Murray Wiki - User contributions [en]

Group Schedule, Spring 2016

2016-05-31T22:15:13Z

Chayes: /* Week 11: 6 Jun - 10 Jun */

This page contains information about various upcoming events that are of interest to the group. __NOTOC__
{| width=60%
|- valign=top
| width=50% |
* [[Schedule|Richard's calendar (travel)]]
| width=50% |
* [[Group Schedule, Winter 2016]]
|}

The schedule for group and subgroup meetings is given below. Contact Richard if you need to change the schedule. Unless otherwise noted, here are the locations of the meetings:

:{| width=100%
|- valign=top
| width=30% |
* Group meetings - 213 ANB
| width=30% |
* Biocircuits subgroup - 111 Keck
| width=30% |
* NCS subgroup - 243 ANB
|}

{| width=100% border=1

|- valign=top
| width=25% |
=== Week 1: 28 Mar - 1 Apr ===
'''NCS: Wed, 9:30a-11a, 121 ANB '''
* Cat McGhan (main)
* Richard Cheng (short)
'''Biocircuits: <s>Tue, 10a-12p</s> Thu, 2p-4p, 114 Steele (library)'''
* Clare Hayes (long)
* Victoria Hsiao (short)

| width=25% |

=== Week 2: 4 Apr - 8 Apr ===
'''Biocircuits: Tue, 10a-12p'''
* Anandh Swaminathan (long)
* Andrew Montequin (short)
'''NCS: Wed, 3:30p-5p'''
* Ioannis Filippidis (main)
* Tung Phan (short)

| width=25% |

=== Week 3: 11 Apr - 15 Apr ===
* Richard out of town

|- valign=top
| width=25% |

=== Week 4: 18 Apr - 22 Apr ===
'''NCS: Wed, 3:30p-5p''' CANCELLED
* <s>Tony Fragoso (main)</s>
* Open (short)
'''Biocircuits: Thu, 10a-12p'''
* Anu Thubagere (long)
* Vipul Singhal (short)

| width=25% |

=== Week 5: 25 Apr - 29 Apr ===
'''Biocircuits: Tue, 10a-12p'''
* James Parkin (long)
* Ania Baetica (short)
'''NCS: Wed, 3:30p-5p'''
* Sumanth Dathathri (main)
* <s>Jon Åge Stakvik (short)</s>

| width=25% |

=== Week 6: 2 May - 6 May ===
'''Biocircuits: Tue, 10a-12p'''
* Shaobin Guo (long)
* Yong Wu (short)
'''NCS: Wed, 3:30p-5p'''
* Daniel Naftalovich (main)
* Jin Ge (short)
* Jon Åge Stakvik (short)

|- valign=top
| width=25% |

=== Week 7: 9 May - 13 May ===
'''Biocircuits: Tue, 10a-12p'''
* Sam Clamons (long)
* Andrey Shur (short)
'''NCS: Wed, 3:30p-5p'''
* Ivan Papusha (main)
* Open (short)

| width=25% |

=== Week 8: 16 May - 19 May ===
* Richard out of town all week
| width=25% |

=== Week 9: 23 May - 26 May ===
No biocircuits meeting this week.

Lab cleanup instead! Tuesday, 11am.

'''NCS: Wed, 3:30p-5p'''
* Jiangang Li (main)
* Ioannis Filippidis (short)
|- valign=top
| width=25% |

=== Week 10: 30 May - 3 Jun ===
'''Biocircuits: Tue, 10a-12p'''
* Tiffany Zhou (long)
* Andrew Montequin (short)
No NCS group meeting

| width=25% |

=== Week 11: 6 Jun - 10 Jun ===
'''Biocircuits: <s>Tue</s> Wed, 10a-12p'''
* Jining Huang (long)
* Alex White (short)

'''Thurs: Biocircuits''' Keck 116, 116A lab move / cleanup, 10a-12p

'''NCS: <s>Tue</s> Wed 121 ANB, 1:30p-3p'''
* Michele Colledanchise (update)
* Richard Cheng (update)
| width=25% |

=== Week 12: 13 Jun - 17 Jun ===
'''Biocircuits: Tue, 10a-12p'''
* William Poole (long)
* Sean Sanchez (short)
'''NCS: Tue, 1:30p-3p'''
* Benson Christalin (main)
* Tung Phan (update)

|- valign=top
| width=25% |

=== Week 13: 20-24 Jun ===
'''NCS: Mon, 1:30p-3p'''
* Jon Åge Stakvik (update)
* Jin Ge (update)

| width=25% |
| width=25% |

|}

Group Schedule, Spring 2016

2016-05-10T19:05:34Z

Chayes: /* Week 9: 23 May - 26 May */

This page contains information about various upcoming events that are of interest to the group. __NOTOC__
{| width=60%
|- valign=top
| width=50% |
* [[Schedule|Richard's calendar (travel)]]
| width=50% |
* [[Group Schedule, Winter 2016]]
|}

The schedule for group and subgroup meetings is given below. Contact Richard if you need to change the schedule. Unless otherwise noted, here are the locations of the meetings:

:{| width=100%
|- valign=top
| width=30% |
* Group meetings - 213 ANB
| width=30% |
* Biocircuits subgroup - 111 Keck
| width=30% |
* NCS subgroup - 243 ANB
|}

{| width=100% border=1

|- valign=top
| width=25% |
=== Week 1: 28 Mar - 1 Apr ===
'''NCS: Wed, 9:30a-11a, 121 ANB '''
* Cat McGhan (main)
* Richard Cheng (short)
'''Biocircuits: <s>Tue, 10a-12p</s> Thu, 2p-4p, 114 Steele (library)'''
* Clare Hayes (long)
* Victoria Hsiao (short)

| width=25% |

=== Week 2: 4 Apr - 8 Apr ===
'''Biocircuits: Tue, 10a-12p'''
* Anandh Swaminathan (long)
* Andrew Montequin (short)
'''NCS: Wed, 3:30p-5p'''
* Ioannis Filippidis (main)
* Tung Phan (short)

| width=25% |

=== Week 3: 11 Apr - 15 Apr ===
* Richard out of town

|- valign=top
| width=25% |

=== Week 4: 18 Apr - 22 Apr ===
'''NCS: Wed, 3:30p-5p''' CANCELLED
* <s>Tony Fragoso (main)</s>
* Open (short)
'''Biocircuits: Thu, 10a-12p'''
* Anu Thubagere (long)
* Vipul Singhal (short)

| width=25% |

=== Week 5: 25 Apr - 29 Apr ===
'''Biocircuits: Tue, 10a-12p'''
* James Parkin (long)
* Ania Baetica (short)
'''NCS: Wed, 3:30p-5p'''
* Sumanth Dathathri (main)
* <s>Jon Åge Stakvik (short)</s>

| width=25% |

=== Week 6: 2 May - 6 May ===
'''Biocircuits: Tue, 10a-12p'''
* Shaobin Guo (long)
* Yong Wu (short)
'''NCS: Wed, 3:30p-5p'''
* Daniel Naftalovich (main)
* Jin Ge (short)
* Jon Åge Stakvik (short)

|- valign=top
| width=25% |

=== Week 7: 9 May - 13 May ===
'''Biocircuits: Tue, 10a-12p'''
* Sam Clamons (long)
* Andrey Shur (short)
'''NCS: Wed, 3:30p-5p'''
* Ivan Papusha (main)
* Open (short)

| width=25% |

=== Week 8: 16 May - 19 May ===
* Richard out of town all week
| width=25% |

=== Week 9: 23 May - 26 May ===
No biocircuits meeting this week.

Lab cleanup instead! Tuesday, 11am.

'''NCS: Wed, 3:30p-5p'''
* Jiangang Li (main)
* Ioannis Filippidis (short)
|- valign=top
| width=25% |

=== Week 10: 30 May - 3 Jun ===
'''Biocircuits: Tue, 10a-12p'''
* Jining Huang (long)
* Andrew Montequin (short)
'''NCS: Tue, 1:30p-3p'''
* Benson Christalin (main)
* Richard Cheng (update)

| width=25% |

=== Week 11: 6 Jun - 10 Jun ===
'''Biocircuits: <s>Tue</s> Wed, 10a-12p'''
* Tiffany Zhou (long)
* Alex White (short)
'''NCS: <s>Tue</s> Wed 121 ANB, 1:30p-3p'''
* Michele Colledanchise (update)
* Tung Phan (update)
| width=25% |

=== Week 12: 13 Jun - 17 Jun ===
'''Biocircuits: Tue, 10a-12p'''
* William Poole (long)
* Sean Sanchez (short)
'''NCS: Tue, 1:30p-3p'''
* Jon Åge Stakvik (update)
* Jin Ge (update)
|}

TX-TL projects, 2015-16

2016-01-27T07:08:38Z

Chayes:

{| style="float: right"
|-
| [[Image:breadboards-process.png|400px]]
|-
| align=center | Overview of the cell-free expression breadboard process.
|}
The overall goal of this research is to build a set of “biomolecular breadboards” to create a systematic, engineering-oriented approach to synthesizing biomolecular circuits that involves developing, modeling, and debugging a sequence of prototype devices, each at increasing levels of complexity and each allowing the incorporation of increasingly realistic operating environments for either in vitro or in vivo applications. We are adapting an existing cell-free toolbox developed at U. Minnesota to create a set of prototyping environments for testing biological circuits. A sequence of increasingly complex environments, ending in prokaryotic cells, is being used to demonstrate the ability to prototype circuits that function in vivo, with iteration in in vitro assays and models to streamline development of predictable, in vivo functionality.

A number of projects are available for 2015-16 for undergraduates interested in contributing to the research progress in this area. Possible projects include:
* '''Variability in circuit performance across extract preparation methods.''' We have seen many situations in which circuits work only in batches of extract produced with certain methods of lysis (bead beating, homogenization, french press, etc). There are no obvious patterns of what types of circuits work in what types of extract, and so there are a lot of interesting speculation about what is going on. Work in this area would require testing existing circuits in different extract batches and then debugging the circuits in the batches where they don't work correctly.
* '''Freeze-drying TX-TL.''' Currently, extract & buffer have to be stored at -80C, making transportation and distribution to non-science facilities difficult. One potential solution is to freeze-dry, or lyophilize, TX-TL, which may preserve activity at higher temperatures. Research will focus on determining optimal lyophilization & storage conditions for TX-TL, and may include trying vacuum sealing, stoppering chambers, or desiccant. Students will also test different types of circuits in TX-TL, to determine how lyophilization effects circuit function. This project may overlap with the Paper-based TX-TL project, as this research includes lyophilizing TX-TL onto paper.
* '''Paper-based TX-TL.''' Currently, TX-TL reactions are run either in plate wells or microcentrifuge tubes, with the fluorescent output of reactions measured in a plate reader. However, recently researchers in the Murray lab have found a way to measure the output of TX-TL reactions with a cellphone, if the TX-TL reactions are on paper. This project focuses on developing paper-based technology for TX-TL, with the aim of eventually being able to run all reactions on paper and read all outputs on a cellphone. Research will include designing paper reaction strips, testing different circuits on the strips, and modifying the cellphone to measure multiple fluorescent and luminescent reporter proteins. This project may overlap with the Freeze-drying TX-TL project, as it may involve lyophilizing TX-TL onto paper.
* '''Colorimetric reporter proteins.''' Currently, the outputs of TX-TL reactions are almost always fluorescent proteins, easy to express in TX-TL and commonly used in biology. However, special excitation-emission filters are needed to measure fluorescence, making it difficult to measure outside of a laboratory setting. Finding a TX-TL output that can be seen by the naked eye, eg. a colored protein or an enzyme-mediated color change, would help enable TX-TL use in the field. Research focuses on testing the functionality of different colorimetric reporters, the LacZ enzyme and varied LacZ substrates in TX-TL. This project may overlap with the Paper-based TX-TL project, as it may include testing successful colorimetric reporter proteins on paper.
* '''Improvements in preparation methods for TX-TL.''' Current preparation methods to make extract for circuit prototyping are low-yield (18 mL per batch). However, alternative preparation methods exist (45 mL per batch) which are significantly less labor-intensive, but are not optimized for circuit prototyping. Research on preparation methods will be conducted to increase yields but match cellular conditions more precisely.

TX-TL projects, 2015-16

2016-01-27T07:08:21Z

Chayes:

{| style="float: right"
|-
| [[Image:breadboards-process.png|400px]]
|-
| align=center | Overview of the cell-free expression breadboard process.
|}
The overall goal of this research is to build a set of “biomolecular breadboards” to create a systematic, engineering-oriented approach to synthesizing biomolecular circuits that involves developing, modeling, and debugging a sequence of prototype devices, each at increasing levels of complexity and each allowing the incorporation of increasingly realistic operating environments for either in vitro or in vivo applications. We are adapting an existing cell-free toolbox developed at U. Minnesota to create a set of prototyping environments for testing biological circuits. A sequence of increasingly complex environments, ending in prokaryotic cells, is being used to demonstrate the ability to prototype circuits that function in vivo, with iteration in in vitro assays and models to streamline development of predictable, in vivo functionality.

A number of projects are available for 2015-16 for undergraduates interested in contributing to the research progress in this area. Possible projects include:
* '''Variability in circuit performance across extract preparation methods.''' We have seen many situations in which circuits work only in batches of extract produced with certain methods of lysis (bead beating, homogenization, french press, etc). There are no obvious patterns of what types of circuits work in what types of extract, and so there are a lot of interesting speculation about what is going on. Work in this area would require testing existing circuits in different extract batches and then debugging the circuits in the batches where they don't work correctly.
* '''Freeze-drying TX-TL.''' Currently, extract & buffer have to be stored at -80C, making transportation and distribution to non-science facilities difficult. One potential solution is to freeze-dry, or lyophilize, TX-TL, which may preserve activity at higher temperatures. Research will focus on determining optimal lyophilization & storage conditions for TX-TL, and may include trying vacuum sealing, stoppering chambers, or desiccant. Students will also test different types of circuits in TX-TL, to determine how lyophilization effects circuit function. This project may overlap with the Paper-based TX-TL project, as this research lyophilizing TX-TL onto paper.
* '''Paper-based TX-TL.''' Currently, TX-TL reactions are run either in plate wells or microcentrifuge tubes, with the fluorescent output of reactions measured in a plate reader. However, recently researchers in the Murray lab have found a way to measure the output of TX-TL reactions with a cellphone, if the TX-TL reactions are on paper. This project focuses on developing paper-based technology for TX-TL, with the aim of eventually being able to run all reactions on paper and read all outputs on a cellphone. Research will include designing paper reaction strips, testing different circuits on the strips, and modifying the cellphone to measure multiple fluorescent and luminescent reporter proteins. This project may overlap with the Freeze-drying TX-TL project, as it may involve lyophilizing TX-TL onto paper.
* '''Colorimetric reporter proteins.''' Currently, the outputs of TX-TL reactions are almost always fluorescent proteins, easy to express in TX-TL and commonly used in biology. However, special excitation-emission filters are needed to measure fluorescence, making it difficult to measure outside of a laboratory setting. Finding a TX-TL output that can be seen by the naked eye, eg. a colored protein or an enzyme-mediated color change, would help enable TX-TL use in the field. Research focuses on testing the functionality of different colorimetric reporters, the LacZ enzyme and varied LacZ substrates in TX-TL. This project may overlap with the Paper-based TX-TL project, as it may include testing successful colorimetric reporter proteins on paper.
* '''Improvements in preparation methods for TX-TL.''' Current preparation methods to make extract for circuit prototyping are low-yield (18 mL per batch). However, alternative preparation methods exist (45 mL per batch) which are significantly less labor-intensive, but are not optimized for circuit prototyping. Research on preparation methods will be conducted to increase yields but match cellular conditions more precisely.

TX-TL projects, 2015-16

2016-01-27T07:07:26Z

Chayes:

{| style="float: right"
|-
| [[Image:breadboards-process.png|400px]]
|-
| align=center | Overview of the cell-free expression breadboard process.
|}
The overall goal of this research is to build a set of “biomolecular breadboards” to create a systematic, engineering-oriented approach to synthesizing biomolecular circuits that involves developing, modeling, and debugging a sequence of prototype devices, each at increasing levels of complexity and each allowing the incorporation of increasingly realistic operating environments for either in vitro or in vivo applications. We are adapting an existing cell-free toolbox developed at U. Minnesota to create a set of prototyping environments for testing biological circuits. A sequence of increasingly complex environments, ending in prokaryotic cells, is being used to demonstrate the ability to prototype circuits that function in vivo, with iteration in in vitro assays and models to streamline development of predictable, in vivo functionality.

A number of projects are available for 2015-16 for undergraduates interested in contributing to the research progress in this area. Possible projects include:
* '''Variability in circuit performance across extract preparation methods.''' We have seen many situations in which circuits work only in batches of extract produced with certain methods of lysis (bead beating, homogenization, french press, etc). There are no obvious patterns of what types of circuits work in what types of extract, and so there are a lot of interesting speculation about what is going on. Work in this area would require testing existing circuits in different extract batches and then debugging the circuits in the batches where they don't work correctly.
* '''Freeze-drying TX-TL.''' Currently, extract & buffer have to be stored at -80C, making transportation and distribution to non-science facilities difficult. One potential solution is to freeze-dry, or lyophilize, TX-TL, which may preserve activity at higher temperatures. Research will focus on determining optimal lyophilization & storage conditions for TX-TL, and may include trying vacuum sealing, stoppering chambers, or desiccant. Students will also test different types of circuits in TX-TL, to determine how lyophilization effects circuit function. This project may overlap with the Paper-based TX-TL project, as this research includes figuring out how to lyophilize TX-TL onto paper.
* '''Paper-based TX-TL.''' Currently, TX-TL reactions are run either in plate wells or microcentrifuge tubes, with the fluorescent output of reactions measured in a plate reader. However, recently researchers in the Murray lab have found a way to measure the output of TX-TL reactions with a cellphone, if the TX-TL reactions are on paper. This project focuses on developing paper-based technology for TX-TL, with the aim of eventually being able to run all reactions on paper and read all outputs on a cellphone. Research will include designing paper reaction strips, testing different circuits on the strips, and modifying the cellphone to measure multiple fluorescent and luminescent reporter proteins. This project may overlap with the Freeze-drying TX-TL project, as it may involve lyophilizing TX-TL onto paper.
* '''Colorimetric reporter proteins.''' Currently, the outputs of TX-TL reactions are almost always fluorescent proteins, easy to express in TX-TL and commonly used in biology. However, special excitation-emission filters are needed to measure fluorescence, making it difficult to measure outside of a laboratory setting. Finding a TX-TL output that can be seen by the naked eye, eg. a colored protein or an enzyme-mediated color change, would help enable TX-TL use in the field. Research focuses on testing the functionality of different colorimetric reporters, the LacZ enzyme and varied LacZ substrates in TX-TL. This project may overlap with the Paper-based TX-TL project, as it may include testing successful colorimetric reporter proteins on paper.
* '''Improvements in preparation methods for TX-TL.''' Current preparation methods to make extract for circuit prototyping are low-yield (18 mL per batch). However, alternative preparation methods exist (45 mL per batch) which are significantly less labor-intensive, but are not optimized for circuit prototyping. Research on preparation methods will be conducted to increase yields but match cellular conditions more precisely.

Research meetings, Jan/Feb 2016

2016-01-19T03:05:02Z

Chayes: /* 29 Jan 2016 (Fri) */

Please sign up for a slot below. __NOTOC__

{| border=1 width=100%
|- valign = top
|
=== 25 Jan 2016 (Mon) ===
* Richard in SF
|
=== 26 Jan 2016 (Tue) ===
* 1-2 pm: Andrey Shur
* 2-3 pm: Anders Knight
* 3-4 pm: Reed McCardell
* 5:30-6:30 pm: Ania Baetica
|

=== 27 Jan 2016 (Wed) ===
* 8:30-9:30 am: Vipul Singhal
* 9:30-10:30 am: Anandh Swaminathan
* 4-5 pm: open
* 5-6 pm: open
|

=== 28 Jan 2016 (Thu) ===
* 5:30-6:30 pm: open
* 6:30-7:30 pm: open
|
=== 29 Jan 2016 (Fri) ===
* 2-3 pm: Victoria Hsiao
* 3-4 pm: Clare
* 4:30-5:30 pm: Ioannis Filippidis
* 5:30-6:30 pm: open
|- valign = top
|

=== 25 Jan 2016 (Mon) ===
* Richard in Hartford
|
=== 2 Feb 2016 (Tue) ===
* 9-10 am: Yong W.
* 2-3 pm: Tony Fragoso
* 3-4 pm: open
* 4-5 pm: open
* 5:30-6:30 pm: Daniel Naftalovich
* 6:30-7:30 pm: Anu Thubagere
|

=== 3 Feb 2016 (Wed) ===
* 8:30-9:30 am: open
* 9:30-10:30 am: open
|
=== 4 Feb 2016 (Thu) ===
* Richard in SF
|
=== 5 Feb 2016 (Fri) ===
* BE visiting day
|}

Group Schedule, Summer 2015

2015-07-20T22:39:41Z

Chayes: /* Week 13: 7 Sep - 11 Sep */

This page contains information about various upcoming events that are of interest to the group. __NOTOC__
{| width=60%
|- valign=top
| width=50% |
* [[Schedule|Richard's calendar (travel)]]
| width=50% |
* [[Group Schedule, Spring 2015]]
|}

The schedule for group and subgroup meetings is given below. Contact Richard if you need to change the schedule. Unless otherwise noted, here are the locations of the meetings:

:{| width=100%
|- valign=top
| width=30% |
* Group meetings - 213 ANB
| width=30% |
* Biocircuits subgroup - 111 Keck
| width=30% |
* NCS subgroup - 243 ANB
|}

{| width=100% border=1

|- valign=top
| width=25% |
=== Week 1: 15 Jun - 19 Jun ===
'''Biocircuits: 15 Jun (Mon), 10a-12p'''
* Yutaka Hori (long)
* Abel Chiao (short)
'''NCS: 17 Jun (Wed), 10:30a-12p'''
* Vasu Raman (main)
* Open (short)
<hr>
* TX-TL workshop, Tue-Fri
| width=25% |

=== Week 2: 22 Jun - 26 Jun ===
'''Biocircuits: 23 Jun (Tue), 10a-12p'''
* Ania Baetica (long)
* Anandh Swaminathan (short)
'''NCS: 24 Jun (Wed), 10:30a-12p'''
* Cat McGhan (main)
* Sumanth Dathathri (short)

| width=25% |

=== Week 3: 29 Jun - 3 Jul ===
'''Biocircuits: 29 Jun (Mon), 10a-12p'''
* Victoria Hsiao (long)
* Anu Thubagere (short)
'''NCS: 29 Jun (Mon), 1:30p-3p'''
* Tony Fragoso (main)
* Cat McGhan (short)
<hr>
* Richard out of town, Tue-Fri (ACC)

|- valign=top
| width=25% |

=== Week 4: 6 Jul - 12 Jul ===
'''Biocircuits: 10 Jul (Fri), 10a-12p'''
* Shaunak Sen (long)
* Emzo de los Santos (short)
'''NCS: 10 Jul (Fri), 1:30p-3p'''
* Scott Livingston
* Open (short)
<hr>
* Richard out of town, Mon-Thu
* Biocircuits lab cleanup, Thursday @ 10 am

| width=25% |

=== Week 5: 13 Jul - 17 Jul ===
'''Biocircuits: 16 Jul (Thu), 10a-12p 114 Steele'''
* Vipul Singhal (long)
* Zach Sun (short)
'''NCS: 17 Jul (Fri), 10:30a-12p'''
* Jiangang Li (main)
* Open (short)

| width=25% |

=== Week 6: 20 Jul - 24 Jul ===
* Richard out of town Mon-Fri (China)

|- valign=top
| width=25% |

=== Week 7: 27 Jul - 31 Jul ===
* Richard out of town Mon-Fri (China)

| width=25% |

=== Week 8: 3 Aug - 7 Aug ===
'''Biocircuits: 4 Aug (Tue), 10a-12p'''
* Enoch Yeung (long)
* Seung Lee (short)
'''NCS: 5 Aug (Wed), 10:30a-12p'''
* Ivan Papusha (main)
* Anthony Gong (short)

| width=25% |

=== Week 9: 10 Aug - 14 Aug ===
'''Biocircuits: 11 Aug (Tue), 10a-12p'''
* Yong Wu (long)
* Ron Pereira (short)
'''NCS: 12 Aug (Wed), 10:30a-12p'''
* Daniel Naftalovich
* Open (short)

|- valign=top
| width=25% |

=== Week 10: 17 Aug - 21 Aug ===
* RMM out of town Mon-Fri (ISAT)
* Biocircuits lab cleanup, Tue @ 10 am
| width=25% |

=== Week 11: 24 Aug - 28 Aug ===
* RMM out of town Mon-Fri (Sweden)
| width=25% |

=== Week 12: 31 Aug - 4 Sep ===
'''Biocircuits: 1 Sep (Tue), 10a-12p'''
* May move to 31 Aug, 10a-12p
* Open (long)
* Shaobin Guo (short)
'''NCS: 2 Sep (Wed), 10:30a-12p'''
* Samira Farahani
* Open (short)

|- valign=top
| width=25% |

=== Week 13: 7 Sep - 11 Sep ===
'''NCS: 7 Sep (Mon), 1:30p-3p'''
* Ioannis Filippidis (main)
* Open (short)
'''Biocircuits: 8 Sep (Tue), 10a-12p'''
* Annual lab safety briefing (Dora Gosen)
* Clare Hayes (short)

| width=25% |

=== Week 14: 14 Sep - 18 Sep ===
* RMM out of town, Mon-Fri (vacation)

| width=25% |

=== Week 15: 21 Sep - 25 Sep ===
'''Biocircuits: 21 Sep (Mon), 10a-12p'''
* (long)
* Sean Sanchez (short)
'''NCS: 24 Sep (Thu), 10:30a-12p'''
* Benson Christalin
* Open (short)
|}

Group Schedule, Summer 2015

2015-07-07T01:23:26Z

Chayes:

This page contains information about various upcoming events that are of interest to the group. __NOTOC__
{| width=60%
|- valign=top
| width=50% |
* [[Schedule|Richard's calendar (travel)]]
| width=50% |
* [[Group Schedule, Spring 2015]]
|}

The schedule for group and subgroup meetings is given below. Contact Richard if you need to change the schedule. Unless otherwise noted, here are the locations of the meetings:

:{| width=100%
|- valign=top
| width=30% |
* Group meetings - 213 ANB
| width=30% |
* Biocircuits subgroup - 111 Keck
| width=30% |
* NCS subgroup - 243 ANB
|}

{| width=100% border=1

|- valign=top
| width=25% |
=== Week 1: 15 Jun - 19 Jun ===
'''Biocircuits: 15 Jun (Mon), 10a-12p'''
* Yutaka Hori (long)
* Abel Chiao (short)
'''NCS: 17 Jun (Wed), 10:30a-12p'''
* Vasu Raman (main)
* Open (short)
<hr>
* TX-TL workshop, Tue-Fri
| width=25% |

=== Week 2: 22 Jun - 26 Jun ===
'''Biocircuits: 23 Jun (Tue), 10a-12p'''
* Ania Baetica (long)
* Anandh Swaminathan (short)
'''NCS: 24 Jun (Wed), 10:30a-12p'''
* Cat McGhan (main)
* Sumanth Dathathri (short)

| width=25% |

=== Week 3: 29 Jun - 3 Jul ===
'''Biocircuits: 29 Jun (Mon), 10a-12p'''
* Victoria Hsiao (long)
* Anu Thubagere (short)
'''NCS: 29 Jun (Mon), 1:30p-3p'''
* Tony Fragoso (main)
* Cat McGhan (short)
<hr>
* Richard out of town, Tue-Fri (ACC)

|- valign=top
| width=25% |

=== Week 4: 6 Jul - 12 Jul ===
'''Biocircuits: 10 Jul (Fri), 10a-12p'''
* Shaunak Sen (long)
* Emzo de los Santos (short)
'''NCS: 10 Jul (Fri), 1:30p-3p'''
* Scott Livingston
* Open (short)
<hr>
* Richard out of town, Mon-Thu
* Biocircuits lab cleanup, Thursday @ 10 am

| width=25% |

=== Week 5: 13 Jul - 17 Jul ===
'''Biocircuits: 16 Jul (Thu), 10a-12p 114 Steele'''
* Vipul Singhal (long)
* Zach Sun (short)
'''NCS: 17 Jul (Fri), 10:30a-12p'''
* Jiangang Li (main)
* Open (short)

| width=25% |

=== Week 6: 20 Jul - 24 Jul ===
* Richard out of town Mon-Fri (China)

|- valign=top
| width=25% |

=== Week 7: 27 Jul - 31 Jul ===
* Richard out of town Mon-Fri (China)

| width=25% |

=== Week 8: 3 Aug - 7 Aug ===
'''Biocircuits: 4 Aug (Tue), 10a-12p'''
* Enoch Yeung (long)
* Seung Lee (short)
'''NCS: 5 Aug (Wed), 10:30a-12p'''
* Ivan Papusha (main)
* Anthony Gong (short)

| width=25% |

=== Week 9: 10 Aug - 14 Aug ===
'''Biocircuits: 11 Aug (Tue), 10a-12p'''
* Yong Wu (long)
* Ron Pereira (short)
'''NCS: 12 Aug (Wed), 10:30a-12p'''
* Ioannis Filippidis
* Open (short)

|- valign=top
| width=25% |

=== Week 10: 17 Aug - 21 Aug ===
* RMM out of town Mon-Fri (ISAT)
* Biocircuits lab cleanup, Tue @ 10 am
| width=25% |

=== Week 11: 24 Aug - 28 Aug ===
* RMM out of town Mon-Fri (Sweden)
| width=25% |

=== Week 12: 31 Aug - 4 Sep ===
'''Biocircuits: 1 Sep (Tue), 10a-12p'''
* May move to 31 Aug, 10a-12p
* Open (long)
* Shaobin Guo (short)
'''NCS: 2 Sep (Wed), 10:30a-12p'''
* Samira Farahani
* Open (short)

|- valign=top
| width=25% |

=== Week 13: 7 Sep - 11 Sep ===
'''NCS: 7 Sep (Mon), 1:30p-3p'''
* Daniel Naftalovich (main)
* Open (short)
'''Biocircuits: 8 Sep (Tue), 10a-12p'''
* Open (long)
* Clare Hayes (short)

| width=25% |

=== Week 14: 14 Sep - 18 Sep ===
* RMM out of town, Mon-Fri (vacation)

| width=25% |

=== Week 15: 21 Sep - 25 Sep ===
'''Biocircuits: 21 Sep (Mon), 10a-12p'''
* (long)
* Sean Sanchez (short)
'''NCS: 24 Sep (Thu), 10:30a-12p'''
* Benson Christalin
* Open (short)
|}

TX-TL Bootcamp, Jun 2015

2015-06-18T17:20:08Z

Chayes: /* Thu morning */

Caltech will be hosting a hands-on "bootcamp" on cell-free prototyping and debugging of biological circuits. This page contains information for the TX-TL workshop, which will take place at Caltech on 16-18 Jun 2015. This workshop is by invitation only. __NOTOC__

=== Workshop goals ===
The purpose of the workshop is to provide participants with a working knowledge of cell-free methods for design of biomolecular circuits, using the TX-TL system developed by Vincent Noireaux at U. Minnesota. By the end of the workshop, participants will be able to:

* Build models and simulate circuits using the TX-TL modeling toolbox (MATLAB-based)
* Assemble and test genetic circuits using linear DNA assembly in a single day
* Test and characterize circuits that are part of our current research activities

=== Summary Schedule ===

The schedule below gives an overview of the activities during the workshop.

{| width=100% border=1
|- valign=top
| width=25% |
==== Tue morning ====

| width=25% |

==== Wed morning ====
9-12 am: Meet in '''111 Keck'''
* Analyzing TX-TL results (from overnight run)
* Presentation: TX-TL using linear DNA
* Lab (136 Keck): Set up Golden Gate reactions

(Optional) Group lunch at Chandler
| width= 25% |

==== Thu morning ====
10 am - Analyze TX-TL results from previous day '''[110 Steele?]'''

10:30 am - Group projects: Set up experiment

12pm: Optional group lunch - Chandler, or walk to Lake street?

| width=25% |

==== Fri morning ====
9 am: Group projects: Create group presentation
|- valign=top
| width= 25% |

==== Tue afternoon ====
11 am: '''Bootcamp starts''', '''111 Keck''' (lunch will be provided)
* Overview of workshop and TX-TL system (Richard)
* Lab safety briefing (Clare)

1:45-5 pm: SURF check-in and orientation
* 1:45-3 pm: SURF checkin
* 1:45-3:45 pm: Housing move in
* 3:45-5 pm: SURF orientation
| width= 25% |

==== Wed afternoon ====
1:30 - 2:30 pm - SURF safety meeting (mandatory)

2:30 pm: Set up PCR reactions for GGA linear DNAs (Clare)

3 pm - Project discussions (with co-mentors) at CDS tea and/or initial experiments

| width= 25% |

==== Thu afternoon ====
Group projects: Set up experiments

| width=25% |

==== Fri afternoon ====
1-3 pm: Group presentations '''(111 Keck)'''

|- valign=top
|

==== Tue evening ====
5-7 pm: SURF BBQ

7 pm: Meet in '''111 Keck'''

Lab session (136 Keck): 7:30-9 pm
* Set up and run first TX-TL reactions

| width=25% |

==== Wed evening ====
5-8 pm: Meet in '''111 Keck'''

* Lab (136 Keck): Set up FFL runs from GGA assembly

| width=25% |

==== Thu evening ====
Group projects: Set up overnight experiments

| width=25% |
|}

Description of tutorials:
* Lab basics - this tutorial is intended for participants who have not had any experience in a molecular biology lab. You will learn how to pipette small volumes of clear fluids, run PCR reactions and run gels. If you have had an undergraduate lab class in biology in the last 10 years, you probably don't need to come.

* MATLAB basics - this tutorial is for participants who have never used the MATLAB program. You will learn how to load and plot data in MATLAB and how to use the SimBiology toolbox for setting up very simple reactions.

* Sequence editing - this tutorial will show how to use a DNA sequence editing program such as Geneious or ApE (we mainly use Geneious). You'll learn how to annotate a sequence, simulate PCR reactions and other similar techniques.

=== Read-ahead material ===

We will assume everyone has watched the following 15 minute video before attending the workshop:
* Z. Z. Sun, C. A. Hayes, J. Shin, F. Caschera, R. M. Murray, V. Noireaux, [http://www.jove.com/video/50762 Protocols for Implementing an Escherichia Coli Based TX-TL Cell-Free Expression System for Synthetic Biology]. ''Journal. of Visualized Experiments'' (JoVE), e50762, doi:10.3791/50762 (2013).

If you have time, we also encourage you to take a look at the following material before arriving:
* J. Shin and V. Noireaux, [http://pubs.acs.org/doi/abs/10.1021/sb200016s An ''E. coli'' cell-free expression toolbox: application to synthetic gene circuits and artificial cells]. ''ACS Synthetic Biology'', 1(1):29–41, 2012.

* Z. Z. Sun, E. Yeung, C. A. Hayes, V. Noireaux and Richard M. Murray, [http://www.cds.caltech.edu/~murray/papers/sun+13-acs_synbio.html Linear DNA for rapid prototyping of synthetic biological circuits in an ''Escherichia coli'' based TX-TL cell-free system]. ''ACS Synthetic Biology'', 2014.

* [http://openwetware.org/wiki/Biomolecular_Breadboards Biomolecular Breadboards pages on OpenWetWare]
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Models Modeling overview] - setting up simulations using MATLAB-based TX-TL toolbox
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Preliminary_Data Preliminary data] - includes linear DNA protection, protein degradation
** [http://openwetware.org/wiki/Biomolecular_Breadboards:More_Info More info] - additional references and presentations on TX-TL

=== Software ===
We will make use of the following software as part of the workshop:
* Microsoft Excel (or Numbers)
* [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE] (free), [http://www.geneious.com Geneious] (free trial)
* [http://www.mathworks.com MATLAB], [http://www.mathworks.com/products/simbiology/ Simbiology]
* [http://sourceforge.net/projects/txtl/ TX-TL modeling toolbox] (requires MATLAB 2010+ and SimBiology]
Participants are encouraged to install this software on their laptops prior to the workshop, but version of the software will also be available on lab computers.

TX-TL Bootcamp, Jun 2015

2015-06-18T01:19:55Z

Chayes: /* Thu morning */

Caltech will be hosting a hands-on "bootcamp" on cell-free prototyping and debugging of biological circuits. This page contains information for the TX-TL workshop, which will take place at Caltech on 16-18 Jun 2015. This workshop is by invitation only. __NOTOC__

=== Workshop goals ===
The purpose of the workshop is to provide participants with a working knowledge of cell-free methods for design of biomolecular circuits, using the TX-TL system developed by Vincent Noireaux at U. Minnesota. By the end of the workshop, participants will be able to:

* Build models and simulate circuits using the TX-TL modeling toolbox (MATLAB-based)
* Assemble and test genetic circuits using linear DNA assembly in a single day
* Test and characterize circuits that are part of our current research activities

=== Summary Schedule ===

The schedule below gives an overview of the activities during the workshop.

{| width=100% border=1
|- valign=top
| width=25% |
==== Tue morning ====

| width=25% |

==== Wed morning ====
9-12 am: Meet in '''111 Keck'''
* Analyzing TX-TL results (from overnight run)
* Presentation: TX-TL using linear DNA
* Lab (136 Keck): Set up Golden Gate reactions

(Optional) Group lunch at Chandler
| width= 25% |

==== Thu morning ====
10 am - Analyze TX-TL results from previous day '''[110 Steele?]'''

10:30 am - Group projects: Set up experiment

12pm: Group lunch

| width=25% |

==== Fri morning ====
9 am: Group projects: Create group presentation
|- valign=top
| width= 25% |

==== Tue afternoon ====
11 am: '''Bootcamp starts''', '''111 Keck''' (lunch will be provided)
* Overview of workshop and TX-TL system (Richard)
* Lab safety briefing (Clare)

1:45-5 pm: SURF check-in and orientation
* 1:45-3 pm: SURF checkin
* 1:45-3:45 pm: Housing move in
* 3:45-5 pm: SURF orientation
| width= 25% |

==== Wed afternoon ====
1:30 - 2:30 pm - SURF safety meeting (mandatory)

2:30 pm: Set up PCR reactions for GGA linear DNAs (Clare)

3 pm - Project discussions (with co-mentors) at CDS tea and/or initial experiments

| width= 25% |

==== Thu afternoon ====
Group projects: Set up experiments

| width=25% |

==== Fri afternoon ====
1-3 pm: Group presentations '''(111 Keck)'''

|- valign=top
|

==== Tue evening ====
5-7 pm: SURF BBQ

7 pm: Meet in '''111 Keck'''

Lab session (136 Keck): 7:30-9 pm
* Set up and run first TX-TL reactions

| width=25% |

==== Wed evening ====
5-8 pm: Meet in '''111 Keck'''

* Lab (136 Keck): Set up FFL runs from GGA assembly

| width=25% |

==== Thu evening ====
Group projects: Set up overnight experiments

| width=25% |
|}

Description of tutorials:
* Lab basics - this tutorial is intended for participants who have not had any experience in a molecular biology lab. You will learn how to pipette small volumes of clear fluids, run PCR reactions and run gels. If you have had an undergraduate lab class in biology in the last 10 years, you probably don't need to come.

* MATLAB basics - this tutorial is for participants who have never used the MATLAB program. You will learn how to load and plot data in MATLAB and how to use the SimBiology toolbox for setting up very simple reactions.

* Sequence editing - this tutorial will show how to use a DNA sequence editing program such as Geneious or ApE (we mainly use Geneious). You'll learn how to annotate a sequence, simulate PCR reactions and other similar techniques.

=== Read-ahead material ===

We will assume everyone has watched the following 15 minute video before attending the workshop:
* Z. Z. Sun, C. A. Hayes, J. Shin, F. Caschera, R. M. Murray, V. Noireaux, [http://www.jove.com/video/50762 Protocols for Implementing an Escherichia Coli Based TX-TL Cell-Free Expression System for Synthetic Biology]. ''Journal. of Visualized Experiments'' (JoVE), e50762, doi:10.3791/50762 (2013).

If you have time, we also encourage you to take a look at the following material before arriving:
* J. Shin and V. Noireaux, [http://pubs.acs.org/doi/abs/10.1021/sb200016s An ''E. coli'' cell-free expression toolbox: application to synthetic gene circuits and artificial cells]. ''ACS Synthetic Biology'', 1(1):29–41, 2012.

* Z. Z. Sun, E. Yeung, C. A. Hayes, V. Noireaux and Richard M. Murray, [http://www.cds.caltech.edu/~murray/papers/sun+13-acs_synbio.html Linear DNA for rapid prototyping of synthetic biological circuits in an ''Escherichia coli'' based TX-TL cell-free system]. ''ACS Synthetic Biology'', 2014.

* [http://openwetware.org/wiki/Biomolecular_Breadboards Biomolecular Breadboards pages on OpenWetWare]
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Models Modeling overview] - setting up simulations using MATLAB-based TX-TL toolbox
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Preliminary_Data Preliminary data] - includes linear DNA protection, protein degradation
** [http://openwetware.org/wiki/Biomolecular_Breadboards:More_Info More info] - additional references and presentations on TX-TL

=== Software ===
We will make use of the following software as part of the workshop:
* Microsoft Excel (or Numbers)
* [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE] (free), [http://www.geneious.com Geneious] (free trial)
* [http://www.mathworks.com MATLAB], [http://www.mathworks.com/products/simbiology/ Simbiology]
* [http://sourceforge.net/projects/txtl/ TX-TL modeling toolbox] (requires MATLAB 2010+ and SimBiology]
Participants are encouraged to install this software on their laptops prior to the workshop, but version of the software will also be available on lab computers.

TX-TL Bootcamp, Jun 2015

2015-06-17T15:51:13Z

Chayes: /* Wed morning */

Caltech will be hosting a hands-on "bootcamp" on cell-free prototyping and debugging of biological circuits. This page contains information for the TX-TL workshop, which will take place at Caltech on 16-18 Jun 2015. This workshop is by invitation only. __NOTOC__

=== Workshop goals ===
The purpose of the workshop is to provide participants with a working knowledge of cell-free methods for design of biomolecular circuits, using the TX-TL system developed by Vincent Noireaux at U. Minnesota. By the end of the workshop, participants will be able to:

* Build models and simulate circuits using the TX-TL modeling toolbox (MATLAB-based)
* Assemble and test genetic circuits using linear DNA assembly in a single day
* Test and characterize circuits that are part of our current research activities

=== Summary Schedule ===

The schedule below gives an overview of the activities during the workshop.

{| width=100% border=1
|- valign=top
| width=25% |
==== Tue morning ====

| width=25% |

==== Wed morning ====
9-12 am: Meet in '''111 Keck'''
* Analyzing TX-TL results (from overnight run)
* Presentation: TX-TL using linear DNA
* Lab (136 Keck): Set up Golden Gate reactions

(Optional) Group lunch at Chandler
| width= 25% |

==== Thu morning ====
9 am - Analyze TX-TL results from previous day '''[110 Steele?]'''

10 am - Group projects: Set up experiment

12pm: Group lunch

| width=25% |

==== Fri morning ====
9 am: Group projects: Create group presentation
|- valign=top
| width= 25% |

==== Tue afternoon ====
11 am: '''Bootcamp starts''', '''111 Keck''' (lunch will be provided)
* Overview of workshop and TX-TL system (Richard)
* Lab safety briefing (Clare)

1:45-5 pm: SURF check-in and orientation
* 1:45-3 pm: SURF checkin
* 1:45-3:45 pm: Housing move in
* 3:45-5 pm: SURF orientation
| width= 25% |

==== Wed afternoon ====
1:30 - 2:30 pm - SURF safety meeting (mandatory)

2:30 pm: Set up PCR reactions for GGA linear DNAs (Clare)

3 pm - Project discussions (with co-mentors) at CDS tea and/or initial experiments

| width= 25% |

==== Thu afternoon ====
Group projects: Set up experiments

| width=25% |

==== Fri afternoon ====
1-3 pm: Group presentations '''(111 Keck)'''

|- valign=top
|

==== Tue evening ====
5-7 pm: SURF BBQ

7 pm: Meet in '''111 Keck'''

Lab session (136 Keck): 7:30-9 pm
* Set up and run first TX-TL reactions

| width=25% |

==== Wed evening ====
5-8 pm: Meet in '''111 Keck'''

* Lab (136 Keck): Set up FFL runs from GGA assembly

| width=25% |

==== Thu evening ====
Group projects: Set up overnight experiments

| width=25% |
|}

Description of tutorials:
* Lab basics - this tutorial is intended for participants who have not had any experience in a molecular biology lab. You will learn how to pipette small volumes of clear fluids, run PCR reactions and run gels. If you have had an undergraduate lab class in biology in the last 10 years, you probably don't need to come.

* MATLAB basics - this tutorial is for participants who have never used the MATLAB program. You will learn how to load and plot data in MATLAB and how to use the SimBiology toolbox for setting up very simple reactions.

* Sequence editing - this tutorial will show how to use a DNA sequence editing program such as Geneious or ApE (we mainly use Geneious). You'll learn how to annotate a sequence, simulate PCR reactions and other similar techniques.

=== Read-ahead material ===

We will assume everyone has watched the following 15 minute video before attending the workshop:
* Z. Z. Sun, C. A. Hayes, J. Shin, F. Caschera, R. M. Murray, V. Noireaux, [http://www.jove.com/video/50762 Protocols for Implementing an Escherichia Coli Based TX-TL Cell-Free Expression System for Synthetic Biology]. ''Journal. of Visualized Experiments'' (JoVE), e50762, doi:10.3791/50762 (2013).

If you have time, we also encourage you to take a look at the following material before arriving:
* J. Shin and V. Noireaux, [http://pubs.acs.org/doi/abs/10.1021/sb200016s An ''E. coli'' cell-free expression toolbox: application to synthetic gene circuits and artificial cells]. ''ACS Synthetic Biology'', 1(1):29–41, 2012.

* Z. Z. Sun, E. Yeung, C. A. Hayes, V. Noireaux and Richard M. Murray, [http://www.cds.caltech.edu/~murray/papers/sun+13-acs_synbio.html Linear DNA for rapid prototyping of synthetic biological circuits in an ''Escherichia coli'' based TX-TL cell-free system]. ''ACS Synthetic Biology'', 2014.

* [http://openwetware.org/wiki/Biomolecular_Breadboards Biomolecular Breadboards pages on OpenWetWare]
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Models Modeling overview] - setting up simulations using MATLAB-based TX-TL toolbox
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Preliminary_Data Preliminary data] - includes linear DNA protection, protein degradation
** [http://openwetware.org/wiki/Biomolecular_Breadboards:More_Info More info] - additional references and presentations on TX-TL

=== Software ===
We will make use of the following software as part of the workshop:
* Microsoft Excel (or Numbers)
* [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE] (free), [http://www.geneious.com Geneious] (free trial)
* [http://www.mathworks.com MATLAB], [http://www.mathworks.com/products/simbiology/ Simbiology]
* [http://sourceforge.net/projects/txtl/ TX-TL modeling toolbox] (requires MATLAB 2010+ and SimBiology]
Participants are encouraged to install this software on their laptops prior to the workshop, but version of the software will also be available on lab computers.

TX-TL Bootcamp, Jun 2015

2015-06-16T18:49:35Z

Chayes: /* Wed morning */

Caltech will be hosting a hands-on "bootcamp" on cell-free prototyping and debugging of biological circuits. This page contains information for the TX-TL workshop, which will take place at Caltech on 16-18 Jun 2015. This workshop is by invitation only. __NOTOC__

=== Workshop goals ===
The purpose of the workshop is to provide participants with a working knowledge of cell-free methods for design of biomolecular circuits, using the TX-TL system developed by Vincent Noireaux at U. Minnesota. By the end of the workshop, participants will be able to:

* Build models and simulate circuits using the TX-TL modeling toolbox (MATLAB-based)
* Assemble and test genetic circuits using linear DNA assembly in a single day
* Test and characterize circuits that are part of our current research activities

=== Summary Schedule ===

The schedule below gives an overview of the activities during the workshop.

{| width=100% border=1
|- valign=top
| width=25% |
==== Tue morning ====

| width=25% |

==== Wed morning ====
9-12 am: Meet in '''111 Keck'''
* Analyzing TX-TL results (from overnight run)
* Presentation: TX-TL using linear DNA
* Lab (136 Keck): Set up Golden Gate reactions

Group lunch at Chandler (when done)
| width= 25% |

==== Thu morning ====
9 am - Analyze TX-TL results from previous day '''[110 Steele?]'''

10 am - Group projects: Set up experiment

12pm: Group lunch

| width=25% |

==== Fri morning ====
9 am: Group projects: Create group presentation
|- valign=top
| width= 25% |

==== Tue afternoon ====
11 am: '''Bootcamp starts''', '''111 Keck''' (lunch will be provided)
* Overview of workshop and TX-TL system (Richard)
* Lab safety briefing (Clare)

1:45-5 pm: SURF check-in and orientation
* 1:45-3 pm: SURF checkin
* 1:45-3:45 pm: Housing move in
* 3:45-5 pm: SURF orientation
| width= 25% |

==== Wed afternoon ====
1:30 - 2:30 pm - SURF safety meeting (mandatory)

2:30 pm: Set up PCR reactions for GGA linear DNAs (Clare)

3 pm - Project discussions (with co-mentors) at CDS tea and/or initial experiments

| width= 25% |

==== Thu afternoon ====
Group projects: Set up experiments

| width=25% |

==== Fri afternoon ====
1-3 pm: Group presentations '''(111 Keck)'''

|- valign=top
|

==== Tue evening ====
5-7 pm: SURF BBQ

7 pm: Meet in '''111 Keck'''

Lab session (136 Keck): 7:30-9 pm
* Set up and run first TX-TL reactions

| width=25% |

==== Wed evening ====
5-8 pm: Meet in '''111 Keck'''

* Lab (136 Keck): Set up FFL runs from GGA assembly

| width=25% |

==== Thu evening ====
Group projects: Set up overnight experiments

| width=25% |
|}

Description of tutorials:
* Lab basics - this tutorial is intended for participants who have not had any experience in a molecular biology lab. You will learn how to pipette small volumes of clear fluids, run PCR reactions and run gels. If you have had an undergraduate lab class in biology in the last 10 years, you probably don't need to come.

* MATLAB basics - this tutorial is for participants who have never used the MATLAB program. You will learn how to load and plot data in MATLAB and how to use the SimBiology toolbox for setting up very simple reactions.

* Sequence editing - this tutorial will show how to use a DNA sequence editing program such as Geneious or ApE (we mainly use Geneious). You'll learn how to annotate a sequence, simulate PCR reactions and other similar techniques.

=== Read-ahead material ===

We will assume everyone has watched the following 15 minute video before attending the workshop:
* Z. Z. Sun, C. A. Hayes, J. Shin, F. Caschera, R. M. Murray, V. Noireaux, [http://www.jove.com/video/50762 Protocols for Implementing an Escherichia Coli Based TX-TL Cell-Free Expression System for Synthetic Biology]. ''Journal. of Visualized Experiments'' (JoVE), e50762, doi:10.3791/50762 (2013).

If you have time, we also encourage you to take a look at the following material before arriving:
* J. Shin and V. Noireaux, [http://pubs.acs.org/doi/abs/10.1021/sb200016s An ''E. coli'' cell-free expression toolbox: application to synthetic gene circuits and artificial cells]. ''ACS Synthetic Biology'', 1(1):29–41, 2012.

* Z. Z. Sun, E. Yeung, C. A. Hayes, V. Noireaux and Richard M. Murray, [http://www.cds.caltech.edu/~murray/papers/sun+13-acs_synbio.html Linear DNA for rapid prototyping of synthetic biological circuits in an ''Escherichia coli'' based TX-TL cell-free system]. ''ACS Synthetic Biology'', 2014.

* [http://openwetware.org/wiki/Biomolecular_Breadboards Biomolecular Breadboards pages on OpenWetWare]
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Models Modeling overview] - setting up simulations using MATLAB-based TX-TL toolbox
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Preliminary_Data Preliminary data] - includes linear DNA protection, protein degradation
** [http://openwetware.org/wiki/Biomolecular_Breadboards:More_Info More info] - additional references and presentations on TX-TL

=== Software ===
We will make use of the following software as part of the workshop:
* Microsoft Excel (or Numbers)
* [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE] (free), [http://www.geneious.com Geneious] (free trial)
* [http://www.mathworks.com MATLAB], [http://www.mathworks.com/products/simbiology/ Simbiology]
* [http://sourceforge.net/projects/txtl/ TX-TL modeling toolbox] (requires MATLAB 2010+ and SimBiology]
Participants are encouraged to install this software on their laptops prior to the workshop, but version of the software will also be available on lab computers.

TX-TL Bootcamp, Jun 2015

2015-06-16T18:18:12Z

Chayes: /* Tue evening */

Caltech will be hosting a hands-on "bootcamp" on cell-free prototyping and debugging of biological circuits. This page contains information for the TX-TL workshop, which will take place at Caltech on 16-18 Jun 2015. This workshop is by invitation only. __NOTOC__

=== Workshop goals ===
The purpose of the workshop is to provide participants with a working knowledge of cell-free methods for design of biomolecular circuits, using the TX-TL system developed by Vincent Noireaux at U. Minnesota. By the end of the workshop, participants will be able to:

* Build models and simulate circuits using the TX-TL modeling toolbox (MATLAB-based)
* Assemble and test genetic circuits using linear DNA assembly in a single day
* Test and characterize circuits that are part of our current research activities

=== Summary Schedule ===

The schedule below gives an overview of the activities during the workshop.

{| width=100% border=1
|- valign=top
| width=25% |
==== Tue morning ====

| width=25% |

==== Wed morning ====
9-12 pm: Meet in '''111 Keck'''
* Analyzing TX-TL results (from overnight run)
* Presentation: TX-TL using linear DNA
* Lab (136 Keck): Set up Golden Gate reactions

Group lunch at Chandler (when done)
| width= 25% |

==== Thu morning ====
9 am - Analyze TX-TL results from previous day '''[110 Steele?]'''

10 am - Group projects: Set up experiment

12pm: Group lunch

| width=25% |

==== Fri morning ====
9 am: Group projects: Create group presentation
|- valign=top
| width= 25% |

==== Tue afternoon ====
11 am: '''Bootcamp starts''', '''111 Keck''' (lunch will be provided)
* Overview of workshop and TX-TL system (Richard)
* Lab safety briefing (Clare)

1:45-5 pm: SURF check-in and orientation
* 1:45-3 pm: SURF checkin
* 1:45-3:45 pm: Housing move in
* 3:45-5 pm: SURF orientation
| width= 25% |

==== Wed afternoon ====
1:30 - 2:30 pm - SURF safety meeting (mandatory)

2:30 pm: Set up PCR reactions for GGA linear DNAs (Clare)

3 pm - Project discussions (with co-mentors) at CDS tea and/or initial experiments

| width= 25% |

==== Thu afternoon ====
Group projects: Set up experiments

| width=25% |

==== Fri afternoon ====
1-3 pm: Group presentations '''(111 Keck)'''

|- valign=top
|

==== Tue evening ====
5-7 pm: SURF BBQ

7 pm: Meet in '''111 Keck'''

Lab session (136 Keck): 7:30-9 pm
* Set up and run first TX-TL reactions

| width=25% |

==== Wed evening ====
5-8 pm: Meet in '''111 Keck'''

* Lab (136 Keck): Set up FFL runs from GGA assembly

| width=25% |

==== Thu evening ====
Group projects: Set up overnight experiments

| width=25% |
|}

Description of tutorials:
* Lab basics - this tutorial is intended for participants who have not had any experience in a molecular biology lab. You will learn how to pipette small volumes of clear fluids, run PCR reactions and run gels. If you have had an undergraduate lab class in biology in the last 10 years, you probably don't need to come.

* MATLAB basics - this tutorial is for participants who have never used the MATLAB program. You will learn how to load and plot data in MATLAB and how to use the SimBiology toolbox for setting up very simple reactions.

* Sequence editing - this tutorial will show how to use a DNA sequence editing program such as Geneious or ApE (we mainly use Geneious). You'll learn how to annotate a sequence, simulate PCR reactions and other similar techniques.

=== Read-ahead material ===

We will assume everyone has watched the following 15 minute video before attending the workshop:
* Z. Z. Sun, C. A. Hayes, J. Shin, F. Caschera, R. M. Murray, V. Noireaux, [http://www.jove.com/video/50762 Protocols for Implementing an Escherichia Coli Based TX-TL Cell-Free Expression System for Synthetic Biology]. ''Journal. of Visualized Experiments'' (JoVE), e50762, doi:10.3791/50762 (2013).

If you have time, we also encourage you to take a look at the following material before arriving:
* J. Shin and V. Noireaux, [http://pubs.acs.org/doi/abs/10.1021/sb200016s An ''E. coli'' cell-free expression toolbox: application to synthetic gene circuits and artificial cells]. ''ACS Synthetic Biology'', 1(1):29–41, 2012.

* Z. Z. Sun, E. Yeung, C. A. Hayes, V. Noireaux and Richard M. Murray, [http://www.cds.caltech.edu/~murray/papers/sun+13-acs_synbio.html Linear DNA for rapid prototyping of synthetic biological circuits in an ''Escherichia coli'' based TX-TL cell-free system]. ''ACS Synthetic Biology'', 2014.

* [http://openwetware.org/wiki/Biomolecular_Breadboards Biomolecular Breadboards pages on OpenWetWare]
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Models Modeling overview] - setting up simulations using MATLAB-based TX-TL toolbox
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Preliminary_Data Preliminary data] - includes linear DNA protection, protein degradation
** [http://openwetware.org/wiki/Biomolecular_Breadboards:More_Info More info] - additional references and presentations on TX-TL

=== Software ===
We will make use of the following software as part of the workshop:
* Microsoft Excel (or Numbers)
* [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE] (free), [http://www.geneious.com Geneious] (free trial)
* [http://www.mathworks.com MATLAB], [http://www.mathworks.com/products/simbiology/ Simbiology]
* [http://sourceforge.net/projects/txtl/ TX-TL modeling toolbox] (requires MATLAB 2010+ and SimBiology]
Participants are encouraged to install this software on their laptops prior to the workshop, but version of the software will also be available on lab computers.

TX-TL Bootcamp, Jun 2015

2015-06-16T18:08:56Z

Chayes: /* Tue evening */

Caltech will be hosting a hands-on "bootcamp" on cell-free prototyping and debugging of biological circuits. This page contains information for the TX-TL workshop, which will take place at Caltech on 16-18 Jun 2015. This workshop is by invitation only. __NOTOC__

=== Workshop goals ===
The purpose of the workshop is to provide participants with a working knowledge of cell-free methods for design of biomolecular circuits, using the TX-TL system developed by Vincent Noireaux at U. Minnesota. By the end of the workshop, participants will be able to:

* Build models and simulate circuits using the TX-TL modeling toolbox (MATLAB-based)
* Assemble and test genetic circuits using linear DNA assembly in a single day
* Test and characterize circuits that are part of our current research activities

=== Summary Schedule ===

The schedule below gives an overview of the activities during the workshop.

{| width=100% border=1
|- valign=top
| width=25% |
==== Tue morning ====

| width=25% |

==== Wed morning ====
9-12 pm: Meet in '''111 Keck'''
* Analyzing TX-TL results (from overnight run)
* Presentation: TX-TL using linear DNA
* Lab (136 Keck): Set up Golden Gate reactions

Group lunch at Chandler (when done)
| width= 25% |

==== Thu morning ====
9 am - Analyze TX-TL results from previous day '''[110 Steele?]'''

10 am - Group projects: Set up experiment

12pm: Group lunch

| width=25% |

==== Fri morning ====
9 am: Group projects: Create group presentation
|- valign=top
| width= 25% |

==== Tue afternoon ====
11 am: '''Bootcamp starts''', '''111 Keck''' (lunch will be provided)
* Overview of workshop and TX-TL system (Richard)
* Lab safety briefing (Clare)

1:45-5 pm: SURF check-in and orientation
* 1:45-3 pm: SURF checkin
* 1:45-3:45 pm: Housing move in
* 3:45-5 pm: SURF orientation
| width= 25% |

==== Wed afternoon ====
1:30 - 2:30 pm - SURF safety meeting (mandatory)

2:30 pm: Set up PCR reactions for GGA linear DNAs (Clare)

3 pm - Project discussions (with co-mentors) at CDS tea and/or initial experiments

| width= 25% |

==== Thu afternoon ====
Group projects: Set up experiments

| width=25% |

==== Fri afternoon ====
1-3 pm: Group presentations '''(111 Keck)'''

|- valign=top
|

==== Tue evening ====
5-7 pm: SURF BBQ

7 pm: Meet in '''111 Keck'''

Lab session: 7-9 pm
* Set up and run first TX-TL reactions

| width=25% |

==== Wed evening ====
5-8 pm: Meet in '''111 Keck'''

* Lab (136 Keck): Set up FFL runs from GGA assembly

| width=25% |

==== Thu evening ====
Group projects: Set up overnight experiments

| width=25% |
|}

Description of tutorials:
* Lab basics - this tutorial is intended for participants who have not had any experience in a molecular biology lab. You will learn how to pipette small volumes of clear fluids, run PCR reactions and run gels. If you have had an undergraduate lab class in biology in the last 10 years, you probably don't need to come.

* MATLAB basics - this tutorial is for participants who have never used the MATLAB program. You will learn how to load and plot data in MATLAB and how to use the SimBiology toolbox for setting up very simple reactions.

* Sequence editing - this tutorial will show how to use a DNA sequence editing program such as Geneious or ApE (we mainly use Geneious). You'll learn how to annotate a sequence, simulate PCR reactions and other similar techniques.

=== Read-ahead material ===

We will assume everyone has watched the following 15 minute video before attending the workshop:
* Z. Z. Sun, C. A. Hayes, J. Shin, F. Caschera, R. M. Murray, V. Noireaux, [http://www.jove.com/video/50762 Protocols for Implementing an Escherichia Coli Based TX-TL Cell-Free Expression System for Synthetic Biology]. ''Journal. of Visualized Experiments'' (JoVE), e50762, doi:10.3791/50762 (2013).

If you have time, we also encourage you to take a look at the following material before arriving:
* J. Shin and V. Noireaux, [http://pubs.acs.org/doi/abs/10.1021/sb200016s An ''E. coli'' cell-free expression toolbox: application to synthetic gene circuits and artificial cells]. ''ACS Synthetic Biology'', 1(1):29–41, 2012.

* Z. Z. Sun, E. Yeung, C. A. Hayes, V. Noireaux and Richard M. Murray, [http://www.cds.caltech.edu/~murray/papers/sun+13-acs_synbio.html Linear DNA for rapid prototyping of synthetic biological circuits in an ''Escherichia coli'' based TX-TL cell-free system]. ''ACS Synthetic Biology'', 2014.

* [http://openwetware.org/wiki/Biomolecular_Breadboards Biomolecular Breadboards pages on OpenWetWare]
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Models Modeling overview] - setting up simulations using MATLAB-based TX-TL toolbox
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Preliminary_Data Preliminary data] - includes linear DNA protection, protein degradation
** [http://openwetware.org/wiki/Biomolecular_Breadboards:More_Info More info] - additional references and presentations on TX-TL

=== Software ===
We will make use of the following software as part of the workshop:
* Microsoft Excel (or Numbers)
* [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE] (free), [http://www.geneious.com Geneious] (free trial)
* [http://www.mathworks.com MATLAB], [http://www.mathworks.com/products/simbiology/ Simbiology]
* [http://sourceforge.net/projects/txtl/ TX-TL modeling toolbox] (requires MATLAB 2010+ and SimBiology]
Participants are encouraged to install this software on their laptops prior to the workshop, but version of the software will also be available on lab computers.

TX-TL Bootcamp, Jun 2015

2015-06-16T17:03:14Z

Chayes: /* Fri afternoon */

Caltech will be hosting a hands-on "bootcamp" on cell-free prototyping and debugging of biological circuits. This page contains information for the TX-TL workshop, which will take place at Caltech on 16-18 Jun 2015. This workshop is by invitation only. __NOTOC__

=== Workshop goals ===
The purpose of the workshop is to provide participants with a working knowledge of cell-free methods for design of biomolecular circuits, using the TX-TL system developed by Vincent Noireaux at U. Minnesota. By the end of the workshop, participants will be able to:

* Build models and simulate circuits using the TX-TL modeling toolbox (MATLAB-based)
* Assemble and test genetic circuits using linear DNA assembly in a single day
* Test and characterize circuits that are part of our current research activities

=== Summary Schedule ===

The schedule below gives an overview of the activities during the workshop.

{| width=100% border=1
|- valign=top
| width=25% |
==== Tue morning ====

| width=25% |

==== Wed morning ====
9-12 pm: Meet in '''111 Keck'''
* Analyzing TX-TL results (from overnight run)
* Presentation: TX-TL using linear DNA
* Lab (136 Keck): Set up Golden Gate reactions

Group lunch at Chandler (when done)
| width= 25% |

==== Thu morning ====
9 am - Analyze TX-TL results from previous day '''[110 Steele]'''

10 am - Group projects: Set up experiment

12pm: Group lunch

| width=25% |

==== Fri morning ====
9 am: Group projects: Create group presentation
|- valign=top
| width= 25% |

==== Tue afternoon ====
11 am: '''Bootcamp starts''', '''213 Annenberg''' (lunch will be provided)
* Overview of workshop and TX-TL system (Richard)
* Lab safety briefing (Clare)

1:45-5 pm: SURF check-in and orientation
* 1:45-3 pm: SURF checkin
* 1:45-3:45 pm: Housing move in
* 3:45-5 pm: SURF orientation
| width= 25% |

==== Wed afternoon ====
1:30 - 2:30 pm - SURF safety meeting (mandatory)

2:30 pm: Set up PCR reactions for GGA linear DNAs (Clare)

3 pm - Project discussions (with co-mentors) at CDS tea and/or initial experiments

| width= 25% |

==== Thu afternoon ====
Group projects: Set up experiments

| width=25% |

==== Fri afternoon ====
1-3 pm: Group presentations '''(111 Keck)'''

|- valign=top
|

==== Tue evening ====
5-7 pm: SURF BBQ

Lab session: 7-9 pm
* Set up and run first TX-TL reactions

| width=25% |
==== Wed evening ====
5-8 pm: Meet in '''111 Keck'''

* Lab (136 Keck): Set up FFL runs from GGA assembly

| width=25% |

==== Thu evening ====
Group projects: Set up overnight experiments

| width=25% |
|}

Description of tutorials:
* Lab basics - this tutorial is intended for participants who have not had any experience in a molecular biology lab. You will learn how to pipette small volumes of clear fluids, run PCR reactions and run gels. If you have had an undergraduate lab class in biology in the last 10 years, you probably don't need to come.

* MATLAB basics - this tutorial is for participants who have never used the MATLAB program. You will learn how to load and plot data in MATLAB and how to use the SimBiology toolbox for setting up very simple reactions.

* Sequence editing - this tutorial will show how to use a DNA sequence editing program such as Geneious or ApE (we mainly use Geneious). You'll learn how to annotate a sequence, simulate PCR reactions and other similar techniques.

=== Read-ahead material ===

We will assume everyone has watched the following 15 minute video before attending the workshop:
* Z. Z. Sun, C. A. Hayes, J. Shin, F. Caschera, R. M. Murray, V. Noireaux, [http://www.jove.com/video/50762 Protocols for Implementing an Escherichia Coli Based TX-TL Cell-Free Expression System for Synthetic Biology]. ''Journal. of Visualized Experiments'' (JoVE), e50762, doi:10.3791/50762 (2013).

If you have time, we also encourage you to take a look at the following material before arriving:
* J. Shin and V. Noireaux, [http://pubs.acs.org/doi/abs/10.1021/sb200016s An ''E. coli'' cell-free expression toolbox: application to synthetic gene circuits and artificial cells]. ''ACS Synthetic Biology'', 1(1):29–41, 2012.

* Z. Z. Sun, E. Yeung, C. A. Hayes, V. Noireaux and Richard M. Murray, [http://www.cds.caltech.edu/~murray/papers/sun+13-acs_synbio.html Linear DNA for rapid prototyping of synthetic biological circuits in an ''Escherichia coli'' based TX-TL cell-free system]. ''ACS Synthetic Biology'', 2014.

* [http://openwetware.org/wiki/Biomolecular_Breadboards Biomolecular Breadboards pages on OpenWetWare]
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Models Modeling overview] - setting up simulations using MATLAB-based TX-TL toolbox
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Preliminary_Data Preliminary data] - includes linear DNA protection, protein degradation
** [http://openwetware.org/wiki/Biomolecular_Breadboards:More_Info More info] - additional references and presentations on TX-TL

=== Software ===
We will make use of the following software as part of the workshop:
* Microsoft Excel (or Numbers)
* [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE] (free), [http://www.geneious.com Geneious] (free trial)
* [http://www.mathworks.com MATLAB], [http://www.mathworks.com/products/simbiology/ Simbiology]
* [http://sourceforge.net/projects/txtl/ TX-TL modeling toolbox] (requires MATLAB 2010+ and SimBiology]
Participants are encouraged to install this software on their laptops prior to the workshop, but version of the software will also be available on lab computers.

TX-TL Bootcamp, Jun 2015

2015-06-16T17:02:52Z

Chayes: /* Thu morning */

Caltech will be hosting a hands-on "bootcamp" on cell-free prototyping and debugging of biological circuits. This page contains information for the TX-TL workshop, which will take place at Caltech on 16-18 Jun 2015. This workshop is by invitation only. __NOTOC__

=== Workshop goals ===
The purpose of the workshop is to provide participants with a working knowledge of cell-free methods for design of biomolecular circuits, using the TX-TL system developed by Vincent Noireaux at U. Minnesota. By the end of the workshop, participants will be able to:

* Build models and simulate circuits using the TX-TL modeling toolbox (MATLAB-based)
* Assemble and test genetic circuits using linear DNA assembly in a single day
* Test and characterize circuits that are part of our current research activities

=== Summary Schedule ===

The schedule below gives an overview of the activities during the workshop.

{| width=100% border=1
|- valign=top
| width=25% |
==== Tue morning ====

| width=25% |

==== Wed morning ====
9-12 pm: Meet in '''111 Keck'''
* Analyzing TX-TL results (from overnight run)
* Presentation: TX-TL using linear DNA
* Lab (136 Keck): Set up Golden Gate reactions

Group lunch at Chandler (when done)
| width= 25% |

==== Thu morning ====
9 am - Analyze TX-TL results from previous day '''[110 Steele]'''

10 am - Group projects: Set up experiment

12pm: Group lunch

| width=25% |

==== Fri morning ====
9 am: Group projects: Create group presentation
|- valign=top
| width= 25% |

==== Tue afternoon ====
11 am: '''Bootcamp starts''', '''213 Annenberg''' (lunch will be provided)
* Overview of workshop and TX-TL system (Richard)
* Lab safety briefing (Clare)

1:45-5 pm: SURF check-in and orientation
* 1:45-3 pm: SURF checkin
* 1:45-3:45 pm: Housing move in
* 3:45-5 pm: SURF orientation
| width= 25% |

==== Wed afternoon ====
1:30 - 2:30 pm - SURF safety meeting (mandatory)

2:30 pm: Set up PCR reactions for GGA linear DNAs (Clare)

3 pm - Project discussions (with co-mentors) at CDS tea and/or initial experiments

| width= 25% |

==== Thu afternoon ====
Group projects: Set up experiments

| width=25% |

==== Fri afternoon ====
1-3 pm: Group presentations

|- valign=top
|

==== Tue evening ====
5-7 pm: SURF BBQ

Lab session: 7-9 pm
* Set up and run first TX-TL reactions

| width=25% |
==== Wed evening ====
5-8 pm: Meet in '''111 Keck'''

* Lab (136 Keck): Set up FFL runs from GGA assembly

| width=25% |

==== Thu evening ====
Group projects: Set up overnight experiments

| width=25% |
|}

Description of tutorials:
* Lab basics - this tutorial is intended for participants who have not had any experience in a molecular biology lab. You will learn how to pipette small volumes of clear fluids, run PCR reactions and run gels. If you have had an undergraduate lab class in biology in the last 10 years, you probably don't need to come.

* MATLAB basics - this tutorial is for participants who have never used the MATLAB program. You will learn how to load and plot data in MATLAB and how to use the SimBiology toolbox for setting up very simple reactions.

* Sequence editing - this tutorial will show how to use a DNA sequence editing program such as Geneious or ApE (we mainly use Geneious). You'll learn how to annotate a sequence, simulate PCR reactions and other similar techniques.

=== Read-ahead material ===

We will assume everyone has watched the following 15 minute video before attending the workshop:
* Z. Z. Sun, C. A. Hayes, J. Shin, F. Caschera, R. M. Murray, V. Noireaux, [http://www.jove.com/video/50762 Protocols for Implementing an Escherichia Coli Based TX-TL Cell-Free Expression System for Synthetic Biology]. ''Journal. of Visualized Experiments'' (JoVE), e50762, doi:10.3791/50762 (2013).

If you have time, we also encourage you to take a look at the following material before arriving:
* J. Shin and V. Noireaux, [http://pubs.acs.org/doi/abs/10.1021/sb200016s An ''E. coli'' cell-free expression toolbox: application to synthetic gene circuits and artificial cells]. ''ACS Synthetic Biology'', 1(1):29–41, 2012.

* Z. Z. Sun, E. Yeung, C. A. Hayes, V. Noireaux and Richard M. Murray, [http://www.cds.caltech.edu/~murray/papers/sun+13-acs_synbio.html Linear DNA for rapid prototyping of synthetic biological circuits in an ''Escherichia coli'' based TX-TL cell-free system]. ''ACS Synthetic Biology'', 2014.

* [http://openwetware.org/wiki/Biomolecular_Breadboards Biomolecular Breadboards pages on OpenWetWare]
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Models Modeling overview] - setting up simulations using MATLAB-based TX-TL toolbox
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Preliminary_Data Preliminary data] - includes linear DNA protection, protein degradation
** [http://openwetware.org/wiki/Biomolecular_Breadboards:More_Info More info] - additional references and presentations on TX-TL

=== Software ===
We will make use of the following software as part of the workshop:
* Microsoft Excel (or Numbers)
* [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE] (free), [http://www.geneious.com Geneious] (free trial)
* [http://www.mathworks.com MATLAB], [http://www.mathworks.com/products/simbiology/ Simbiology]
* [http://sourceforge.net/projects/txtl/ TX-TL modeling toolbox] (requires MATLAB 2010+ and SimBiology]
Participants are encouraged to install this software on their laptops prior to the workshop, but version of the software will also be available on lab computers.

TX-TL Bootcamp, Jun 2015

2015-06-16T17:02:36Z

Chayes: /* Wed evening */

Caltech will be hosting a hands-on "bootcamp" on cell-free prototyping and debugging of biological circuits. This page contains information for the TX-TL workshop, which will take place at Caltech on 16-18 Jun 2015. This workshop is by invitation only. __NOTOC__

=== Workshop goals ===
The purpose of the workshop is to provide participants with a working knowledge of cell-free methods for design of biomolecular circuits, using the TX-TL system developed by Vincent Noireaux at U. Minnesota. By the end of the workshop, participants will be able to:

* Build models and simulate circuits using the TX-TL modeling toolbox (MATLAB-based)
* Assemble and test genetic circuits using linear DNA assembly in a single day
* Test and characterize circuits that are part of our current research activities

=== Summary Schedule ===

The schedule below gives an overview of the activities during the workshop.

{| width=100% border=1
|- valign=top
| width=25% |
==== Tue morning ====

| width=25% |

==== Wed morning ====
9-12 pm: Meet in '''111 Keck'''
* Analyzing TX-TL results (from overnight run)
* Presentation: TX-TL using linear DNA
* Lab (136 Keck): Set up Golden Gate reactions

Group lunch at Chandler (when done)
| width= 25% |

==== Thu morning ====
9 am - Analyze TX-TL results from previous day [110 Steele]

10 am - Group projects: Set up experiment

12pm: Group lunch

| width=25% |

==== Fri morning ====
9 am: Group projects: Create group presentation
|- valign=top
| width= 25% |

==== Tue afternoon ====
11 am: '''Bootcamp starts''', '''213 Annenberg''' (lunch will be provided)
* Overview of workshop and TX-TL system (Richard)
* Lab safety briefing (Clare)

1:45-5 pm: SURF check-in and orientation
* 1:45-3 pm: SURF checkin
* 1:45-3:45 pm: Housing move in
* 3:45-5 pm: SURF orientation
| width= 25% |

==== Wed afternoon ====
1:30 - 2:30 pm - SURF safety meeting (mandatory)

2:30 pm: Set up PCR reactions for GGA linear DNAs (Clare)

3 pm - Project discussions (with co-mentors) at CDS tea and/or initial experiments

| width= 25% |

==== Thu afternoon ====
Group projects: Set up experiments

| width=25% |

==== Fri afternoon ====
1-3 pm: Group presentations

|- valign=top
|

==== Tue evening ====
5-7 pm: SURF BBQ

Lab session: 7-9 pm
* Set up and run first TX-TL reactions

| width=25% |
==== Wed evening ====
5-8 pm: Meet in '''111 Keck'''

* Lab (136 Keck): Set up FFL runs from GGA assembly

| width=25% |

==== Thu evening ====
Group projects: Set up overnight experiments

| width=25% |
|}

Description of tutorials:
* Lab basics - this tutorial is intended for participants who have not had any experience in a molecular biology lab. You will learn how to pipette small volumes of clear fluids, run PCR reactions and run gels. If you have had an undergraduate lab class in biology in the last 10 years, you probably don't need to come.

* MATLAB basics - this tutorial is for participants who have never used the MATLAB program. You will learn how to load and plot data in MATLAB and how to use the SimBiology toolbox for setting up very simple reactions.

* Sequence editing - this tutorial will show how to use a DNA sequence editing program such as Geneious or ApE (we mainly use Geneious). You'll learn how to annotate a sequence, simulate PCR reactions and other similar techniques.

=== Read-ahead material ===

We will assume everyone has watched the following 15 minute video before attending the workshop:
* Z. Z. Sun, C. A. Hayes, J. Shin, F. Caschera, R. M. Murray, V. Noireaux, [http://www.jove.com/video/50762 Protocols for Implementing an Escherichia Coli Based TX-TL Cell-Free Expression System for Synthetic Biology]. ''Journal. of Visualized Experiments'' (JoVE), e50762, doi:10.3791/50762 (2013).

If you have time, we also encourage you to take a look at the following material before arriving:
* J. Shin and V. Noireaux, [http://pubs.acs.org/doi/abs/10.1021/sb200016s An ''E. coli'' cell-free expression toolbox: application to synthetic gene circuits and artificial cells]. ''ACS Synthetic Biology'', 1(1):29–41, 2012.

* Z. Z. Sun, E. Yeung, C. A. Hayes, V. Noireaux and Richard M. Murray, [http://www.cds.caltech.edu/~murray/papers/sun+13-acs_synbio.html Linear DNA for rapid prototyping of synthetic biological circuits in an ''Escherichia coli'' based TX-TL cell-free system]. ''ACS Synthetic Biology'', 2014.

* [http://openwetware.org/wiki/Biomolecular_Breadboards Biomolecular Breadboards pages on OpenWetWare]
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Models Modeling overview] - setting up simulations using MATLAB-based TX-TL toolbox
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Preliminary_Data Preliminary data] - includes linear DNA protection, protein degradation
** [http://openwetware.org/wiki/Biomolecular_Breadboards:More_Info More info] - additional references and presentations on TX-TL

=== Software ===
We will make use of the following software as part of the workshop:
* Microsoft Excel (or Numbers)
* [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE] (free), [http://www.geneious.com Geneious] (free trial)
* [http://www.mathworks.com MATLAB], [http://www.mathworks.com/products/simbiology/ Simbiology]
* [http://sourceforge.net/projects/txtl/ TX-TL modeling toolbox] (requires MATLAB 2010+ and SimBiology]
Participants are encouraged to install this software on their laptops prior to the workshop, but version of the software will also be available on lab computers.

TX-TL Bootcamp, Jun 2015

2015-06-16T17:02:13Z

Chayes: /* Wed evening */

Caltech will be hosting a hands-on "bootcamp" on cell-free prototyping and debugging of biological circuits. This page contains information for the TX-TL workshop, which will take place at Caltech on 16-18 Jun 2015. This workshop is by invitation only. __NOTOC__

=== Workshop goals ===
The purpose of the workshop is to provide participants with a working knowledge of cell-free methods for design of biomolecular circuits, using the TX-TL system developed by Vincent Noireaux at U. Minnesota. By the end of the workshop, participants will be able to:

* Build models and simulate circuits using the TX-TL modeling toolbox (MATLAB-based)
* Assemble and test genetic circuits using linear DNA assembly in a single day
* Test and characterize circuits that are part of our current research activities

=== Summary Schedule ===

The schedule below gives an overview of the activities during the workshop.

{| width=100% border=1
|- valign=top
| width=25% |
==== Tue morning ====

| width=25% |

==== Wed morning ====
9-12 pm: Meet in '''111 Keck'''
* Analyzing TX-TL results (from overnight run)
* Presentation: TX-TL using linear DNA
* Lab (136 Keck): Set up Golden Gate reactions

Group lunch at Chandler (when done)
| width= 25% |

==== Thu morning ====
9 am - Analyze TX-TL results from previous day [110 Steele]

10 am - Group projects: Set up experiment

12pm: Group lunch

| width=25% |

==== Fri morning ====
9 am: Group projects: Create group presentation
|- valign=top
| width= 25% |

==== Tue afternoon ====
11 am: '''Bootcamp starts''', '''213 Annenberg''' (lunch will be provided)
* Overview of workshop and TX-TL system (Richard)
* Lab safety briefing (Clare)

1:45-5 pm: SURF check-in and orientation
* 1:45-3 pm: SURF checkin
* 1:45-3:45 pm: Housing move in
* 3:45-5 pm: SURF orientation
| width= 25% |

==== Wed afternoon ====
1:30 - 2:30 pm - SURF safety meeting (mandatory)

2:30 pm: Set up PCR reactions for GGA linear DNAs (Clare)

3 pm - Project discussions (with co-mentors) at CDS tea and/or initial experiments

| width= 25% |

==== Thu afternoon ====
Group projects: Set up experiments

| width=25% |

==== Fri afternoon ====
1-3 pm: Group presentations

|- valign=top
|

==== Tue evening ====
5-7 pm: SURF BBQ

Lab session: 7-9 pm
* Set up and run first TX-TL reactions

| width=25% |
==== Wed evening ====
5-8 pm: Meet in '''111 Keck'''

Set up FFL runs from GGA assembly

| width=25% |

==== Thu evening ====
Group projects: Set up overnight experiments

| width=25% |
|}

Description of tutorials:
* Lab basics - this tutorial is intended for participants who have not had any experience in a molecular biology lab. You will learn how to pipette small volumes of clear fluids, run PCR reactions and run gels. If you have had an undergraduate lab class in biology in the last 10 years, you probably don't need to come.

* MATLAB basics - this tutorial is for participants who have never used the MATLAB program. You will learn how to load and plot data in MATLAB and how to use the SimBiology toolbox for setting up very simple reactions.

* Sequence editing - this tutorial will show how to use a DNA sequence editing program such as Geneious or ApE (we mainly use Geneious). You'll learn how to annotate a sequence, simulate PCR reactions and other similar techniques.

=== Read-ahead material ===

We will assume everyone has watched the following 15 minute video before attending the workshop:
* Z. Z. Sun, C. A. Hayes, J. Shin, F. Caschera, R. M. Murray, V. Noireaux, [http://www.jove.com/video/50762 Protocols for Implementing an Escherichia Coli Based TX-TL Cell-Free Expression System for Synthetic Biology]. ''Journal. of Visualized Experiments'' (JoVE), e50762, doi:10.3791/50762 (2013).

If you have time, we also encourage you to take a look at the following material before arriving:
* J. Shin and V. Noireaux, [http://pubs.acs.org/doi/abs/10.1021/sb200016s An ''E. coli'' cell-free expression toolbox: application to synthetic gene circuits and artificial cells]. ''ACS Synthetic Biology'', 1(1):29–41, 2012.

* Z. Z. Sun, E. Yeung, C. A. Hayes, V. Noireaux and Richard M. Murray, [http://www.cds.caltech.edu/~murray/papers/sun+13-acs_synbio.html Linear DNA for rapid prototyping of synthetic biological circuits in an ''Escherichia coli'' based TX-TL cell-free system]. ''ACS Synthetic Biology'', 2014.

* [http://openwetware.org/wiki/Biomolecular_Breadboards Biomolecular Breadboards pages on OpenWetWare]
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Models Modeling overview] - setting up simulations using MATLAB-based TX-TL toolbox
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Preliminary_Data Preliminary data] - includes linear DNA protection, protein degradation
** [http://openwetware.org/wiki/Biomolecular_Breadboards:More_Info More info] - additional references and presentations on TX-TL

=== Software ===
We will make use of the following software as part of the workshop:
* Microsoft Excel (or Numbers)
* [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE] (free), [http://www.geneious.com Geneious] (free trial)
* [http://www.mathworks.com MATLAB], [http://www.mathworks.com/products/simbiology/ Simbiology]
* [http://sourceforge.net/projects/txtl/ TX-TL modeling toolbox] (requires MATLAB 2010+ and SimBiology]
Participants are encouraged to install this software on their laptops prior to the workshop, but version of the software will also be available on lab computers.

TX-TL Bootcamp, Jun 2015

2015-06-16T17:01:32Z

Chayes: /* Wed morning */

Caltech will be hosting a hands-on "bootcamp" on cell-free prototyping and debugging of biological circuits. This page contains information for the TX-TL workshop, which will take place at Caltech on 16-18 Jun 2015. This workshop is by invitation only. __NOTOC__

=== Workshop goals ===
The purpose of the workshop is to provide participants with a working knowledge of cell-free methods for design of biomolecular circuits, using the TX-TL system developed by Vincent Noireaux at U. Minnesota. By the end of the workshop, participants will be able to:

* Build models and simulate circuits using the TX-TL modeling toolbox (MATLAB-based)
* Assemble and test genetic circuits using linear DNA assembly in a single day
* Test and characterize circuits that are part of our current research activities

=== Summary Schedule ===

The schedule below gives an overview of the activities during the workshop.

{| width=100% border=1
|- valign=top
| width=25% |
==== Tue morning ====

| width=25% |

==== Wed morning ====
9-12 pm: Meet in '''111 Keck'''
* Analyzing TX-TL results (from overnight run)
* Presentation: TX-TL using linear DNA
* Lab (136 Keck): Set up Golden Gate reactions

Group lunch at Chandler (when done)
| width= 25% |

==== Thu morning ====
9 am - Analyze TX-TL results from previous day [110 Steele]

10 am - Group projects: Set up experiment

12pm: Group lunch

| width=25% |

==== Fri morning ====
9 am: Group projects: Create group presentation
|- valign=top
| width= 25% |

==== Tue afternoon ====
11 am: '''Bootcamp starts''', '''213 Annenberg''' (lunch will be provided)
* Overview of workshop and TX-TL system (Richard)
* Lab safety briefing (Clare)

1:45-5 pm: SURF check-in and orientation
* 1:45-3 pm: SURF checkin
* 1:45-3:45 pm: Housing move in
* 3:45-5 pm: SURF orientation
| width= 25% |

==== Wed afternoon ====
1:30 - 2:30 pm - SURF safety meeting (mandatory)

2:30 pm: Set up PCR reactions for GGA linear DNAs (Clare)

3 pm - Project discussions (with co-mentors) at CDS tea and/or initial experiments

| width= 25% |

==== Thu afternoon ====
Group projects: Set up experiments

| width=25% |

==== Fri afternoon ====
1-3 pm: Group presentations

|- valign=top
|

==== Tue evening ====
5-7 pm: SURF BBQ

Lab session: 7-9 pm
* Set up and run first TX-TL reactions

| width=25% |
==== Wed evening ====
5-8 pm - Set up FFL runs from GGA assembly

| width=25% |
==== Thu evening ====
Group projects: Set up overnight experiments

| width=25% |
|}

Description of tutorials:
* Lab basics - this tutorial is intended for participants who have not had any experience in a molecular biology lab. You will learn how to pipette small volumes of clear fluids, run PCR reactions and run gels. If you have had an undergraduate lab class in biology in the last 10 years, you probably don't need to come.

* MATLAB basics - this tutorial is for participants who have never used the MATLAB program. You will learn how to load and plot data in MATLAB and how to use the SimBiology toolbox for setting up very simple reactions.

* Sequence editing - this tutorial will show how to use a DNA sequence editing program such as Geneious or ApE (we mainly use Geneious). You'll learn how to annotate a sequence, simulate PCR reactions and other similar techniques.

=== Read-ahead material ===

We will assume everyone has watched the following 15 minute video before attending the workshop:
* Z. Z. Sun, C. A. Hayes, J. Shin, F. Caschera, R. M. Murray, V. Noireaux, [http://www.jove.com/video/50762 Protocols for Implementing an Escherichia Coli Based TX-TL Cell-Free Expression System for Synthetic Biology]. ''Journal. of Visualized Experiments'' (JoVE), e50762, doi:10.3791/50762 (2013).

If you have time, we also encourage you to take a look at the following material before arriving:
* J. Shin and V. Noireaux, [http://pubs.acs.org/doi/abs/10.1021/sb200016s An ''E. coli'' cell-free expression toolbox: application to synthetic gene circuits and artificial cells]. ''ACS Synthetic Biology'', 1(1):29–41, 2012.

* Z. Z. Sun, E. Yeung, C. A. Hayes, V. Noireaux and Richard M. Murray, [http://www.cds.caltech.edu/~murray/papers/sun+13-acs_synbio.html Linear DNA for rapid prototyping of synthetic biological circuits in an ''Escherichia coli'' based TX-TL cell-free system]. ''ACS Synthetic Biology'', 2014.

* [http://openwetware.org/wiki/Biomolecular_Breadboards Biomolecular Breadboards pages on OpenWetWare]
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Models Modeling overview] - setting up simulations using MATLAB-based TX-TL toolbox
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Preliminary_Data Preliminary data] - includes linear DNA protection, protein degradation
** [http://openwetware.org/wiki/Biomolecular_Breadboards:More_Info More info] - additional references and presentations on TX-TL

=== Software ===
We will make use of the following software as part of the workshop:
* Microsoft Excel (or Numbers)
* [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE] (free), [http://www.geneious.com Geneious] (free trial)
* [http://www.mathworks.com MATLAB], [http://www.mathworks.com/products/simbiology/ Simbiology]
* [http://sourceforge.net/projects/txtl/ TX-TL modeling toolbox] (requires MATLAB 2010+ and SimBiology]
Participants are encouraged to install this software on their laptops prior to the workshop, but version of the software will also be available on lab computers.

TX-TL Bootcamp, Jun 2015

2015-06-16T17:00:14Z

Chayes: /* Tue afternoon */

Caltech will be hosting a hands-on "bootcamp" on cell-free prototyping and debugging of biological circuits. This page contains information for the TX-TL workshop, which will take place at Caltech on 16-18 Jun 2015. This workshop is by invitation only. __NOTOC__

=== Workshop goals ===
The purpose of the workshop is to provide participants with a working knowledge of cell-free methods for design of biomolecular circuits, using the TX-TL system developed by Vincent Noireaux at U. Minnesota. By the end of the workshop, participants will be able to:

* Build models and simulate circuits using the TX-TL modeling toolbox (MATLAB-based)
* Assemble and test genetic circuits using linear DNA assembly in a single day
* Test and characterize circuits that are part of our current research activities

=== Summary Schedule ===

The schedule below gives an overview of the activities during the workshop.

{| width=100% border=1
|- valign=top
| width=25% |
==== Tue morning ====

| width=25% |

==== Wed morning ====
9-12 pm: Meet in 110 Steele
* Analyzing TX-TL results (from overnight run)
* Presentation: TX-TL using linear DNA
* Lab (136 Keck): Set up Golden Gate reactions

Group lunch at Chandler (when done)
| width= 25% |

==== Thu morning ====
9 am - Analyze TX-TL results from previous day [110 Steele]

10 am - Group projects: Set up experiment

12pm: Group lunch

| width=25% |

==== Fri morning ====
9 am: Group projects: Create group presentation
|- valign=top
| width= 25% |

==== Tue afternoon ====
11 am: '''Bootcamp starts''', '''213 Annenberg''' (lunch will be provided)
* Overview of workshop and TX-TL system (Richard)
* Lab safety briefing (Clare)

1:45-5 pm: SURF check-in and orientation
* 1:45-3 pm: SURF checkin
* 1:45-3:45 pm: Housing move in
* 3:45-5 pm: SURF orientation
| width= 25% |

==== Wed afternoon ====
1:30 - 2:30 pm - SURF safety meeting (mandatory)

2:30 pm: Set up PCR reactions for GGA linear DNAs (Clare)

3 pm - Project discussions (with co-mentors) at CDS tea and/or initial experiments

| width= 25% |

==== Thu afternoon ====
Group projects: Set up experiments

| width=25% |

==== Fri afternoon ====
1-3 pm: Group presentations

|- valign=top
|

==== Tue evening ====
5-7 pm: SURF BBQ

Lab session: 7-9 pm
* Set up and run first TX-TL reactions

| width=25% |
==== Wed evening ====
5-8 pm - Set up FFL runs from GGA assembly

| width=25% |
==== Thu evening ====
Group projects: Set up overnight experiments

| width=25% |
|}

Description of tutorials:
* Lab basics - this tutorial is intended for participants who have not had any experience in a molecular biology lab. You will learn how to pipette small volumes of clear fluids, run PCR reactions and run gels. If you have had an undergraduate lab class in biology in the last 10 years, you probably don't need to come.

* MATLAB basics - this tutorial is for participants who have never used the MATLAB program. You will learn how to load and plot data in MATLAB and how to use the SimBiology toolbox for setting up very simple reactions.

* Sequence editing - this tutorial will show how to use a DNA sequence editing program such as Geneious or ApE (we mainly use Geneious). You'll learn how to annotate a sequence, simulate PCR reactions and other similar techniques.

=== Read-ahead material ===

We will assume everyone has watched the following 15 minute video before attending the workshop:
* Z. Z. Sun, C. A. Hayes, J. Shin, F. Caschera, R. M. Murray, V. Noireaux, [http://www.jove.com/video/50762 Protocols for Implementing an Escherichia Coli Based TX-TL Cell-Free Expression System for Synthetic Biology]. ''Journal. of Visualized Experiments'' (JoVE), e50762, doi:10.3791/50762 (2013).

If you have time, we also encourage you to take a look at the following material before arriving:
* J. Shin and V. Noireaux, [http://pubs.acs.org/doi/abs/10.1021/sb200016s An ''E. coli'' cell-free expression toolbox: application to synthetic gene circuits and artificial cells]. ''ACS Synthetic Biology'', 1(1):29–41, 2012.

* Z. Z. Sun, E. Yeung, C. A. Hayes, V. Noireaux and Richard M. Murray, [http://www.cds.caltech.edu/~murray/papers/sun+13-acs_synbio.html Linear DNA for rapid prototyping of synthetic biological circuits in an ''Escherichia coli'' based TX-TL cell-free system]. ''ACS Synthetic Biology'', 2014.

* [http://openwetware.org/wiki/Biomolecular_Breadboards Biomolecular Breadboards pages on OpenWetWare]
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Models Modeling overview] - setting up simulations using MATLAB-based TX-TL toolbox
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Preliminary_Data Preliminary data] - includes linear DNA protection, protein degradation
** [http://openwetware.org/wiki/Biomolecular_Breadboards:More_Info More info] - additional references and presentations on TX-TL

=== Software ===
We will make use of the following software as part of the workshop:
* Microsoft Excel (or Numbers)
* [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE] (free), [http://www.geneious.com Geneious] (free trial)
* [http://www.mathworks.com MATLAB], [http://www.mathworks.com/products/simbiology/ Simbiology]
* [http://sourceforge.net/projects/txtl/ TX-TL modeling toolbox] (requires MATLAB 2010+ and SimBiology]
Participants are encouraged to install this software on their laptops prior to the workshop, but version of the software will also be available on lab computers.

TX-TL Bootcamp, Jun 2015

2015-06-12T00:11:16Z

Chayes: /* Summary Schedule */

Caltech will be hosting a hands-on "bootcamp" on cell-free prototyping and debugging of biological circuits. This page contains information for the TX-TL workshop, which will take place at Caltech on 16-18 Jun 2015. This workshop is by invitation only. __NOTOC__

=== Workshop goals ===
The purpose of the workshop is to provide participants with a working knowledge of cell-free methods for design of biomolecular circuits, using the TX-TL system developed by Vincent Noireaux at U. Minnesota. By the end of the workshop, participants will be able to:

* Build models and simulate circuits using the TX-TL modeling toolbox (MATLAB-based)
* Assemble and test genetic circuits using linear DNA assembly in a single day
* Test and characterize circuits that are part of our current research activities

=== Summary Schedule ===

The schedule below gives an overview of the activities during the workshop.

{| width=100% border=1
|- valign=top
| width=25% |
==== Tue morning ====

| width=25% |

==== Wed morning ====
9-12 pm: Meet in 110 Steele
* Analyzing TX-TL results (from overnight run)
* Presentation: TX-TL using linear DNA
* Lab (136 Keck): Set up Golden Gate reactions

Group lunch at Chandler (when done)
| width= 25% |

==== Thu morning ====
9 am - Analyze TX-TL results from previous day [110 Steele]

10 am - Group projects: Set up experiment

12pm: Group lunch

| width=25% |

==== Fri morning ====
9 am: Group projects: Create group presentation
|- valign=top
| width= 25% |

==== Tue afternoon ====
11 am: '''Bootcamp starts''', 110 Steele (lunch will be provided)
* Overview of workshop and TX-TL system (Richard)
* Lab safety briefing (Clare)

1:45-5 pm: SURF check-in and orientation
* 1:45-3 pm: SURF checkin
* 1:45-3:45 pm: Housing move in
* 3:45-5 pm: SURF orientation
| width= 25% |

==== Wed afternoon ====
1:30 - 2:30 pm - SURF safety meeting (mandatory)

2:30 pm: Set up PCR reactions for GGA linear DNAs (Clare)

3 pm - Project discussions (with co-mentors) at CDS tea and/or initial experiments

| width= 25% |

==== Thu afternoon ====
Group projects: Set up experiments

| width=25% |

==== Fri afternoon ====
1-3 pm: Group presentations

|- valign=top
|

==== Tue evening ====
5-7 pm: SURF BBQ

Lab session: 7-9 pm
* Set up and run first TX-TL reactions

| width=25% |
==== Wed evening ====
5-8 pm - Set up FFL runs from GGA assembly

| width=25% |
==== Thu evening ====
Group projects: Set up overnight experiments

| width=25% |
|}

Description of tutorials:
* Lab basics - this tutorial is intended for participants who have not had any experience in a molecular biology lab. You will learn how to pipette small volumes of clear fluids, run PCR reactions and run gels. If you have had an undergraduate lab class in biology in the last 10 years, you probably don't need to come.

* MATLAB basics - this tutorial is for participants who have never used the MATLAB program. You will learn how to load and plot data in MATLAB and how to use the SimBiology toolbox for setting up very simple reactions.

* Sequence editing - this tutorial will show how to use a DNA sequence editing program such as Geneious or ApE (we mainly use Geneious). You'll learn how to annotate a sequence, simulate PCR reactions and other similar techniques.

=== Read-ahead material ===

We will assume everyone has watched the following 15 minute video before attending the workshop:
* Z. Z. Sun, C. A. Hayes, J. Shin, F. Caschera, R. M. Murray, V. Noireaux, [http://www.jove.com/video/50762 Protocols for Implementing an Escherichia Coli Based TX-TL Cell-Free Expression System for Synthetic Biology]. ''Journal. of Visualized Experiments'' (JoVE), e50762, doi:10.3791/50762 (2013).

If you have time, we also encourage you to take a look at the following material before arriving:
* J. Shin and V. Noireaux, [http://pubs.acs.org/doi/abs/10.1021/sb200016s An ''E. coli'' cell-free expression toolbox: application to synthetic gene circuits and artificial cells]. ''ACS Synthetic Biology'', 1(1):29–41, 2012.

* Z. Z. Sun, E. Yeung, C. A. Hayes, V. Noireaux and Richard M. Murray, [http://www.cds.caltech.edu/~murray/papers/sun+13-acs_synbio.html Linear DNA for rapid prototyping of synthetic biological circuits in an ''Escherichia coli'' based TX-TL cell-free system]. ''ACS Synthetic Biology'', 2014.

* [http://openwetware.org/wiki/Biomolecular_Breadboards Biomolecular Breadboards pages on OpenWetWare]
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Models Modeling overview] - setting up simulations using MATLAB-based TX-TL toolbox
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Preliminary_Data Preliminary data] - includes linear DNA protection, protein degradation
** [http://openwetware.org/wiki/Biomolecular_Breadboards:More_Info More info] - additional references and presentations on TX-TL

=== Software ===
We will make use of the following software as part of the workshop:
* Microsoft Excel (or Numbers)
* [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE] (free), [http://www.geneious.com Geneious] (free trial)
* [http://www.mathworks.com MATLAB], [http://www.mathworks.com/products/simbiology/ Simbiology]
* [http://sourceforge.net/projects/txtl/ TX-TL modeling toolbox] (requires MATLAB 2010+ and SimBiology]
Participants are encouraged to install this software on their laptops prior to the workshop, but version of the software will also be available on lab computers.

TX-TL Bootcamp, Jun 2015

2015-06-12T00:10:25Z

Chayes: Undo revision 18571 by Chayes (talk)

Caltech will be hosting a hands-on "bootcamp" on cell-free prototyping and debugging of biological circuits. This page contains information for the TX-TL workshop, which will take place at Caltech on 16-18 Jun 2015. This workshop is by invitation only. __NOTOC__

=== Workshop goals ===
The purpose of the workshop is to provide participants with a working knowledge of cell-free methods for design of biomolecular circuits, using the TX-TL system developed by Vincent Noireaux at U. Minnesota. By the end of the workshop, participants will be able to:

* Build models and simulate circuits using the TX-TL modeling toolbox (MATLAB-based)
* Assemble and test genetic circuits using linear DNA assembly in a single day
* Test and characterize circuits that are part of our current research activities

=== Summary Schedule ===

The schedule below gives an overview of the activities during the workshop.

{| width=100% border=1
|- valign=top
| width=25% |
==== Tue morning ====
9-11 am: Optional tutorials (details below):
* Lab basics - meet in 110 Steele
| width=25% |

==== Wed morning ====
9-12 pm: Meet in 110 Steele
* Analyzing TX-TL results (from overnight run)
* Presentation: TX-TL using linear DNA
* Lab (136 Keck): Set up Golden Gate reactions

Group lunch at Chandler (when done)
| width= 25% |

==== Thu morning ====
9 am - Analyze TX-TL results from previous day [110 Steele]

10 am - Group projects: Set up experiment

12pm: Group lunch

| width=25% |

==== Fri morning ====
9 am: Group projects: Create group presentation
|- valign=top
| width= 25% |

==== Tue afternoon ====
11 am: '''Bootcamp starts''', 110 Steele (lunch will be provided)
* Overview of workshop and TX-TL system (Richard)
* Lab safety briefing (Clare)

1:45-5 pm: SURF check-in and orientation
* 1:45-3 pm: SURF checkin
* 1:45-3:45 pm: Housing move in
* 3:45-5 pm: SURF orientation
| width= 25% |

==== Wed afternoon ====
1:30 - 2:30 pm - SURF safety meeting (mandatory)

2:30 pm: Set up PCR reactions for GGA linear DNAs (Clare)

3 pm - Project discussions (with co-mentors) at CDS tea and/or initial experiments

| width= 25% |

==== Thu afternoon ====
Group projects: Set up experiments

| width=25% |

==== Fri afternoon ====
1-3 pm: Group presentations

|- valign=top
|

==== Tue evening ====
5-7 pm: SURF BBQ

Lab session: 7-9 pm
* Set up and run first TX-TL reactions

| width=25% |
==== Wed evening ====
5-8 pm - Set up FFL runs from GGA assembly

| width=25% |
==== Thu evening ====
Group projects: Set up overnight experiments

| width=25% |
|}

Description of tutorials:
* Lab basics - this tutorial is intended for participants who have not had any experience in a molecular biology lab. You will learn how to pipette small volumes of clear fluids, run PCR reactions and run gels. If you have had an undergraduate lab class in biology in the last 10 years, you probably don't need to come.

* MATLAB basics - this tutorial is for participants who have never used the MATLAB program. You will learn how to load and plot data in MATLAB and how to use the SimBiology toolbox for setting up very simple reactions.

* Sequence editing - this tutorial will show how to use a DNA sequence editing program such as Geneious or ApE (we mainly use Geneious). You'll learn how to annotate a sequence, simulate PCR reactions and other similar techniques.

=== Read-ahead material ===

We will assume everyone has watched the following 15 minute video before attending the workshop:
* Z. Z. Sun, C. A. Hayes, J. Shin, F. Caschera, R. M. Murray, V. Noireaux, [http://www.jove.com/video/50762 Protocols for Implementing an Escherichia Coli Based TX-TL Cell-Free Expression System for Synthetic Biology]. ''Journal. of Visualized Experiments'' (JoVE), e50762, doi:10.3791/50762 (2013).

If you have time, we also encourage you to take a look at the following material before arriving:
* J. Shin and V. Noireaux, [http://pubs.acs.org/doi/abs/10.1021/sb200016s An ''E. coli'' cell-free expression toolbox: application to synthetic gene circuits and artificial cells]. ''ACS Synthetic Biology'', 1(1):29–41, 2012.

* Z. Z. Sun, E. Yeung, C. A. Hayes, V. Noireaux and Richard M. Murray, [http://www.cds.caltech.edu/~murray/papers/sun+13-acs_synbio.html Linear DNA for rapid prototyping of synthetic biological circuits in an ''Escherichia coli'' based TX-TL cell-free system]. ''ACS Synthetic Biology'', 2014.

* [http://openwetware.org/wiki/Biomolecular_Breadboards Biomolecular Breadboards pages on OpenWetWare]
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Models Modeling overview] - setting up simulations using MATLAB-based TX-TL toolbox
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Preliminary_Data Preliminary data] - includes linear DNA protection, protein degradation
** [http://openwetware.org/wiki/Biomolecular_Breadboards:More_Info More info] - additional references and presentations on TX-TL

=== Software ===
We will make use of the following software as part of the workshop:
* Microsoft Excel (or Numbers)
* [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE] (free), [http://www.geneious.com Geneious] (free trial)
* [http://www.mathworks.com MATLAB], [http://www.mathworks.com/products/simbiology/ Simbiology]
* [http://sourceforge.net/projects/txtl/ TX-TL modeling toolbox] (requires MATLAB 2010+ and SimBiology]
Participants are encouraged to install this software on their laptops prior to the workshop, but version of the software will also be available on lab computers.

TX-TL Bootcamp, Jun 2015

2015-06-12T00:10:00Z

Chayes: /* Tue morning */

Caltech will be hosting a hands-on "bootcamp" on cell-free prototyping and debugging of biological circuits. This page contains information for the TX-TL workshop, which will take place at Caltech on 16-18 Jun 2015. This workshop is by invitation only. __NOTOC__

=== Workshop goals ===
The purpose of the workshop is to provide participants with a working knowledge of cell-free methods for design of biomolecular circuits, using the TX-TL system developed by Vincent Noireaux at U. Minnesota. By the end of the workshop, participants will be able to:

* Build models and simulate circuits using the TX-TL modeling toolbox (MATLAB-based)
* Assemble and test genetic circuits using linear DNA assembly in a single day
* Test and characterize circuits that are part of our current research activities

=== Summary Schedule ===

The schedule below gives an overview of the activities during the workshop.

{| width=100% border=1
|- valign=top
| width=25% |
==== Tue morning ====

==== Wed morning ====
9-12 pm: Meet in 110 Steele
* Analyzing TX-TL results (from overnight run)
* Presentation: TX-TL using linear DNA
* Lab (136 Keck): Set up Golden Gate reactions

Group lunch at Chandler (when done)
| width= 25% |

==== Thu morning ====
9 am - Analyze TX-TL results from previous day [110 Steele]

10 am - Group projects: Set up experiment

12pm: Group lunch

| width=25% |

==== Fri morning ====
9 am: Group projects: Create group presentation
|- valign=top
| width= 25% |

==== Tue afternoon ====
11 am: '''Bootcamp starts''', 110 Steele (lunch will be provided)
* Overview of workshop and TX-TL system (Richard)
* Lab safety briefing (Clare)

1:45-5 pm: SURF check-in and orientation
* 1:45-3 pm: SURF checkin
* 1:45-3:45 pm: Housing move in
* 3:45-5 pm: SURF orientation
| width= 25% |

==== Wed afternoon ====
1:30 - 2:30 pm - SURF safety meeting (mandatory)

2:30 pm: Set up PCR reactions for GGA linear DNAs (Clare)

3 pm - Project discussions (with co-mentors) at CDS tea and/or initial experiments

| width= 25% |

==== Thu afternoon ====
Group projects: Set up experiments

| width=25% |

==== Fri afternoon ====
1-3 pm: Group presentations

|- valign=top
|

==== Tue evening ====
5-7 pm: SURF BBQ

Lab session: 7-9 pm
* Set up and run first TX-TL reactions

| width=25% |
==== Wed evening ====
5-8 pm - Set up FFL runs from GGA assembly

| width=25% |
==== Thu evening ====
Group projects: Set up overnight experiments

| width=25% |
|}

Description of tutorials:
* Lab basics - this tutorial is intended for participants who have not had any experience in a molecular biology lab. You will learn how to pipette small volumes of clear fluids, run PCR reactions and run gels. If you have had an undergraduate lab class in biology in the last 10 years, you probably don't need to come.

* MATLAB basics - this tutorial is for participants who have never used the MATLAB program. You will learn how to load and plot data in MATLAB and how to use the SimBiology toolbox for setting up very simple reactions.

* Sequence editing - this tutorial will show how to use a DNA sequence editing program such as Geneious or ApE (we mainly use Geneious). You'll learn how to annotate a sequence, simulate PCR reactions and other similar techniques.

=== Read-ahead material ===

We will assume everyone has watched the following 15 minute video before attending the workshop:
* Z. Z. Sun, C. A. Hayes, J. Shin, F. Caschera, R. M. Murray, V. Noireaux, [http://www.jove.com/video/50762 Protocols for Implementing an Escherichia Coli Based TX-TL Cell-Free Expression System for Synthetic Biology]. ''Journal. of Visualized Experiments'' (JoVE), e50762, doi:10.3791/50762 (2013).

If you have time, we also encourage you to take a look at the following material before arriving:
* J. Shin and V. Noireaux, [http://pubs.acs.org/doi/abs/10.1021/sb200016s An ''E. coli'' cell-free expression toolbox: application to synthetic gene circuits and artificial cells]. ''ACS Synthetic Biology'', 1(1):29–41, 2012.

* Z. Z. Sun, E. Yeung, C. A. Hayes, V. Noireaux and Richard M. Murray, [http://www.cds.caltech.edu/~murray/papers/sun+13-acs_synbio.html Linear DNA for rapid prototyping of synthetic biological circuits in an ''Escherichia coli'' based TX-TL cell-free system]. ''ACS Synthetic Biology'', 2014.

* [http://openwetware.org/wiki/Biomolecular_Breadboards Biomolecular Breadboards pages on OpenWetWare]
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Models Modeling overview] - setting up simulations using MATLAB-based TX-TL toolbox
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Preliminary_Data Preliminary data] - includes linear DNA protection, protein degradation
** [http://openwetware.org/wiki/Biomolecular_Breadboards:More_Info More info] - additional references and presentations on TX-TL

=== Software ===
We will make use of the following software as part of the workshop:
* Microsoft Excel (or Numbers)
* [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE] (free), [http://www.geneious.com Geneious] (free trial)
* [http://www.mathworks.com MATLAB], [http://www.mathworks.com/products/simbiology/ Simbiology]
* [http://sourceforge.net/projects/txtl/ TX-TL modeling toolbox] (requires MATLAB 2010+ and SimBiology]
Participants are encouraged to install this software on their laptops prior to the workshop, but version of the software will also be available on lab computers.

TX-TL Bootcamp, Jun 2015

2015-06-08T22:21:03Z

Chayes: /* Wed morning */

Caltech will be hosting a hands-on "bootcamp" on cell-free prototyping and debugging of biological circuits. This page contains information for the TX-TL workshop, which will take place at Caltech on 16-18 Jun 2015. This workshop is by invitation only. __NOTOC__

=== Workshop goals ===
The purpose of the workshop is to provide participants with a working knowledge of cell-free methods for design of biomolecular circuits, using the TX-TL system developed by Vincent Noireaux at U. Minnesota. By the end of the workshop, participants will be able to:

* Build models and simulate circuits using the TX-TL modeling toolbox (MATLAB-based)
* Assemble and test genetic circuits using linear DNA assembly in a single day
* Test and characterize circuits that are part of our current research activities

=== Summary Schedule ===

The schedule below gives an overview of the activities during the workshop.

{| width=100% border=1
|- valign=top
| width=25% |
==== Tue morning ====
9-11 am: Optional tutorials (details below):
* Lab basics - meet in 110 Steele
| width=25% |

==== Wed morning ====
9-12 pm: Meet in 110 Steele
* Analyzing TX-TL results (from overnight run)
* Presentation: TX-TL using linear DNA
* Lab (136 Keck): Set up Golden Gate reactions

Group lunch at Chandler (when done)
| width= 25% |

==== Thu morning ====
9 am - Analyze TX-TL results from previous day [110 Steele]

10 am - Group projects: Set up experiment

12pm: Group lunch

| width=25% |

==== Fri morning ====
9 am: Group projects: Create group presentation
|- valign=top
| width= 25% |

==== Tue afternoon ====
11 am: '''Bootcamp starts''', 110 Steele (lunch will be provided)
* Overview of workshop and TX-TL system (Richard)
* Lab safety briefing (Clare)

1:45-5 pm: SURF check-in and orientation
* 1:45-3 pm: SURF checkin
* 1:45-3:45 pm: Housing move in
* 3:45-5 pm: SURF orientation
| width= 25% |

==== Wed afternoon ====
1:30 - 2:30 pm - SURF safety meeting (mandatory)

2:30 pm: Set up PCR reactions for GGA linear DNAs (Clare)

3 pm - Project discussions (with co-mentors) at CDS tea and/or initial experiments

| width= 25% |

==== Thu afternoon ====
Group projects: Set up experiments

| width=25% |

==== Fri afternoon ====
1-3 pm: Group presentations

|- valign=top
|

==== Tue evening ====
5-7 pm: SURF BBQ

Lab session: 7-9 pm
* Set up and run first TX-TL reactions

| width=25% |
==== Wed evening ====
5-8 pm - Set up FFL runs from GGA assembly

| width=25% |
==== Thu evening ====
Group projects: Set up overnight experiments

| width=25% |
|}

Description of tutorials:
* Lab basics - this tutorial is intended for participants who have not had any experience in a molecular biology lab. You will learn how to pipette small volumes of clear fluids, run PCR reactions and run gels. If you have had an undergraduate lab class in biology in the last 10 years, you probably don't need to come.

* MATLAB basics - this tutorial is for participants who have never used the MATLAB program. You will learn how to load and plot data in MATLAB and how to use the SimBiology toolbox for setting up very simple reactions.

* Sequence editing - this tutorial will show how to use a DNA sequence editing program such as Geneious or ApE (we mainly use Geneious). You'll learn how to annotate a sequence, simulate PCR reactions and other similar techniques.

=== Read-ahead material ===

We will assume everyone has watched the following 15 minute video before attending the workshop:
* Z. Z. Sun, C. A. Hayes, J. Shin, F. Caschera, R. M. Murray, V. Noireaux, [http://www.jove.com/video/50762 Protocols for Implementing an Escherichia Coli Based TX-TL Cell-Free Expression System for Synthetic Biology]. ''Journal. of Visualized Experiments'' (JoVE), e50762, doi:10.3791/50762 (2013).

If you have time, we also encourage you to take a look at the following material before arriving:
* J. Shin and V. Noireaux, [http://pubs.acs.org/doi/abs/10.1021/sb200016s An ''E. coli'' cell-free expression toolbox: application to synthetic gene circuits and artificial cells]. ''ACS Synthetic Biology'', 1(1):29–41, 2012.

* Z. Z. Sun, E. Yeung, C. A. Hayes, V. Noireaux and Richard M. Murray, [http://www.cds.caltech.edu/~murray/papers/sun+13-acs_synbio.html Linear DNA for rapid prototyping of synthetic biological circuits in an ''Escherichia coli'' based TX-TL cell-free system]. ''ACS Synthetic Biology'', 2014.

* [http://openwetware.org/wiki/Biomolecular_Breadboards Biomolecular Breadboards pages on OpenWetWare]
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Models Modeling overview] - setting up simulations using MATLAB-based TX-TL toolbox
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Preliminary_Data Preliminary data] - includes linear DNA protection, protein degradation
** [http://openwetware.org/wiki/Biomolecular_Breadboards:More_Info More info] - additional references and presentations on TX-TL

=== Software ===
We will make use of the following software as part of the workshop:
* Microsoft Excel (or Numbers)
* [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE] (free), [http://www.geneious.com Geneious] (free trial)
* [http://www.mathworks.com MATLAB], [http://www.mathworks.com/products/simbiology/ Simbiology]
* [http://sourceforge.net/projects/txtl/ TX-TL modeling toolbox] (requires MATLAB 2010+ and SimBiology]
Participants are encouraged to install this software on their laptops prior to the workshop, but version of the software will also be available on lab computers.

TX-TL Bootcamp, Jun 2015

2015-06-05T00:17:31Z

Chayes: /* Thu afternoon */

Caltech will be hosting a hands-on "bootcamp" on cell-free prototyping and debugging of biological circuits. This page contains information for the TX-TL workshop, which will take place at Caltech on 16-18 Jun 2015. This workshop is by invitation only. __NOTOC__

=== Workshop goals ===
The purpose of the workshop is to provide participants with a working knowledge of cell-free methods for design of biomolecular circuits, using the TX-TL system developed by Vincent Noireaux at U. Minnesota. By the end of the workshop, participants will be able to:

* Build models and simulate circuits using the TX-TL modeling toolbox (MATLAB-based)
* Assemble and test genetic circuits using linear DNA assembly in a single day
* Test and characterize circuits that are part of our current research activities

=== Summary Schedule ===

The schedule below gives an overview of the activities during the workshop.

{| width=100% border=1
|- valign=top
| width=25% |
==== Tue morning ====
9-11 am: Optional tutorials (details below):
* Lab basics - meet in 111 Keck
| width=25% |

==== Wed morning ====
9-12 pm: Meet in 111 Keck
* Analyzing TX-TL results (from overnight run)
* TX-TL using linear DNA
* Lab (136 Keck): Set up Golden Gate reactions

Group lunch at Chandler (when done)
| width= 25% |

==== Thu morning ====
9 am - Analyze TX-TL results from previous day [111 Keck]

10 am - Group projects: Set up experiment

12pm: Group lunch

| width=25% |

==== Fri morning ====
9 am: Group projects: Create group presentation
|- valign=top
| width= 25% |

==== Tue afternoon ====
11 am: '''Bootcamp starts''', 111 Keck (lunch will be provided)
* Overview of workshop and TX-TL system (Richard)
* Lab safety briefing (Clare)

1:45-5 pm: SURF check-in and orientation
* 1:45-3 pm: SURF checkin
* 1:45-3:45 pm: Housing move in
* 3:45-5 pm: SURF orientation
| width= 25% |

==== Wed afternoon ====
1:30 - 2:30 pm - SURF safety meeting (mandatory)

2:30 pm: Set up PCR reactions for GGA linear DNAs (Clare)

3 pm - Project discussions (with co-mentors) at CDS tea and/or initial experiments

| width= 25% |

==== Thu afternoon ====
Group projects: Set up experiments

| width=25% |

==== Fri afternoon ====
1-3 pm: Group presentations

|- valign=top
|

==== Tue evening ====
5-7 pm: SURF BBQ

Lab session: 7-9 pm
* Set up and run first TX-TL reactions

| width=25% |
==== Wed evening ====
5-8 pm - Set up FFL runs from GGA assembly

| width=25% |
==== Thu evening ====
Group projects: Set up overnight experiments

| width=25% |
|}

Description of tutorials:
* Lab basics - this tutorial is intended for participants who have not had any experience in a molecular biology lab. You will learn how to pipette small volumes of clear fluids, run PCR reactions and run gels. If you have had an undergraduate lab class in biology in the last 10 years, you probably don't need to come.

* MATLAB basics - this tutorial is for participants who have never used the MATLAB program. You will learn how to load and plot data in MATLAB and how to use the SimBiology toolbox for setting up very simple reactions.

* Sequence editing - this tutorial will show how to use a DNA sequence editing program such as Geneious or ApE (we mainly use Geneious). You'll learn how to annotate a sequence, simulate PCR reactions and other similar techniques.

=== Read-ahead material ===

We will assume everyone has watched the following 15 minute video before attending the workshop:
* Z. Z. Sun, C. A. Hayes, J. Shin, F. Caschera, R. M. Murray, V. Noireaux, [http://www.jove.com/video/50762 Protocols for Implementing an Escherichia Coli Based TX-TL Cell-Free Expression System for Synthetic Biology]. ''Journal. of Visualized Experiments'' (JoVE), e50762, doi:10.3791/50762 (2013).

If you have time, we also encourage you to take a look at the following material before arriving:
* J. Shin and V. Noireaux, [http://pubs.acs.org/doi/abs/10.1021/sb200016s An ''E. coli'' cell-free expression toolbox: application to synthetic gene circuits and artificial cells]. ''ACS Synthetic Biology'', 1(1):29–41, 2012.

* Z. Z. Sun, E. Yeung, C. A. Hayes, V. Noireaux and Richard M. Murray, [http://www.cds.caltech.edu/~murray/papers/sun+13-acs_synbio.html Linear DNA for rapid prototyping of synthetic biological circuits in an ''Escherichia coli'' based TX-TL cell-free system]. ''ACS Synthetic Biology'', 2014.

* [http://openwetware.org/wiki/Biomolecular_Breadboards Biomolecular Breadboards pages on OpenWetWare]
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Models Modeling overview] - setting up simulations using MATLAB-based TX-TL toolbox
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Preliminary_Data Preliminary data] - includes linear DNA protection, protein degradation
** [http://openwetware.org/wiki/Biomolecular_Breadboards:More_Info More info] - additional references and presentations on TX-TL

=== Software ===
We will make use of the following software as part of the workshop:
* Microsoft Excel (or Numbers)
* [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE] (free), [http://www.geneious.com Geneious] (free trial)
* [http://www.mathworks.com MATLAB], [http://www.mathworks.com/products/simbiology/ Simbiology]
* [http://sourceforge.net/projects/txtl/ TX-TL modeling toolbox] (requires MATLAB 2010+ and SimBiology]
Participants are encouraged to install this software on their laptops prior to the workshop, but version of the software will also be available on lab computers.

TX-TL Bootcamp, Jun 2015

2015-06-05T00:17:19Z

Chayes: /* Thu morning */

Caltech will be hosting a hands-on "bootcamp" on cell-free prototyping and debugging of biological circuits. This page contains information for the TX-TL workshop, which will take place at Caltech on 16-18 Jun 2015. This workshop is by invitation only. __NOTOC__

=== Workshop goals ===
The purpose of the workshop is to provide participants with a working knowledge of cell-free methods for design of biomolecular circuits, using the TX-TL system developed by Vincent Noireaux at U. Minnesota. By the end of the workshop, participants will be able to:

* Build models and simulate circuits using the TX-TL modeling toolbox (MATLAB-based)
* Assemble and test genetic circuits using linear DNA assembly in a single day
* Test and characterize circuits that are part of our current research activities

=== Summary Schedule ===

The schedule below gives an overview of the activities during the workshop.

{| width=100% border=1
|- valign=top
| width=25% |
==== Tue morning ====
9-11 am: Optional tutorials (details below):
* Lab basics - meet in 111 Keck
| width=25% |

==== Wed morning ====
9-12 pm: Meet in 111 Keck
* Analyzing TX-TL results (from overnight run)
* TX-TL using linear DNA
* Lab (136 Keck): Set up Golden Gate reactions

Group lunch at Chandler (when done)
| width= 25% |

==== Thu morning ====
9 am - Analyze TX-TL results from previous day [111 Keck]

10 am - Group projects: Set up experiment

12pm: Group lunch

| width=25% |

==== Fri morning ====
9 am: Group projects: Create group presentation
|- valign=top
| width= 25% |

==== Tue afternoon ====
11 am: '''Bootcamp starts''', 111 Keck (lunch will be provided)
* Overview of workshop and TX-TL system (Richard)
* Lab safety briefing (Clare)

1:45-5 pm: SURF check-in and orientation
* 1:45-3 pm: SURF checkin
* 1:45-3:45 pm: Housing move in
* 3:45-5 pm: SURF orientation
| width= 25% |

==== Wed afternoon ====
1:30 - 2:30 pm - SURF safety meeting (mandatory)

2:30 pm: Set up PCR reactions for GGA linear DNAs (Clare)

3 pm - Project discussions (with co-mentors) at CDS tea and/or initial experiments

| width= 25% |

==== Thu afternoon ====
Group lunch?

Group projects: Set up experiments

| width=25% |

==== Fri afternoon ====
1-3 pm: Group presentations

|- valign=top
|

==== Tue evening ====
5-7 pm: SURF BBQ

Lab session: 7-9 pm
* Set up and run first TX-TL reactions

| width=25% |
==== Wed evening ====
5-8 pm - Set up FFL runs from GGA assembly

| width=25% |
==== Thu evening ====
Group projects: Set up overnight experiments

| width=25% |
|}

Description of tutorials:
* Lab basics - this tutorial is intended for participants who have not had any experience in a molecular biology lab. You will learn how to pipette small volumes of clear fluids, run PCR reactions and run gels. If you have had an undergraduate lab class in biology in the last 10 years, you probably don't need to come.

* MATLAB basics - this tutorial is for participants who have never used the MATLAB program. You will learn how to load and plot data in MATLAB and how to use the SimBiology toolbox for setting up very simple reactions.

* Sequence editing - this tutorial will show how to use a DNA sequence editing program such as Geneious or ApE (we mainly use Geneious). You'll learn how to annotate a sequence, simulate PCR reactions and other similar techniques.

=== Read-ahead material ===

We will assume everyone has watched the following 15 minute video before attending the workshop:
* Z. Z. Sun, C. A. Hayes, J. Shin, F. Caschera, R. M. Murray, V. Noireaux, [http://www.jove.com/video/50762 Protocols for Implementing an Escherichia Coli Based TX-TL Cell-Free Expression System for Synthetic Biology]. ''Journal. of Visualized Experiments'' (JoVE), e50762, doi:10.3791/50762 (2013).

If you have time, we also encourage you to take a look at the following material before arriving:
* J. Shin and V. Noireaux, [http://pubs.acs.org/doi/abs/10.1021/sb200016s An ''E. coli'' cell-free expression toolbox: application to synthetic gene circuits and artificial cells]. ''ACS Synthetic Biology'', 1(1):29–41, 2012.

* Z. Z. Sun, E. Yeung, C. A. Hayes, V. Noireaux and Richard M. Murray, [http://www.cds.caltech.edu/~murray/papers/sun+13-acs_synbio.html Linear DNA for rapid prototyping of synthetic biological circuits in an ''Escherichia coli'' based TX-TL cell-free system]. ''ACS Synthetic Biology'', 2014.

* [http://openwetware.org/wiki/Biomolecular_Breadboards Biomolecular Breadboards pages on OpenWetWare]
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Models Modeling overview] - setting up simulations using MATLAB-based TX-TL toolbox
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Preliminary_Data Preliminary data] - includes linear DNA protection, protein degradation
** [http://openwetware.org/wiki/Biomolecular_Breadboards:More_Info More info] - additional references and presentations on TX-TL

=== Software ===
We will make use of the following software as part of the workshop:
* Microsoft Excel (or Numbers)
* [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE] (free), [http://www.geneious.com Geneious] (free trial)
* [http://www.mathworks.com MATLAB], [http://www.mathworks.com/products/simbiology/ Simbiology]
* [http://sourceforge.net/projects/txtl/ TX-TL modeling toolbox] (requires MATLAB 2010+ and SimBiology]
Participants are encouraged to install this software on their laptops prior to the workshop, but version of the software will also be available on lab computers.

TX-TL Bootcamp, Jun 2015

2015-06-05T00:10:10Z

Chayes: /* Thu afternoon */

Caltech will be hosting a hands-on "bootcamp" on cell-free prototyping and debugging of biological circuits. This page contains information for the TX-TL workshop, which will take place at Caltech on 16-18 Jun 2015. This workshop is by invitation only. __NOTOC__

=== Workshop goals ===
The purpose of the workshop is to provide participants with a working knowledge of cell-free methods for design of biomolecular circuits, using the TX-TL system developed by Vincent Noireaux at U. Minnesota. By the end of the workshop, participants will be able to:

* Build models and simulate circuits using the TX-TL modeling toolbox (MATLAB-based)
* Assemble and test genetic circuits using linear DNA assembly in a single day
* Test and characterize circuits that are part of our current research activities

=== Summary Schedule ===

The schedule below gives an overview of the activities during the workshop.

{| width=100% border=1
|- valign=top
| width=25% |
==== Tue morning ====
9-11 am: Optional tutorials (details below):
* Lab basics - meet in 111 Keck
| width=25% |

==== Wed morning ====
9-12 pm: Meet in 111 Keck
* Analyzing TX-TL results (from overnight run)
* TX-TL using linear DNA
* Lab (136 Keck): Set up Golden Gate reactions

Group lunch at Chandler (when done)
| width= 25% |

==== Thu morning ====
9:00a - Analyze TX-TL results from previous day [111 Keck]

10:00a - Group projects: Set up experiment

| width=25% |

==== Fri morning ====
9 am: Group projects: Create group presentation
|- valign=top
| width= 25% |

==== Tue afternoon ====
11 am: '''Bootcamp starts''', 111 Keck (lunch will be provided)
* Overview of workshop and TX-TL system (Richard)
* Lab safety briefing (Clare)

1:45-5 pm: SURF check-in and orientation
* 1:45-3 pm: SURF checkin
* 1:45-3:45 pm: Housing move in
* 3:45-5 pm: SURF orientation
| width= 25% |

==== Wed afternoon ====
1:30 - 2:30 pm - SURF safety meeting (mandatory)

2:30 pm: Set up PCR reactions for GGA linear DNAs (Clare)

3 pm - Project discussions (with co-mentors) at CDS tea and/or initial experiments

| width= 25% |

==== Thu afternoon ====
Group lunch?

Group projects: Set up experiments

| width=25% |

==== Fri afternoon ====
1-3 pm: Group presentations

|- valign=top
|

==== Tue evening ====
5-7 pm: SURF BBQ

Lab session: 7-9 pm
* Set up and run first TX-TL reactions

| width=25% |
==== Wed evening ====
5-8 pm - Set up FFL runs from GGA assembly

| width=25% |
==== Thu evening ====
Group projects: Set up overnight experiments

| width=25% |
|}

Description of tutorials:
* Lab basics - this tutorial is intended for participants who have not had any experience in a molecular biology lab. You will learn how to pipette small volumes of clear fluids, run PCR reactions and run gels. If you have had an undergraduate lab class in biology in the last 10 years, you probably don't need to come.

* MATLAB basics - this tutorial is for participants who have never used the MATLAB program. You will learn how to load and plot data in MATLAB and how to use the SimBiology toolbox for setting up very simple reactions.

* Sequence editing - this tutorial will show how to use a DNA sequence editing program such as Geneious or ApE (we mainly use Geneious). You'll learn how to annotate a sequence, simulate PCR reactions and other similar techniques.

=== Read-ahead material ===

We will assume everyone has watched the following 15 minute video before attending the workshop:
* Z. Z. Sun, C. A. Hayes, J. Shin, F. Caschera, R. M. Murray, V. Noireaux, [http://www.jove.com/video/50762 Protocols for Implementing an Escherichia Coli Based TX-TL Cell-Free Expression System for Synthetic Biology]. ''Journal. of Visualized Experiments'' (JoVE), e50762, doi:10.3791/50762 (2013).

If you have time, we also encourage you to take a look at the following material before arriving:
* J. Shin and V. Noireaux, [http://pubs.acs.org/doi/abs/10.1021/sb200016s An ''E. coli'' cell-free expression toolbox: application to synthetic gene circuits and artificial cells]. ''ACS Synthetic Biology'', 1(1):29–41, 2012.

* Z. Z. Sun, E. Yeung, C. A. Hayes, V. Noireaux and Richard M. Murray, [http://www.cds.caltech.edu/~murray/papers/sun+13-acs_synbio.html Linear DNA for rapid prototyping of synthetic biological circuits in an ''Escherichia coli'' based TX-TL cell-free system]. ''ACS Synthetic Biology'', 2014.

* [http://openwetware.org/wiki/Biomolecular_Breadboards Biomolecular Breadboards pages on OpenWetWare]
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Models Modeling overview] - setting up simulations using MATLAB-based TX-TL toolbox
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Preliminary_Data Preliminary data] - includes linear DNA protection, protein degradation
** [http://openwetware.org/wiki/Biomolecular_Breadboards:More_Info More info] - additional references and presentations on TX-TL

=== Software ===
We will make use of the following software as part of the workshop:
* Microsoft Excel (or Numbers)
* [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE] (free), [http://www.geneious.com Geneious] (free trial)
* [http://www.mathworks.com MATLAB], [http://www.mathworks.com/products/simbiology/ Simbiology]
* [http://sourceforge.net/projects/txtl/ TX-TL modeling toolbox] (requires MATLAB 2010+ and SimBiology]
Participants are encouraged to install this software on their laptops prior to the workshop, but version of the software will also be available on lab computers.

TX-TL Bootcamp, Jun 2015

2015-06-05T00:10:01Z

Chayes: /* Thu morning */

Caltech will be hosting a hands-on "bootcamp" on cell-free prototyping and debugging of biological circuits. This page contains information for the TX-TL workshop, which will take place at Caltech on 16-18 Jun 2015. This workshop is by invitation only. __NOTOC__

=== Workshop goals ===
The purpose of the workshop is to provide participants with a working knowledge of cell-free methods for design of biomolecular circuits, using the TX-TL system developed by Vincent Noireaux at U. Minnesota. By the end of the workshop, participants will be able to:

* Build models and simulate circuits using the TX-TL modeling toolbox (MATLAB-based)
* Assemble and test genetic circuits using linear DNA assembly in a single day
* Test and characterize circuits that are part of our current research activities

=== Summary Schedule ===

The schedule below gives an overview of the activities during the workshop.

{| width=100% border=1
|- valign=top
| width=25% |
==== Tue morning ====
9-11 am: Optional tutorials (details below):
* Lab basics - meet in 111 Keck
| width=25% |

==== Wed morning ====
9-12 pm: Meet in 111 Keck
* Analyzing TX-TL results (from overnight run)
* TX-TL using linear DNA
* Lab (136 Keck): Set up Golden Gate reactions

Group lunch at Chandler (when done)
| width= 25% |

==== Thu morning ====
9:00a - Analyze TX-TL results from previous day [111 Keck]

10:00a - Group projects: Set up experiment

| width=25% |

==== Fri morning ====
9 am: Group projects: Create group presentation
|- valign=top
| width= 25% |

==== Tue afternoon ====
11 am: '''Bootcamp starts''', 111 Keck (lunch will be provided)
* Overview of workshop and TX-TL system (Richard)
* Lab safety briefing (Clare)

1:45-5 pm: SURF check-in and orientation
* 1:45-3 pm: SURF checkin
* 1:45-3:45 pm: Housing move in
* 3:45-5 pm: SURF orientation
| width= 25% |

==== Wed afternoon ====
1:30 - 2:30 pm - SURF safety meeting (mandatory)

2:30 pm: Set up PCR reactions for GGA linear DNAs (Clare)

3 pm - Project discussions (with co-mentors) at CDS tea and/or initial experiments

| width= 25% |

==== Thu afternoon ====
Group lunch?

Group projects: Set up second/third experiments

| width=25% |

==== Fri afternoon ====
1-3 pm: Group presentations

|- valign=top
|

==== Tue evening ====
5-7 pm: SURF BBQ

Lab session: 7-9 pm
* Set up and run first TX-TL reactions

| width=25% |
==== Wed evening ====
5-8 pm - Set up FFL runs from GGA assembly

| width=25% |
==== Thu evening ====
Group projects: Set up overnight experiments

| width=25% |
|}

Description of tutorials:
* Lab basics - this tutorial is intended for participants who have not had any experience in a molecular biology lab. You will learn how to pipette small volumes of clear fluids, run PCR reactions and run gels. If you have had an undergraduate lab class in biology in the last 10 years, you probably don't need to come.

* MATLAB basics - this tutorial is for participants who have never used the MATLAB program. You will learn how to load and plot data in MATLAB and how to use the SimBiology toolbox for setting up very simple reactions.

* Sequence editing - this tutorial will show how to use a DNA sequence editing program such as Geneious or ApE (we mainly use Geneious). You'll learn how to annotate a sequence, simulate PCR reactions and other similar techniques.

=== Read-ahead material ===

We will assume everyone has watched the following 15 minute video before attending the workshop:
* Z. Z. Sun, C. A. Hayes, J. Shin, F. Caschera, R. M. Murray, V. Noireaux, [http://www.jove.com/video/50762 Protocols for Implementing an Escherichia Coli Based TX-TL Cell-Free Expression System for Synthetic Biology]. ''Journal. of Visualized Experiments'' (JoVE), e50762, doi:10.3791/50762 (2013).

If you have time, we also encourage you to take a look at the following material before arriving:
* J. Shin and V. Noireaux, [http://pubs.acs.org/doi/abs/10.1021/sb200016s An ''E. coli'' cell-free expression toolbox: application to synthetic gene circuits and artificial cells]. ''ACS Synthetic Biology'', 1(1):29–41, 2012.

* Z. Z. Sun, E. Yeung, C. A. Hayes, V. Noireaux and Richard M. Murray, [http://www.cds.caltech.edu/~murray/papers/sun+13-acs_synbio.html Linear DNA for rapid prototyping of synthetic biological circuits in an ''Escherichia coli'' based TX-TL cell-free system]. ''ACS Synthetic Biology'', 2014.

* [http://openwetware.org/wiki/Biomolecular_Breadboards Biomolecular Breadboards pages on OpenWetWare]
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Models Modeling overview] - setting up simulations using MATLAB-based TX-TL toolbox
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Preliminary_Data Preliminary data] - includes linear DNA protection, protein degradation
** [http://openwetware.org/wiki/Biomolecular_Breadboards:More_Info More info] - additional references and presentations on TX-TL

=== Software ===
We will make use of the following software as part of the workshop:
* Microsoft Excel (or Numbers)
* [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE] (free), [http://www.geneious.com Geneious] (free trial)
* [http://www.mathworks.com MATLAB], [http://www.mathworks.com/products/simbiology/ Simbiology]
* [http://sourceforge.net/projects/txtl/ TX-TL modeling toolbox] (requires MATLAB 2010+ and SimBiology]
Participants are encouraged to install this software on their laptops prior to the workshop, but version of the software will also be available on lab computers.

TX-TL Bootcamp, Jun 2015

2015-06-05T00:03:39Z

Chayes: /* Thu evening */

Caltech will be hosting a hands-on "bootcamp" on cell-free prototyping and debugging of biological circuits. This page contains information for the TX-TL workshop, which will take place at Caltech on 16-18 Jun 2015. This workshop is by invitation only. __NOTOC__

=== Workshop goals ===
The purpose of the workshop is to provide participants with a working knowledge of cell-free methods for design of biomolecular circuits, using the TX-TL system developed by Vincent Noireaux at U. Minnesota. By the end of the workshop, participants will be able to:

* Build models and simulate circuits using the TX-TL modeling toolbox (MATLAB-based)
* Assemble and test genetic circuits using linear DNA assembly in a single day
* Test and characterize circuits that are part of our current research activities

=== Summary Schedule ===

The schedule below gives an overview of the activities during the workshop.

{| width=100% border=1
|- valign=top
| width=25% |
==== Tue morning ====
9-11 am: Optional tutorials (details below):
* Lab basics - meet in 111 Keck
| width=25% |

==== Wed morning ====
9-12 pm: Meet in 111 Keck
* Analyzing TX-TL results (from overnight run)
* TX-TL using linear DNA
* Lab (136 Keck): Set up Golden Gate reactions

Group lunch at Chandler (when done)
| width= 25% |

==== Thu morning ====
9:00a - Analyze TX-TL results from previous day [111 Keck]

10:00a - Group projects: Set up first experiment

| width=25% |

==== Fri morning ====
9 am: Group projects: Create group presentation
|- valign=top
| width= 25% |

==== Tue afternoon ====
11 am: '''Bootcamp starts''', 111 Keck (lunch will be provided)
* Overview of workshop and TX-TL system (Richard)
* Lab safety briefing (Clare)

1:45-5 pm: SURF check-in and orientation
* 1:45-3 pm: SURF checkin
* 1:45-3:45 pm: Housing move in
* 3:45-5 pm: SURF orientation
| width= 25% |

==== Wed afternoon ====
1:30 - 2:30 pm - SURF safety meeting (mandatory)

2:30 pm: Set up PCR reactions for GGA linear DNAs (Clare)

3 pm - Project discussions (with co-mentors) at CDS tea and/or initial experiments

| width= 25% |

==== Thu afternoon ====
Group lunch?

Group projects: Set up second/third experiments

| width=25% |

==== Fri afternoon ====
1-3 pm: Group presentations

|- valign=top
|

==== Tue evening ====
5-7 pm: SURF BBQ

Lab session: 7-9 pm
* Set up and run first TX-TL reactions

| width=25% |
==== Wed evening ====
5-8 pm - Set up FFL runs from GGA assembly

| width=25% |
==== Thu evening ====
Group projects: Set up overnight experiments

| width=25% |
|}

Description of tutorials:
* Lab basics - this tutorial is intended for participants who have not had any experience in a molecular biology lab. You will learn how to pipette small volumes of clear fluids, run PCR reactions and run gels. If you have had an undergraduate lab class in biology in the last 10 years, you probably don't need to come.

* MATLAB basics - this tutorial is for participants who have never used the MATLAB program. You will learn how to load and plot data in MATLAB and how to use the SimBiology toolbox for setting up very simple reactions.

* Sequence editing - this tutorial will show how to use a DNA sequence editing program such as Geneious or ApE (we mainly use Geneious). You'll learn how to annotate a sequence, simulate PCR reactions and other similar techniques.

=== Read-ahead material ===

We will assume everyone has watched the following 15 minute video before attending the workshop:
* Z. Z. Sun, C. A. Hayes, J. Shin, F. Caschera, R. M. Murray, V. Noireaux, [http://www.jove.com/video/50762 Protocols for Implementing an Escherichia Coli Based TX-TL Cell-Free Expression System for Synthetic Biology]. ''Journal. of Visualized Experiments'' (JoVE), e50762, doi:10.3791/50762 (2013).

If you have time, we also encourage you to take a look at the following material before arriving:
* J. Shin and V. Noireaux, [http://pubs.acs.org/doi/abs/10.1021/sb200016s An ''E. coli'' cell-free expression toolbox: application to synthetic gene circuits and artificial cells]. ''ACS Synthetic Biology'', 1(1):29–41, 2012.

* Z. Z. Sun, E. Yeung, C. A. Hayes, V. Noireaux and Richard M. Murray, [http://www.cds.caltech.edu/~murray/papers/sun+13-acs_synbio.html Linear DNA for rapid prototyping of synthetic biological circuits in an ''Escherichia coli'' based TX-TL cell-free system]. ''ACS Synthetic Biology'', 2014.

* [http://openwetware.org/wiki/Biomolecular_Breadboards Biomolecular Breadboards pages on OpenWetWare]
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Models Modeling overview] - setting up simulations using MATLAB-based TX-TL toolbox
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Preliminary_Data Preliminary data] - includes linear DNA protection, protein degradation
** [http://openwetware.org/wiki/Biomolecular_Breadboards:More_Info More info] - additional references and presentations on TX-TL

=== Software ===
We will make use of the following software as part of the workshop:
* Microsoft Excel (or Numbers)
* [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE] (free), [http://www.geneious.com Geneious] (free trial)
* [http://www.mathworks.com MATLAB], [http://www.mathworks.com/products/simbiology/ Simbiology]
* [http://sourceforge.net/projects/txtl/ TX-TL modeling toolbox] (requires MATLAB 2010+ and SimBiology]
Participants are encouraged to install this software on their laptops prior to the workshop, but version of the software will also be available on lab computers.

TX-TL Bootcamp, Jun 2015

2015-06-05T00:03:31Z

Chayes: /* Thu afternoon */

Caltech will be hosting a hands-on "bootcamp" on cell-free prototyping and debugging of biological circuits. This page contains information for the TX-TL workshop, which will take place at Caltech on 16-18 Jun 2015. This workshop is by invitation only. __NOTOC__

=== Workshop goals ===
The purpose of the workshop is to provide participants with a working knowledge of cell-free methods for design of biomolecular circuits, using the TX-TL system developed by Vincent Noireaux at U. Minnesota. By the end of the workshop, participants will be able to:

* Build models and simulate circuits using the TX-TL modeling toolbox (MATLAB-based)
* Assemble and test genetic circuits using linear DNA assembly in a single day
* Test and characterize circuits that are part of our current research activities

=== Summary Schedule ===

The schedule below gives an overview of the activities during the workshop.

{| width=100% border=1
|- valign=top
| width=25% |
==== Tue morning ====
9-11 am: Optional tutorials (details below):
* Lab basics - meet in 111 Keck
| width=25% |

==== Wed morning ====
9-12 pm: Meet in 111 Keck
* Analyzing TX-TL results (from overnight run)
* TX-TL using linear DNA
* Lab (136 Keck): Set up Golden Gate reactions

Group lunch at Chandler (when done)
| width= 25% |

==== Thu morning ====
9:00a - Analyze TX-TL results from previous day [111 Keck]

10:00a - Group projects: Set up first experiment

| width=25% |

==== Fri morning ====
9 am: Group projects: Create group presentation
|- valign=top
| width= 25% |

==== Tue afternoon ====
11 am: '''Bootcamp starts''', 111 Keck (lunch will be provided)
* Overview of workshop and TX-TL system (Richard)
* Lab safety briefing (Clare)

1:45-5 pm: SURF check-in and orientation
* 1:45-3 pm: SURF checkin
* 1:45-3:45 pm: Housing move in
* 3:45-5 pm: SURF orientation
| width= 25% |

==== Wed afternoon ====
1:30 - 2:30 pm - SURF safety meeting (mandatory)

2:30 pm: Set up PCR reactions for GGA linear DNAs (Clare)

3 pm - Project discussions (with co-mentors) at CDS tea and/or initial experiments

| width= 25% |

==== Thu afternoon ====
Group lunch?

Group projects: Set up second/third experiments

| width=25% |

==== Fri afternoon ====
1-3 pm: Group presentations

|- valign=top
|

==== Tue evening ====
5-7 pm: SURF BBQ

Lab session: 7-9 pm
* Set up and run first TX-TL reactions

| width=25% |
==== Wed evening ====
5-8 pm - Set up FFL runs from GGA assembly

| width=25% |
==== Thu evening ====
Group dinner?

Group projects: Set up overnight experiments

| width=25% |
|}

Description of tutorials:
* Lab basics - this tutorial is intended for participants who have not had any experience in a molecular biology lab. You will learn how to pipette small volumes of clear fluids, run PCR reactions and run gels. If you have had an undergraduate lab class in biology in the last 10 years, you probably don't need to come.

* MATLAB basics - this tutorial is for participants who have never used the MATLAB program. You will learn how to load and plot data in MATLAB and how to use the SimBiology toolbox for setting up very simple reactions.

* Sequence editing - this tutorial will show how to use a DNA sequence editing program such as Geneious or ApE (we mainly use Geneious). You'll learn how to annotate a sequence, simulate PCR reactions and other similar techniques.

=== Read-ahead material ===

We will assume everyone has watched the following 15 minute video before attending the workshop:
* Z. Z. Sun, C. A. Hayes, J. Shin, F. Caschera, R. M. Murray, V. Noireaux, [http://www.jove.com/video/50762 Protocols for Implementing an Escherichia Coli Based TX-TL Cell-Free Expression System for Synthetic Biology]. ''Journal. of Visualized Experiments'' (JoVE), e50762, doi:10.3791/50762 (2013).

If you have time, we also encourage you to take a look at the following material before arriving:
* J. Shin and V. Noireaux, [http://pubs.acs.org/doi/abs/10.1021/sb200016s An ''E. coli'' cell-free expression toolbox: application to synthetic gene circuits and artificial cells]. ''ACS Synthetic Biology'', 1(1):29–41, 2012.

* Z. Z. Sun, E. Yeung, C. A. Hayes, V. Noireaux and Richard M. Murray, [http://www.cds.caltech.edu/~murray/papers/sun+13-acs_synbio.html Linear DNA for rapid prototyping of synthetic biological circuits in an ''Escherichia coli'' based TX-TL cell-free system]. ''ACS Synthetic Biology'', 2014.

* [http://openwetware.org/wiki/Biomolecular_Breadboards Biomolecular Breadboards pages on OpenWetWare]
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Models Modeling overview] - setting up simulations using MATLAB-based TX-TL toolbox
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Preliminary_Data Preliminary data] - includes linear DNA protection, protein degradation
** [http://openwetware.org/wiki/Biomolecular_Breadboards:More_Info More info] - additional references and presentations on TX-TL

=== Software ===
We will make use of the following software as part of the workshop:
* Microsoft Excel (or Numbers)
* [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE] (free), [http://www.geneious.com Geneious] (free trial)
* [http://www.mathworks.com MATLAB], [http://www.mathworks.com/products/simbiology/ Simbiology]
* [http://sourceforge.net/projects/txtl/ TX-TL modeling toolbox] (requires MATLAB 2010+ and SimBiology]
Participants are encouraged to install this software on their laptops prior to the workshop, but version of the software will also be available on lab computers.

TX-TL Bootcamp, Jun 2015

2015-06-05T00:01:44Z

Chayes: /* Fri morning */

Caltech will be hosting a hands-on "bootcamp" on cell-free prototyping and debugging of biological circuits. This page contains information for the TX-TL workshop, which will take place at Caltech on 16-18 Jun 2015. This workshop is by invitation only. __NOTOC__

=== Workshop goals ===
The purpose of the workshop is to provide participants with a working knowledge of cell-free methods for design of biomolecular circuits, using the TX-TL system developed by Vincent Noireaux at U. Minnesota. By the end of the workshop, participants will be able to:

* Build models and simulate circuits using the TX-TL modeling toolbox (MATLAB-based)
* Assemble and test genetic circuits using linear DNA assembly in a single day
* Test and characterize circuits that are part of our current research activities

=== Summary Schedule ===

The schedule below gives an overview of the activities during the workshop.

{| width=100% border=1
|- valign=top
| width=25% |
==== Tue morning ====
9-11 am: Optional tutorials (details below):
* Lab basics - meet in 111 Keck
| width=25% |

==== Wed morning ====
9-12 pm: Meet in 111 Keck
* Analyzing TX-TL results (from overnight run)
* TX-TL using linear DNA
* Lab (136 Keck): Set up Golden Gate reactions

Group lunch at Chandler (when done)
| width= 25% |

==== Thu morning ====
9:00a - Analyze TX-TL results from previous day [111 Keck]

10:00a - Group projects: Set up first experiment

| width=25% |

==== Fri morning ====
9 am: Group projects: Create group presentation
|- valign=top
| width= 25% |

==== Tue afternoon ====
11 am: '''Bootcamp starts''', 111 Keck (lunch will be provided)
* Overview of workshop and TX-TL system (Richard)
* Lab safety briefing (Clare)

1:45-5 pm: SURF check-in and orientation
* 1:45-3 pm: SURF checkin
* 1:45-3:45 pm: Housing move in
* 3:45-5 pm: SURF orientation
| width= 25% |

==== Wed afternoon ====
1:30 - 2:30 pm - SURF safety meeting (mandatory)

2:30 pm: Set up PCR reactions for GGA linear DNAs (Clare)

3 pm - Project discussions (with co-mentors) at CDS tea and/or initial experiments

| width= 25% |

==== Thu afternoon ====
Group projects: Set up second/third experiments

| width=25% |

==== Fri afternoon ====
1-3 pm: Group presentations

|- valign=top
|

==== Tue evening ====
5-7 pm: SURF BBQ

Lab session: 7-9 pm
* Set up and run first TX-TL reactions

| width=25% |
==== Wed evening ====
5-8 pm - Set up FFL runs from GGA assembly

| width=25% |
==== Thu evening ====
Group dinner?

Group projects: Set up overnight experiments

| width=25% |
|}

Description of tutorials:
* Lab basics - this tutorial is intended for participants who have not had any experience in a molecular biology lab. You will learn how to pipette small volumes of clear fluids, run PCR reactions and run gels. If you have had an undergraduate lab class in biology in the last 10 years, you probably don't need to come.

* MATLAB basics - this tutorial is for participants who have never used the MATLAB program. You will learn how to load and plot data in MATLAB and how to use the SimBiology toolbox for setting up very simple reactions.

* Sequence editing - this tutorial will show how to use a DNA sequence editing program such as Geneious or ApE (we mainly use Geneious). You'll learn how to annotate a sequence, simulate PCR reactions and other similar techniques.

=== Read-ahead material ===

We will assume everyone has watched the following 15 minute video before attending the workshop:
* Z. Z. Sun, C. A. Hayes, J. Shin, F. Caschera, R. M. Murray, V. Noireaux, [http://www.jove.com/video/50762 Protocols for Implementing an Escherichia Coli Based TX-TL Cell-Free Expression System for Synthetic Biology]. ''Journal. of Visualized Experiments'' (JoVE), e50762, doi:10.3791/50762 (2013).

If you have time, we also encourage you to take a look at the following material before arriving:
* J. Shin and V. Noireaux, [http://pubs.acs.org/doi/abs/10.1021/sb200016s An ''E. coli'' cell-free expression toolbox: application to synthetic gene circuits and artificial cells]. ''ACS Synthetic Biology'', 1(1):29–41, 2012.

* Z. Z. Sun, E. Yeung, C. A. Hayes, V. Noireaux and Richard M. Murray, [http://www.cds.caltech.edu/~murray/papers/sun+13-acs_synbio.html Linear DNA for rapid prototyping of synthetic biological circuits in an ''Escherichia coli'' based TX-TL cell-free system]. ''ACS Synthetic Biology'', 2014.

* [http://openwetware.org/wiki/Biomolecular_Breadboards Biomolecular Breadboards pages on OpenWetWare]
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Models Modeling overview] - setting up simulations using MATLAB-based TX-TL toolbox
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Preliminary_Data Preliminary data] - includes linear DNA protection, protein degradation
** [http://openwetware.org/wiki/Biomolecular_Breadboards:More_Info More info] - additional references and presentations on TX-TL

=== Software ===
We will make use of the following software as part of the workshop:
* Microsoft Excel (or Numbers)
* [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE] (free), [http://www.geneious.com Geneious] (free trial)
* [http://www.mathworks.com MATLAB], [http://www.mathworks.com/products/simbiology/ Simbiology]
* [http://sourceforge.net/projects/txtl/ TX-TL modeling toolbox] (requires MATLAB 2010+ and SimBiology]
Participants are encouraged to install this software on their laptops prior to the workshop, but version of the software will also be available on lab computers.

TX-TL Bootcamp, Jun 2015

2015-06-05T00:01:19Z

Chayes: /* Thu evening */

Caltech will be hosting a hands-on "bootcamp" on cell-free prototyping and debugging of biological circuits. This page contains information for the TX-TL workshop, which will take place at Caltech on 16-18 Jun 2015. This workshop is by invitation only. __NOTOC__

=== Workshop goals ===
The purpose of the workshop is to provide participants with a working knowledge of cell-free methods for design of biomolecular circuits, using the TX-TL system developed by Vincent Noireaux at U. Minnesota. By the end of the workshop, participants will be able to:

* Build models and simulate circuits using the TX-TL modeling toolbox (MATLAB-based)
* Assemble and test genetic circuits using linear DNA assembly in a single day
* Test and characterize circuits that are part of our current research activities

=== Summary Schedule ===

The schedule below gives an overview of the activities during the workshop.

{| width=100% border=1
|- valign=top
| width=25% |
==== Tue morning ====
9-11 am: Optional tutorials (details below):
* Lab basics - meet in 111 Keck
| width=25% |

==== Wed morning ====
9-12 pm: Meet in 111 Keck
* Analyzing TX-TL results (from overnight run)
* TX-TL using linear DNA
* Lab (136 Keck): Set up Golden Gate reactions

Group lunch at Chandler (when done)
| width= 25% |

==== Thu morning ====
9:00a - Analyze TX-TL results from previous day [111 Keck]

10:00a - Group projects: Set up first experiment

| width=25% |

==== Fri morning ====
9 am: Meet with group and create presentation
|- valign=top
| width= 25% |

==== Tue afternoon ====
11 am: '''Bootcamp starts''', 111 Keck (lunch will be provided)
* Overview of workshop and TX-TL system (Richard)
* Lab safety briefing (Clare)

1:45-5 pm: SURF check-in and orientation
* 1:45-3 pm: SURF checkin
* 1:45-3:45 pm: Housing move in
* 3:45-5 pm: SURF orientation
| width= 25% |

==== Wed afternoon ====
1:30 - 2:30 pm - SURF safety meeting (mandatory)

2:30 pm: Set up PCR reactions for GGA linear DNAs (Clare)

3 pm - Project discussions (with co-mentors) at CDS tea and/or initial experiments

| width= 25% |

==== Thu afternoon ====
Group projects: Set up second/third experiments

| width=25% |

==== Fri afternoon ====
1-3 pm: Group presentations

|- valign=top
|

==== Tue evening ====
5-7 pm: SURF BBQ

Lab session: 7-9 pm
* Set up and run first TX-TL reactions

| width=25% |
==== Wed evening ====
5-8 pm - Set up FFL runs from GGA assembly

| width=25% |
==== Thu evening ====
Group dinner?

Group projects: Set up overnight experiments

| width=25% |
|}

Description of tutorials:
* Lab basics - this tutorial is intended for participants who have not had any experience in a molecular biology lab. You will learn how to pipette small volumes of clear fluids, run PCR reactions and run gels. If you have had an undergraduate lab class in biology in the last 10 years, you probably don't need to come.

* MATLAB basics - this tutorial is for participants who have never used the MATLAB program. You will learn how to load and plot data in MATLAB and how to use the SimBiology toolbox for setting up very simple reactions.

* Sequence editing - this tutorial will show how to use a DNA sequence editing program such as Geneious or ApE (we mainly use Geneious). You'll learn how to annotate a sequence, simulate PCR reactions and other similar techniques.

=== Read-ahead material ===

We will assume everyone has watched the following 15 minute video before attending the workshop:
* Z. Z. Sun, C. A. Hayes, J. Shin, F. Caschera, R. M. Murray, V. Noireaux, [http://www.jove.com/video/50762 Protocols for Implementing an Escherichia Coli Based TX-TL Cell-Free Expression System for Synthetic Biology]. ''Journal. of Visualized Experiments'' (JoVE), e50762, doi:10.3791/50762 (2013).

If you have time, we also encourage you to take a look at the following material before arriving:
* J. Shin and V. Noireaux, [http://pubs.acs.org/doi/abs/10.1021/sb200016s An ''E. coli'' cell-free expression toolbox: application to synthetic gene circuits and artificial cells]. ''ACS Synthetic Biology'', 1(1):29–41, 2012.

* Z. Z. Sun, E. Yeung, C. A. Hayes, V. Noireaux and Richard M. Murray, [http://www.cds.caltech.edu/~murray/papers/sun+13-acs_synbio.html Linear DNA for rapid prototyping of synthetic biological circuits in an ''Escherichia coli'' based TX-TL cell-free system]. ''ACS Synthetic Biology'', 2014.

* [http://openwetware.org/wiki/Biomolecular_Breadboards Biomolecular Breadboards pages on OpenWetWare]
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Models Modeling overview] - setting up simulations using MATLAB-based TX-TL toolbox
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Preliminary_Data Preliminary data] - includes linear DNA protection, protein degradation
** [http://openwetware.org/wiki/Biomolecular_Breadboards:More_Info More info] - additional references and presentations on TX-TL

=== Software ===
We will make use of the following software as part of the workshop:
* Microsoft Excel (or Numbers)
* [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE] (free), [http://www.geneious.com Geneious] (free trial)
* [http://www.mathworks.com MATLAB], [http://www.mathworks.com/products/simbiology/ Simbiology]
* [http://sourceforge.net/projects/txtl/ TX-TL modeling toolbox] (requires MATLAB 2010+ and SimBiology]
Participants are encouraged to install this software on their laptops prior to the workshop, but version of the software will also be available on lab computers.

TX-TL Bootcamp, Jun 2015

2015-06-05T00:00:49Z

Chayes: /* Fri afternoon */

Caltech will be hosting a hands-on "bootcamp" on cell-free prototyping and debugging of biological circuits. This page contains information for the TX-TL workshop, which will take place at Caltech on 16-18 Jun 2015. This workshop is by invitation only. __NOTOC__

=== Workshop goals ===
The purpose of the workshop is to provide participants with a working knowledge of cell-free methods for design of biomolecular circuits, using the TX-TL system developed by Vincent Noireaux at U. Minnesota. By the end of the workshop, participants will be able to:

* Build models and simulate circuits using the TX-TL modeling toolbox (MATLAB-based)
* Assemble and test genetic circuits using linear DNA assembly in a single day
* Test and characterize circuits that are part of our current research activities

=== Summary Schedule ===

The schedule below gives an overview of the activities during the workshop.

{| width=100% border=1
|- valign=top
| width=25% |
==== Tue morning ====
9-11 am: Optional tutorials (details below):
* Lab basics - meet in 111 Keck
| width=25% |

==== Wed morning ====
9-12 pm: Meet in 111 Keck
* Analyzing TX-TL results (from overnight run)
* TX-TL using linear DNA
* Lab (136 Keck): Set up Golden Gate reactions

Group lunch at Chandler (when done)
| width= 25% |

==== Thu morning ====
9:00a - Analyze TX-TL results from previous day [111 Keck]

10:00a - Group projects: Set up first experiment

| width=25% |

==== Fri morning ====
9 am: Meet with group and create presentation
|- valign=top
| width= 25% |

==== Tue afternoon ====
11 am: '''Bootcamp starts''', 111 Keck (lunch will be provided)
* Overview of workshop and TX-TL system (Richard)
* Lab safety briefing (Clare)

1:45-5 pm: SURF check-in and orientation
* 1:45-3 pm: SURF checkin
* 1:45-3:45 pm: Housing move in
* 3:45-5 pm: SURF orientation
| width= 25% |

==== Wed afternoon ====
1:30 - 2:30 pm - SURF safety meeting (mandatory)

2:30 pm: Set up PCR reactions for GGA linear DNAs (Clare)

3 pm - Project discussions (with co-mentors) at CDS tea and/or initial experiments

| width= 25% |

==== Thu afternoon ====
Group projects: Set up second/third experiments

| width=25% |

==== Fri afternoon ====
1-3 pm: Group presentations

|- valign=top
|

==== Tue evening ====
5-7 pm: SURF BBQ

Lab session: 7-9 pm
* Set up and run first TX-TL reactions

| width=25% |
==== Wed evening ====
5-8 pm - Set up FFL runs from GGA assembly

| width=25% |
==== Thu evening ====
Group dinner?

Set up overnight experiments

| width=25% |
|}

Description of tutorials:
* Lab basics - this tutorial is intended for participants who have not had any experience in a molecular biology lab. You will learn how to pipette small volumes of clear fluids, run PCR reactions and run gels. If you have had an undergraduate lab class in biology in the last 10 years, you probably don't need to come.

* MATLAB basics - this tutorial is for participants who have never used the MATLAB program. You will learn how to load and plot data in MATLAB and how to use the SimBiology toolbox for setting up very simple reactions.

* Sequence editing - this tutorial will show how to use a DNA sequence editing program such as Geneious or ApE (we mainly use Geneious). You'll learn how to annotate a sequence, simulate PCR reactions and other similar techniques.

=== Read-ahead material ===

We will assume everyone has watched the following 15 minute video before attending the workshop:
* Z. Z. Sun, C. A. Hayes, J. Shin, F. Caschera, R. M. Murray, V. Noireaux, [http://www.jove.com/video/50762 Protocols for Implementing an Escherichia Coli Based TX-TL Cell-Free Expression System for Synthetic Biology]. ''Journal. of Visualized Experiments'' (JoVE), e50762, doi:10.3791/50762 (2013).

If you have time, we also encourage you to take a look at the following material before arriving:
* J. Shin and V. Noireaux, [http://pubs.acs.org/doi/abs/10.1021/sb200016s An ''E. coli'' cell-free expression toolbox: application to synthetic gene circuits and artificial cells]. ''ACS Synthetic Biology'', 1(1):29–41, 2012.

* Z. Z. Sun, E. Yeung, C. A. Hayes, V. Noireaux and Richard M. Murray, [http://www.cds.caltech.edu/~murray/papers/sun+13-acs_synbio.html Linear DNA for rapid prototyping of synthetic biological circuits in an ''Escherichia coli'' based TX-TL cell-free system]. ''ACS Synthetic Biology'', 2014.

* [http://openwetware.org/wiki/Biomolecular_Breadboards Biomolecular Breadboards pages on OpenWetWare]
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Models Modeling overview] - setting up simulations using MATLAB-based TX-TL toolbox
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Preliminary_Data Preliminary data] - includes linear DNA protection, protein degradation
** [http://openwetware.org/wiki/Biomolecular_Breadboards:More_Info More info] - additional references and presentations on TX-TL

=== Software ===
We will make use of the following software as part of the workshop:
* Microsoft Excel (or Numbers)
* [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE] (free), [http://www.geneious.com Geneious] (free trial)
* [http://www.mathworks.com MATLAB], [http://www.mathworks.com/products/simbiology/ Simbiology]
* [http://sourceforge.net/projects/txtl/ TX-TL modeling toolbox] (requires MATLAB 2010+ and SimBiology]
Participants are encouraged to install this software on their laptops prior to the workshop, but version of the software will also be available on lab computers.

TX-TL Bootcamp, Jun 2015

2015-06-05T00:00:22Z

Chayes: /* Fri morning */

Caltech will be hosting a hands-on "bootcamp" on cell-free prototyping and debugging of biological circuits. This page contains information for the TX-TL workshop, which will take place at Caltech on 16-18 Jun 2015. This workshop is by invitation only. __NOTOC__

=== Workshop goals ===
The purpose of the workshop is to provide participants with a working knowledge of cell-free methods for design of biomolecular circuits, using the TX-TL system developed by Vincent Noireaux at U. Minnesota. By the end of the workshop, participants will be able to:

* Build models and simulate circuits using the TX-TL modeling toolbox (MATLAB-based)
* Assemble and test genetic circuits using linear DNA assembly in a single day
* Test and characterize circuits that are part of our current research activities

=== Summary Schedule ===

The schedule below gives an overview of the activities during the workshop.

{| width=100% border=1
|- valign=top
| width=25% |
==== Tue morning ====
9-11 am: Optional tutorials (details below):
* Lab basics - meet in 111 Keck
| width=25% |

==== Wed morning ====
9-12 pm: Meet in 111 Keck
* Analyzing TX-TL results (from overnight run)
* TX-TL using linear DNA
* Lab (136 Keck): Set up Golden Gate reactions

Group lunch at Chandler (when done)
| width= 25% |

==== Thu morning ====
9:00a - Analyze TX-TL results from previous day [111 Keck]

10:00a - Group projects: Set up first experiment

| width=25% |

==== Fri morning ====
9 am: Meet with group and create presentation
|- valign=top
| width= 25% |

==== Tue afternoon ====
11 am: '''Bootcamp starts''', 111 Keck (lunch will be provided)
* Overview of workshop and TX-TL system (Richard)
* Lab safety briefing (Clare)

1:45-5 pm: SURF check-in and orientation
* 1:45-3 pm: SURF checkin
* 1:45-3:45 pm: Housing move in
* 3:45-5 pm: SURF orientation
| width= 25% |

==== Wed afternoon ====
1:30 - 2:30 pm - SURF safety meeting (mandatory)

2:30 pm: Set up PCR reactions for GGA linear DNAs (Clare)

3 pm - Project discussions (with co-mentors) at CDS tea and/or initial experiments

| width= 25% |

==== Thu afternoon ====
Group projects: Set up second/third experiments

| width=25% |

==== Fri afternoon ====

Adjourn by 4 pm
|- valign=top
|

==== Tue evening ====
5-7 pm: SURF BBQ

Lab session: 7-9 pm
* Set up and run first TX-TL reactions

| width=25% |
==== Wed evening ====
5-8 pm - Set up FFL runs from GGA assembly

| width=25% |
==== Thu evening ====
Group dinner?

Set up overnight experiments

| width=25% |
|}

Description of tutorials:
* Lab basics - this tutorial is intended for participants who have not had any experience in a molecular biology lab. You will learn how to pipette small volumes of clear fluids, run PCR reactions and run gels. If you have had an undergraduate lab class in biology in the last 10 years, you probably don't need to come.

* MATLAB basics - this tutorial is for participants who have never used the MATLAB program. You will learn how to load and plot data in MATLAB and how to use the SimBiology toolbox for setting up very simple reactions.

* Sequence editing - this tutorial will show how to use a DNA sequence editing program such as Geneious or ApE (we mainly use Geneious). You'll learn how to annotate a sequence, simulate PCR reactions and other similar techniques.

=== Read-ahead material ===

We will assume everyone has watched the following 15 minute video before attending the workshop:
* Z. Z. Sun, C. A. Hayes, J. Shin, F. Caschera, R. M. Murray, V. Noireaux, [http://www.jove.com/video/50762 Protocols for Implementing an Escherichia Coli Based TX-TL Cell-Free Expression System for Synthetic Biology]. ''Journal. of Visualized Experiments'' (JoVE), e50762, doi:10.3791/50762 (2013).

If you have time, we also encourage you to take a look at the following material before arriving:
* J. Shin and V. Noireaux, [http://pubs.acs.org/doi/abs/10.1021/sb200016s An ''E. coli'' cell-free expression toolbox: application to synthetic gene circuits and artificial cells]. ''ACS Synthetic Biology'', 1(1):29–41, 2012.

* Z. Z. Sun, E. Yeung, C. A. Hayes, V. Noireaux and Richard M. Murray, [http://www.cds.caltech.edu/~murray/papers/sun+13-acs_synbio.html Linear DNA for rapid prototyping of synthetic biological circuits in an ''Escherichia coli'' based TX-TL cell-free system]. ''ACS Synthetic Biology'', 2014.

* [http://openwetware.org/wiki/Biomolecular_Breadboards Biomolecular Breadboards pages on OpenWetWare]
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Models Modeling overview] - setting up simulations using MATLAB-based TX-TL toolbox
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Preliminary_Data Preliminary data] - includes linear DNA protection, protein degradation
** [http://openwetware.org/wiki/Biomolecular_Breadboards:More_Info More info] - additional references and presentations on TX-TL

=== Software ===
We will make use of the following software as part of the workshop:
* Microsoft Excel (or Numbers)
* [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE] (free), [http://www.geneious.com Geneious] (free trial)
* [http://www.mathworks.com MATLAB], [http://www.mathworks.com/products/simbiology/ Simbiology]
* [http://sourceforge.net/projects/txtl/ TX-TL modeling toolbox] (requires MATLAB 2010+ and SimBiology]
Participants are encouraged to install this software on their laptops prior to the workshop, but version of the software will also be available on lab computers.

TX-TL Bootcamp, Jun 2015

2015-06-04T23:53:45Z

Chayes: /* Thu evening */

Caltech will be hosting a hands-on "bootcamp" on cell-free prototyping and debugging of biological circuits. This page contains information for the TX-TL workshop, which will take place at Caltech on 16-18 Jun 2015. This workshop is by invitation only. __NOTOC__

=== Workshop goals ===
The purpose of the workshop is to provide participants with a working knowledge of cell-free methods for design of biomolecular circuits, using the TX-TL system developed by Vincent Noireaux at U. Minnesota. By the end of the workshop, participants will be able to:

* Build models and simulate circuits using the TX-TL modeling toolbox (MATLAB-based)
* Assemble and test genetic circuits using linear DNA assembly in a single day
* Test and characterize circuits that are part of our current research activities

=== Summary Schedule ===

The schedule below gives an overview of the activities during the workshop.

{| width=100% border=1
|- valign=top
| width=25% |
==== Tue morning ====
9-11 am: Optional tutorials (details below):
* Lab basics - meet in 111 Keck
| width=25% |

==== Wed morning ====
9-12 pm: Meet in 111 Keck
* Analyzing TX-TL results (from overnight run)
* TX-TL using linear DNA
* Lab (136 Keck): Set up Golden Gate reactions

Group lunch at Chandler (when done)
| width= 25% |

==== Thu morning ====
9:00a - Analyze TX-TL results from previous day [111 Keck]

10:00a - Group projects: Set up first experiment

| width=25% |

==== Fri morning ====

|- valign=top
| width= 25% |
==== Tue afternoon ====
11 am: '''Bootcamp starts''', 111 Keck (lunch will be provided)
* Overview of workshop and TX-TL system (Richard)
* Lab safety briefing (Clare)

1:45-5 pm: SURF check-in and orientation
* 1:45-3 pm: SURF checkin
* 1:45-3:45 pm: Housing move in
* 3:45-5 pm: SURF orientation
| width= 25% |

==== Wed afternoon ====
1:30 - 2:30 pm - SURF safety meeting (mandatory)

2:30 pm: Set up PCR reactions for GGA linear DNAs (Clare)

3 pm - Project discussions (with co-mentors) at CDS tea and/or initial experiments

| width= 25% |

==== Thu afternoon ====
Group projects: Set up second/third experiments

| width=25% |

==== Fri afternoon ====

Adjourn by 4 pm
|- valign=top
|

==== Tue evening ====
5-7 pm: SURF BBQ

Lab session: 7-9 pm
* Set up and run first TX-TL reactions

| width=25% |
==== Wed evening ====
5-8 pm - Set up FFL runs from GGA assembly

| width=25% |
==== Thu evening ====
Group dinner?

Set up overnight experiments

| width=25% |
|}

Description of tutorials:
* Lab basics - this tutorial is intended for participants who have not had any experience in a molecular biology lab. You will learn how to pipette small volumes of clear fluids, run PCR reactions and run gels. If you have had an undergraduate lab class in biology in the last 10 years, you probably don't need to come.

* MATLAB basics - this tutorial is for participants who have never used the MATLAB program. You will learn how to load and plot data in MATLAB and how to use the SimBiology toolbox for setting up very simple reactions.

* Sequence editing - this tutorial will show how to use a DNA sequence editing program such as Geneious or ApE (we mainly use Geneious). You'll learn how to annotate a sequence, simulate PCR reactions and other similar techniques.

=== Read-ahead material ===

We will assume everyone has watched the following 15 minute video before attending the workshop:
* Z. Z. Sun, C. A. Hayes, J. Shin, F. Caschera, R. M. Murray, V. Noireaux, [http://www.jove.com/video/50762 Protocols for Implementing an Escherichia Coli Based TX-TL Cell-Free Expression System for Synthetic Biology]. ''Journal. of Visualized Experiments'' (JoVE), e50762, doi:10.3791/50762 (2013).

If you have time, we also encourage you to take a look at the following material before arriving:
* J. Shin and V. Noireaux, [http://pubs.acs.org/doi/abs/10.1021/sb200016s An ''E. coli'' cell-free expression toolbox: application to synthetic gene circuits and artificial cells]. ''ACS Synthetic Biology'', 1(1):29–41, 2012.

* Z. Z. Sun, E. Yeung, C. A. Hayes, V. Noireaux and Richard M. Murray, [http://www.cds.caltech.edu/~murray/papers/sun+13-acs_synbio.html Linear DNA for rapid prototyping of synthetic biological circuits in an ''Escherichia coli'' based TX-TL cell-free system]. ''ACS Synthetic Biology'', 2014.

* [http://openwetware.org/wiki/Biomolecular_Breadboards Biomolecular Breadboards pages on OpenWetWare]
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Models Modeling overview] - setting up simulations using MATLAB-based TX-TL toolbox
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Preliminary_Data Preliminary data] - includes linear DNA protection, protein degradation
** [http://openwetware.org/wiki/Biomolecular_Breadboards:More_Info More info] - additional references and presentations on TX-TL

=== Software ===
We will make use of the following software as part of the workshop:
* Microsoft Excel (or Numbers)
* [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE] (free), [http://www.geneious.com Geneious] (free trial)
* [http://www.mathworks.com MATLAB], [http://www.mathworks.com/products/simbiology/ Simbiology]
* [http://sourceforge.net/projects/txtl/ TX-TL modeling toolbox] (requires MATLAB 2010+ and SimBiology]
Participants are encouraged to install this software on their laptops prior to the workshop, but version of the software will also be available on lab computers.

TX-TL Bootcamp, Jun 2015

2015-06-04T23:41:29Z

Chayes: /* Thu afternoon */

Caltech will be hosting a hands-on "bootcamp" on cell-free prototyping and debugging of biological circuits. This page contains information for the TX-TL workshop, which will take place at Caltech on 16-18 Jun 2015. This workshop is by invitation only. __NOTOC__

=== Workshop goals ===
The purpose of the workshop is to provide participants with a working knowledge of cell-free methods for design of biomolecular circuits, using the TX-TL system developed by Vincent Noireaux at U. Minnesota. By the end of the workshop, participants will be able to:

* Build models and simulate circuits using the TX-TL modeling toolbox (MATLAB-based)
* Assemble and test genetic circuits using linear DNA assembly in a single day
* Test and characterize circuits that are part of our current research activities

=== Summary Schedule ===

The schedule below gives an overview of the activities during the workshop.

{| width=100% border=1
|- valign=top
| width=25% |
==== Tue morning ====
9-11 am: Optional tutorials (details below):
* Lab basics - meet in 111 Keck
| width=25% |

==== Wed morning ====
9-12 pm: Meet in 111 Keck
* Analyzing TX-TL results (from overnight run)
* TX-TL using linear DNA
* Lab (136 Keck): Set up Golden Gate reactions

Group lunch at Chandler (when done)
| width= 25% |

==== Thu morning ====
9:00a - Analyze TX-TL results from previous day [111 Keck]

10:00a - Group projects: Set up first experiment

| width=25% |

==== Fri morning ====

|- valign=top
| width= 25% |
==== Tue afternoon ====
11 am: '''Bootcamp starts''', 111 Keck (lunch will be provided)
* Overview of workshop and TX-TL system (Richard)
* Lab safety briefing (Clare)

1:45-5 pm: SURF check-in and orientation
* 1:45-3 pm: SURF checkin
* 1:45-3:45 pm: Housing move in
* 3:45-5 pm: SURF orientation
| width= 25% |

==== Wed afternoon ====
1:30 - 2:30 pm - SURF safety meeting (mandatory)

2:30 pm: Set up PCR reactions for GGA linear DNAs (Clare)

3 pm - Project discussions (with co-mentors) at CDS tea and/or initial experiments

| width= 25% |

==== Thu afternoon ====
Group projects: Set up second/third experiments

| width=25% |

==== Fri afternoon ====

Adjourn by 4 pm
|- valign=top
|

==== Tue evening ====
5-7 pm: SURF BBQ

Lab session: 7-9 pm
* Set up and run first TX-TL reactions

| width=25% |
==== Wed evening ====
5-8 pm - Set up FFL runs from GGA assembly

| width=25% |
==== Thu evening ====
Group dinner?

Optional: Set up overnight experiments

| width=25% |
|}

Description of tutorials:
* Lab basics - this tutorial is intended for participants who have not had any experience in a molecular biology lab. You will learn how to pipette small volumes of clear fluids, run PCR reactions and run gels. If you have had an undergraduate lab class in biology in the last 10 years, you probably don't need to come.

* MATLAB basics - this tutorial is for participants who have never used the MATLAB program. You will learn how to load and plot data in MATLAB and how to use the SimBiology toolbox for setting up very simple reactions.

* Sequence editing - this tutorial will show how to use a DNA sequence editing program such as Geneious or ApE (we mainly use Geneious). You'll learn how to annotate a sequence, simulate PCR reactions and other similar techniques.

=== Read-ahead material ===

We will assume everyone has watched the following 15 minute video before attending the workshop:
* Z. Z. Sun, C. A. Hayes, J. Shin, F. Caschera, R. M. Murray, V. Noireaux, [http://www.jove.com/video/50762 Protocols for Implementing an Escherichia Coli Based TX-TL Cell-Free Expression System for Synthetic Biology]. ''Journal. of Visualized Experiments'' (JoVE), e50762, doi:10.3791/50762 (2013).

If you have time, we also encourage you to take a look at the following material before arriving:
* J. Shin and V. Noireaux, [http://pubs.acs.org/doi/abs/10.1021/sb200016s An ''E. coli'' cell-free expression toolbox: application to synthetic gene circuits and artificial cells]. ''ACS Synthetic Biology'', 1(1):29–41, 2012.

* Z. Z. Sun, E. Yeung, C. A. Hayes, V. Noireaux and Richard M. Murray, [http://www.cds.caltech.edu/~murray/papers/sun+13-acs_synbio.html Linear DNA for rapid prototyping of synthetic biological circuits in an ''Escherichia coli'' based TX-TL cell-free system]. ''ACS Synthetic Biology'', 2014.

* [http://openwetware.org/wiki/Biomolecular_Breadboards Biomolecular Breadboards pages on OpenWetWare]
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Models Modeling overview] - setting up simulations using MATLAB-based TX-TL toolbox
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Preliminary_Data Preliminary data] - includes linear DNA protection, protein degradation
** [http://openwetware.org/wiki/Biomolecular_Breadboards:More_Info More info] - additional references and presentations on TX-TL

=== Software ===
We will make use of the following software as part of the workshop:
* Microsoft Excel (or Numbers)
* [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE] (free), [http://www.geneious.com Geneious] (free trial)
* [http://www.mathworks.com MATLAB], [http://www.mathworks.com/products/simbiology/ Simbiology]
* [http://sourceforge.net/projects/txtl/ TX-TL modeling toolbox] (requires MATLAB 2010+ and SimBiology]
Participants are encouraged to install this software on their laptops prior to the workshop, but version of the software will also be available on lab computers.

TX-TL Bootcamp, Jun 2015

2015-06-04T23:41:13Z

Chayes: /* Thu evening */

Caltech will be hosting a hands-on "bootcamp" on cell-free prototyping and debugging of biological circuits. This page contains information for the TX-TL workshop, which will take place at Caltech on 16-18 Jun 2015. This workshop is by invitation only. __NOTOC__

=== Workshop goals ===
The purpose of the workshop is to provide participants with a working knowledge of cell-free methods for design of biomolecular circuits, using the TX-TL system developed by Vincent Noireaux at U. Minnesota. By the end of the workshop, participants will be able to:

* Build models and simulate circuits using the TX-TL modeling toolbox (MATLAB-based)
* Assemble and test genetic circuits using linear DNA assembly in a single day
* Test and characterize circuits that are part of our current research activities

=== Summary Schedule ===

The schedule below gives an overview of the activities during the workshop.

{| width=100% border=1
|- valign=top
| width=25% |
==== Tue morning ====
9-11 am: Optional tutorials (details below):
* Lab basics - meet in 111 Keck
| width=25% |

==== Wed morning ====
9-12 pm: Meet in 111 Keck
* Analyzing TX-TL results (from overnight run)
* TX-TL using linear DNA
* Lab (136 Keck): Set up Golden Gate reactions

Group lunch at Chandler (when done)
| width= 25% |

==== Thu morning ====
9:00a - Analyze TX-TL results from previous day [111 Keck]

10:00a - Group projects: Set up first experiment

| width=25% |

==== Fri morning ====

|- valign=top
| width= 25% |
==== Tue afternoon ====
11 am: '''Bootcamp starts''', 111 Keck (lunch will be provided)
* Overview of workshop and TX-TL system (Richard)
* Lab safety briefing (Clare)

1:45-5 pm: SURF check-in and orientation
* 1:45-3 pm: SURF checkin
* 1:45-3:45 pm: Housing move in
* 3:45-5 pm: SURF orientation
| width= 25% |

==== Wed afternoon ====
1:30 - 2:30 pm - SURF safety meeting (mandatory)

2:30 pm: Set up PCR reactions for GGA linear DNAs (Clare)

3 pm - Project discussions (with co-mentors) at CDS tea and/or initial experiments

| width= 25% |

==== Thu afternoon ====
Group projects: Set up second experiment

| width=25% |

==== Fri afternoon ====

Adjourn by 4 pm
|- valign=top
|

==== Tue evening ====
5-7 pm: SURF BBQ

Lab session: 7-9 pm
* Set up and run first TX-TL reactions

| width=25% |
==== Wed evening ====
5-8 pm - Set up FFL runs from GGA assembly

| width=25% |
==== Thu evening ====
Group dinner?

Optional: Set up overnight experiments

| width=25% |
|}

Description of tutorials:
* Lab basics - this tutorial is intended for participants who have not had any experience in a molecular biology lab. You will learn how to pipette small volumes of clear fluids, run PCR reactions and run gels. If you have had an undergraduate lab class in biology in the last 10 years, you probably don't need to come.

* MATLAB basics - this tutorial is for participants who have never used the MATLAB program. You will learn how to load and plot data in MATLAB and how to use the SimBiology toolbox for setting up very simple reactions.

* Sequence editing - this tutorial will show how to use a DNA sequence editing program such as Geneious or ApE (we mainly use Geneious). You'll learn how to annotate a sequence, simulate PCR reactions and other similar techniques.

=== Read-ahead material ===

We will assume everyone has watched the following 15 minute video before attending the workshop:
* Z. Z. Sun, C. A. Hayes, J. Shin, F. Caschera, R. M. Murray, V. Noireaux, [http://www.jove.com/video/50762 Protocols for Implementing an Escherichia Coli Based TX-TL Cell-Free Expression System for Synthetic Biology]. ''Journal. of Visualized Experiments'' (JoVE), e50762, doi:10.3791/50762 (2013).

If you have time, we also encourage you to take a look at the following material before arriving:
* J. Shin and V. Noireaux, [http://pubs.acs.org/doi/abs/10.1021/sb200016s An ''E. coli'' cell-free expression toolbox: application to synthetic gene circuits and artificial cells]. ''ACS Synthetic Biology'', 1(1):29–41, 2012.

* Z. Z. Sun, E. Yeung, C. A. Hayes, V. Noireaux and Richard M. Murray, [http://www.cds.caltech.edu/~murray/papers/sun+13-acs_synbio.html Linear DNA for rapid prototyping of synthetic biological circuits in an ''Escherichia coli'' based TX-TL cell-free system]. ''ACS Synthetic Biology'', 2014.

* [http://openwetware.org/wiki/Biomolecular_Breadboards Biomolecular Breadboards pages on OpenWetWare]
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Models Modeling overview] - setting up simulations using MATLAB-based TX-TL toolbox
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Preliminary_Data Preliminary data] - includes linear DNA protection, protein degradation
** [http://openwetware.org/wiki/Biomolecular_Breadboards:More_Info More info] - additional references and presentations on TX-TL

=== Software ===
We will make use of the following software as part of the workshop:
* Microsoft Excel (or Numbers)
* [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE] (free), [http://www.geneious.com Geneious] (free trial)
* [http://www.mathworks.com MATLAB], [http://www.mathworks.com/products/simbiology/ Simbiology]
* [http://sourceforge.net/projects/txtl/ TX-TL modeling toolbox] (requires MATLAB 2010+ and SimBiology]
Participants are encouraged to install this software on their laptops prior to the workshop, but version of the software will also be available on lab computers.

TX-TL Bootcamp, Jun 2015

2015-06-04T23:39:30Z

Chayes: /* Thu afternoon */

Caltech will be hosting a hands-on "bootcamp" on cell-free prototyping and debugging of biological circuits. This page contains information for the TX-TL workshop, which will take place at Caltech on 16-18 Jun 2015. This workshop is by invitation only. __NOTOC__

=== Workshop goals ===
The purpose of the workshop is to provide participants with a working knowledge of cell-free methods for design of biomolecular circuits, using the TX-TL system developed by Vincent Noireaux at U. Minnesota. By the end of the workshop, participants will be able to:

* Build models and simulate circuits using the TX-TL modeling toolbox (MATLAB-based)
* Assemble and test genetic circuits using linear DNA assembly in a single day
* Test and characterize circuits that are part of our current research activities

=== Summary Schedule ===

The schedule below gives an overview of the activities during the workshop.

{| width=100% border=1
|- valign=top
| width=25% |
==== Tue morning ====
9-11 am: Optional tutorials (details below):
* Lab basics - meet in 111 Keck
| width=25% |

==== Wed morning ====
9-12 pm: Meet in 111 Keck
* Analyzing TX-TL results (from overnight run)
* TX-TL using linear DNA
* Lab (136 Keck): Set up Golden Gate reactions

Group lunch at Chandler (when done)
| width= 25% |

==== Thu morning ====
9:00a - Analyze TX-TL results from previous day [111 Keck]

10:00a - Group projects: Set up first experiment

| width=25% |

==== Fri morning ====

|- valign=top
| width= 25% |
==== Tue afternoon ====
11 am: '''Bootcamp starts''', 111 Keck (lunch will be provided)
* Overview of workshop and TX-TL system (Richard)
* Lab safety briefing (Clare)

1:45-5 pm: SURF check-in and orientation
* 1:45-3 pm: SURF checkin
* 1:45-3:45 pm: Housing move in
* 3:45-5 pm: SURF orientation
| width= 25% |

==== Wed afternoon ====
1:30 - 2:30 pm - SURF safety meeting (mandatory)

2:30 pm: Set up PCR reactions for GGA linear DNAs (Clare)

3 pm - Project discussions (with co-mentors) at CDS tea and/or initial experiments

| width= 25% |

==== Thu afternoon ====
Group projects: Set up second experiment

| width=25% |

==== Fri afternoon ====

Adjourn by 4 pm
|- valign=top
|

==== Tue evening ====
5-7 pm: SURF BBQ

Lab session: 7-9 pm
* Set up and run first TX-TL reactions

| width=25% |
==== Wed evening ====
5-8 pm - Set up FFL runs from GGA assembly

| width=25% |
==== Thu evening ====
| width=25% |
|}

Description of tutorials:
* Lab basics - this tutorial is intended for participants who have not had any experience in a molecular biology lab. You will learn how to pipette small volumes of clear fluids, run PCR reactions and run gels. If you have had an undergraduate lab class in biology in the last 10 years, you probably don't need to come.

* MATLAB basics - this tutorial is for participants who have never used the MATLAB program. You will learn how to load and plot data in MATLAB and how to use the SimBiology toolbox for setting up very simple reactions.

* Sequence editing - this tutorial will show how to use a DNA sequence editing program such as Geneious or ApE (we mainly use Geneious). You'll learn how to annotate a sequence, simulate PCR reactions and other similar techniques.

=== Read-ahead material ===

We will assume everyone has watched the following 15 minute video before attending the workshop:
* Z. Z. Sun, C. A. Hayes, J. Shin, F. Caschera, R. M. Murray, V. Noireaux, [http://www.jove.com/video/50762 Protocols for Implementing an Escherichia Coli Based TX-TL Cell-Free Expression System for Synthetic Biology]. ''Journal. of Visualized Experiments'' (JoVE), e50762, doi:10.3791/50762 (2013).

If you have time, we also encourage you to take a look at the following material before arriving:
* J. Shin and V. Noireaux, [http://pubs.acs.org/doi/abs/10.1021/sb200016s An ''E. coli'' cell-free expression toolbox: application to synthetic gene circuits and artificial cells]. ''ACS Synthetic Biology'', 1(1):29–41, 2012.

* Z. Z. Sun, E. Yeung, C. A. Hayes, V. Noireaux and Richard M. Murray, [http://www.cds.caltech.edu/~murray/papers/sun+13-acs_synbio.html Linear DNA for rapid prototyping of synthetic biological circuits in an ''Escherichia coli'' based TX-TL cell-free system]. ''ACS Synthetic Biology'', 2014.

* [http://openwetware.org/wiki/Biomolecular_Breadboards Biomolecular Breadboards pages on OpenWetWare]
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Models Modeling overview] - setting up simulations using MATLAB-based TX-TL toolbox
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Preliminary_Data Preliminary data] - includes linear DNA protection, protein degradation
** [http://openwetware.org/wiki/Biomolecular_Breadboards:More_Info More info] - additional references and presentations on TX-TL

=== Software ===
We will make use of the following software as part of the workshop:
* Microsoft Excel (or Numbers)
* [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE] (free), [http://www.geneious.com Geneious] (free trial)
* [http://www.mathworks.com MATLAB], [http://www.mathworks.com/products/simbiology/ Simbiology]
* [http://sourceforge.net/projects/txtl/ TX-TL modeling toolbox] (requires MATLAB 2010+ and SimBiology]
Participants are encouraged to install this software on their laptops prior to the workshop, but version of the software will also be available on lab computers.

TX-TL Bootcamp, Jun 2015

2015-06-04T23:39:13Z

Chayes: /* Thu morning */

Caltech will be hosting a hands-on "bootcamp" on cell-free prototyping and debugging of biological circuits. This page contains information for the TX-TL workshop, which will take place at Caltech on 16-18 Jun 2015. This workshop is by invitation only. __NOTOC__

=== Workshop goals ===
The purpose of the workshop is to provide participants with a working knowledge of cell-free methods for design of biomolecular circuits, using the TX-TL system developed by Vincent Noireaux at U. Minnesota. By the end of the workshop, participants will be able to:

* Build models and simulate circuits using the TX-TL modeling toolbox (MATLAB-based)
* Assemble and test genetic circuits using linear DNA assembly in a single day
* Test and characterize circuits that are part of our current research activities

=== Summary Schedule ===

The schedule below gives an overview of the activities during the workshop.

{| width=100% border=1
|- valign=top
| width=25% |
==== Tue morning ====
9-11 am: Optional tutorials (details below):
* Lab basics - meet in 111 Keck
| width=25% |

==== Wed morning ====
9-12 pm: Meet in 111 Keck
* Analyzing TX-TL results (from overnight run)
* TX-TL using linear DNA
* Lab (136 Keck): Set up Golden Gate reactions

Group lunch at Chandler (when done)
| width= 25% |

==== Thu morning ====
9:00a - Analyze TX-TL results from previous day [111 Keck]

10:00a - Group projects: Set up first experiment

| width=25% |

==== Fri morning ====

|- valign=top
| width= 25% |
==== Tue afternoon ====
11 am: '''Bootcamp starts''', 111 Keck (lunch will be provided)
* Overview of workshop and TX-TL system (Richard)
* Lab safety briefing (Clare)

1:45-5 pm: SURF check-in and orientation
* 1:45-3 pm: SURF checkin
* 1:45-3:45 pm: Housing move in
* 3:45-5 pm: SURF orientation
| width= 25% |

==== Wed afternoon ====
1:30 - 2:30 pm - SURF safety meeting (mandatory)

2:30 pm: Set up PCR reactions for GGA linear DNAs (Clare)

3 pm - Project discussions (with co-mentors) at CDS tea and/or initial experiments

| width= 25% |

==== Thu afternoon ====
Set up characterization runs

| width=25% |
==== Fri afternoon ====

Adjourn by 4 pm
|- valign=top
|

==== Tue evening ====
5-7 pm: SURF BBQ

Lab session: 7-9 pm
* Set up and run first TX-TL reactions

| width=25% |
==== Wed evening ====
5-8 pm - Set up FFL runs from GGA assembly

| width=25% |
==== Thu evening ====
| width=25% |
|}

Description of tutorials:
* Lab basics - this tutorial is intended for participants who have not had any experience in a molecular biology lab. You will learn how to pipette small volumes of clear fluids, run PCR reactions and run gels. If you have had an undergraduate lab class in biology in the last 10 years, you probably don't need to come.

* MATLAB basics - this tutorial is for participants who have never used the MATLAB program. You will learn how to load and plot data in MATLAB and how to use the SimBiology toolbox for setting up very simple reactions.

* Sequence editing - this tutorial will show how to use a DNA sequence editing program such as Geneious or ApE (we mainly use Geneious). You'll learn how to annotate a sequence, simulate PCR reactions and other similar techniques.

=== Read-ahead material ===

We will assume everyone has watched the following 15 minute video before attending the workshop:
* Z. Z. Sun, C. A. Hayes, J. Shin, F. Caschera, R. M. Murray, V. Noireaux, [http://www.jove.com/video/50762 Protocols for Implementing an Escherichia Coli Based TX-TL Cell-Free Expression System for Synthetic Biology]. ''Journal. of Visualized Experiments'' (JoVE), e50762, doi:10.3791/50762 (2013).

If you have time, we also encourage you to take a look at the following material before arriving:
* J. Shin and V. Noireaux, [http://pubs.acs.org/doi/abs/10.1021/sb200016s An ''E. coli'' cell-free expression toolbox: application to synthetic gene circuits and artificial cells]. ''ACS Synthetic Biology'', 1(1):29–41, 2012.

* Z. Z. Sun, E. Yeung, C. A. Hayes, V. Noireaux and Richard M. Murray, [http://www.cds.caltech.edu/~murray/papers/sun+13-acs_synbio.html Linear DNA for rapid prototyping of synthetic biological circuits in an ''Escherichia coli'' based TX-TL cell-free system]. ''ACS Synthetic Biology'', 2014.

* [http://openwetware.org/wiki/Biomolecular_Breadboards Biomolecular Breadboards pages on OpenWetWare]
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Models Modeling overview] - setting up simulations using MATLAB-based TX-TL toolbox
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Preliminary_Data Preliminary data] - includes linear DNA protection, protein degradation
** [http://openwetware.org/wiki/Biomolecular_Breadboards:More_Info More info] - additional references and presentations on TX-TL

=== Software ===
We will make use of the following software as part of the workshop:
* Microsoft Excel (or Numbers)
* [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE] (free), [http://www.geneious.com Geneious] (free trial)
* [http://www.mathworks.com MATLAB], [http://www.mathworks.com/products/simbiology/ Simbiology]
* [http://sourceforge.net/projects/txtl/ TX-TL modeling toolbox] (requires MATLAB 2010+ and SimBiology]
Participants are encouraged to install this software on their laptops prior to the workshop, but version of the software will also be available on lab computers.

TX-TL Bootcamp, Jun 2015

2015-06-04T23:39:06Z

Chayes: /* Thu morning */

Caltech will be hosting a hands-on "bootcamp" on cell-free prototyping and debugging of biological circuits. This page contains information for the TX-TL workshop, which will take place at Caltech on 16-18 Jun 2015. This workshop is by invitation only. __NOTOC__

=== Workshop goals ===
The purpose of the workshop is to provide participants with a working knowledge of cell-free methods for design of biomolecular circuits, using the TX-TL system developed by Vincent Noireaux at U. Minnesota. By the end of the workshop, participants will be able to:

* Build models and simulate circuits using the TX-TL modeling toolbox (MATLAB-based)
* Assemble and test genetic circuits using linear DNA assembly in a single day
* Test and characterize circuits that are part of our current research activities

=== Summary Schedule ===

The schedule below gives an overview of the activities during the workshop.

{| width=100% border=1
|- valign=top
| width=25% |
==== Tue morning ====
9-11 am: Optional tutorials (details below):
* Lab basics - meet in 111 Keck
| width=25% |

==== Wed morning ====
9-12 pm: Meet in 111 Keck
* Analyzing TX-TL results (from overnight run)
* TX-TL using linear DNA
* Lab (136 Keck): Set up Golden Gate reactions

Group lunch at Chandler (when done)
| width= 25% |

==== Thu morning ====
9:00a - Analyze TX-TL results from previous day [111 Keck]
10:00a - Group projects: Set up first experiment

| width=25% |

==== Fri morning ====

|- valign=top
| width= 25% |
==== Tue afternoon ====
11 am: '''Bootcamp starts''', 111 Keck (lunch will be provided)
* Overview of workshop and TX-TL system (Richard)
* Lab safety briefing (Clare)

1:45-5 pm: SURF check-in and orientation
* 1:45-3 pm: SURF checkin
* 1:45-3:45 pm: Housing move in
* 3:45-5 pm: SURF orientation
| width= 25% |

==== Wed afternoon ====
1:30 - 2:30 pm - SURF safety meeting (mandatory)

2:30 pm: Set up PCR reactions for GGA linear DNAs (Clare)

3 pm - Project discussions (with co-mentors) at CDS tea and/or initial experiments

| width= 25% |

==== Thu afternoon ====
Set up characterization runs

| width=25% |
==== Fri afternoon ====

Adjourn by 4 pm
|- valign=top
|

==== Tue evening ====
5-7 pm: SURF BBQ

Lab session: 7-9 pm
* Set up and run first TX-TL reactions

| width=25% |
==== Wed evening ====
5-8 pm - Set up FFL runs from GGA assembly

| width=25% |
==== Thu evening ====
| width=25% |
|}

Description of tutorials:
* Lab basics - this tutorial is intended for participants who have not had any experience in a molecular biology lab. You will learn how to pipette small volumes of clear fluids, run PCR reactions and run gels. If you have had an undergraduate lab class in biology in the last 10 years, you probably don't need to come.

* MATLAB basics - this tutorial is for participants who have never used the MATLAB program. You will learn how to load and plot data in MATLAB and how to use the SimBiology toolbox for setting up very simple reactions.

* Sequence editing - this tutorial will show how to use a DNA sequence editing program such as Geneious or ApE (we mainly use Geneious). You'll learn how to annotate a sequence, simulate PCR reactions and other similar techniques.

=== Read-ahead material ===

We will assume everyone has watched the following 15 minute video before attending the workshop:
* Z. Z. Sun, C. A. Hayes, J. Shin, F. Caschera, R. M. Murray, V. Noireaux, [http://www.jove.com/video/50762 Protocols for Implementing an Escherichia Coli Based TX-TL Cell-Free Expression System for Synthetic Biology]. ''Journal. of Visualized Experiments'' (JoVE), e50762, doi:10.3791/50762 (2013).

If you have time, we also encourage you to take a look at the following material before arriving:
* J. Shin and V. Noireaux, [http://pubs.acs.org/doi/abs/10.1021/sb200016s An ''E. coli'' cell-free expression toolbox: application to synthetic gene circuits and artificial cells]. ''ACS Synthetic Biology'', 1(1):29–41, 2012.

* Z. Z. Sun, E. Yeung, C. A. Hayes, V. Noireaux and Richard M. Murray, [http://www.cds.caltech.edu/~murray/papers/sun+13-acs_synbio.html Linear DNA for rapid prototyping of synthetic biological circuits in an ''Escherichia coli'' based TX-TL cell-free system]. ''ACS Synthetic Biology'', 2014.

* [http://openwetware.org/wiki/Biomolecular_Breadboards Biomolecular Breadboards pages on OpenWetWare]
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Models Modeling overview] - setting up simulations using MATLAB-based TX-TL toolbox
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Preliminary_Data Preliminary data] - includes linear DNA protection, protein degradation
** [http://openwetware.org/wiki/Biomolecular_Breadboards:More_Info More info] - additional references and presentations on TX-TL

=== Software ===
We will make use of the following software as part of the workshop:
* Microsoft Excel (or Numbers)
* [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE] (free), [http://www.geneious.com Geneious] (free trial)
* [http://www.mathworks.com MATLAB], [http://www.mathworks.com/products/simbiology/ Simbiology]
* [http://sourceforge.net/projects/txtl/ TX-TL modeling toolbox] (requires MATLAB 2010+ and SimBiology]
Participants are encouraged to install this software on their laptops prior to the workshop, but version of the software will also be available on lab computers.

TX-TL Bootcamp, Jun 2015

2015-06-04T23:38:33Z

Chayes: Undo revision 18534 by Chayes (talk)

Caltech will be hosting a hands-on "bootcamp" on cell-free prototyping and debugging of biological circuits. This page contains information for the TX-TL workshop, which will take place at Caltech on 16-18 Jun 2015. This workshop is by invitation only. __NOTOC__

=== Workshop goals ===
The purpose of the workshop is to provide participants with a working knowledge of cell-free methods for design of biomolecular circuits, using the TX-TL system developed by Vincent Noireaux at U. Minnesota. By the end of the workshop, participants will be able to:

* Build models and simulate circuits using the TX-TL modeling toolbox (MATLAB-based)
* Assemble and test genetic circuits using linear DNA assembly in a single day
* Test and characterize circuits that are part of our current research activities

=== Summary Schedule ===

The schedule below gives an overview of the activities during the workshop.

{| width=100% border=1
|- valign=top
| width=25% |
==== Tue morning ====
9-11 am: Optional tutorials (details below):
* Lab basics - meet in 111 Keck
| width=25% |

==== Wed morning ====
9-12 pm: Meet in 111 Keck
* Analyzing TX-TL results (from overnight run)
* TX-TL using linear DNA
* Lab (136 Keck): Set up Golden Gate reactions

Group lunch at Chandler (when done)
| width= 25% |

==== Thu morning ====
9:00a - Analyze TX-TL results from previous day [111 Keck]
10:00a - Plan out circuits designs to build and test (with mentors)

| width=25% |
==== Fri morning ====

|- valign=top
| width= 25% |
==== Tue afternoon ====
11 am: '''Bootcamp starts''', 111 Keck (lunch will be provided)
* Overview of workshop and TX-TL system (Richard)
* Lab safety briefing (Clare)

1:45-5 pm: SURF check-in and orientation
* 1:45-3 pm: SURF checkin
* 1:45-3:45 pm: Housing move in
* 3:45-5 pm: SURF orientation
| width= 25% |

==== Wed afternoon ====
1:30 - 2:30 pm - SURF safety meeting (mandatory)

2:30 pm: Set up PCR reactions for GGA linear DNAs (Clare)

3 pm - Project discussions (with co-mentors) at CDS tea and/or initial experiments

| width= 25% |

==== Thu afternoon ====
Set up characterization runs

| width=25% |
==== Fri afternoon ====

Adjourn by 4 pm
|- valign=top
|

==== Tue evening ====
5-7 pm: SURF BBQ

Lab session: 7-9 pm
* Set up and run first TX-TL reactions

| width=25% |
==== Wed evening ====
5-8 pm - Set up FFL runs from GGA assembly

| width=25% |
==== Thu evening ====
| width=25% |
|}

Description of tutorials:
* Lab basics - this tutorial is intended for participants who have not had any experience in a molecular biology lab. You will learn how to pipette small volumes of clear fluids, run PCR reactions and run gels. If you have had an undergraduate lab class in biology in the last 10 years, you probably don't need to come.

* MATLAB basics - this tutorial is for participants who have never used the MATLAB program. You will learn how to load and plot data in MATLAB and how to use the SimBiology toolbox for setting up very simple reactions.

* Sequence editing - this tutorial will show how to use a DNA sequence editing program such as Geneious or ApE (we mainly use Geneious). You'll learn how to annotate a sequence, simulate PCR reactions and other similar techniques.

=== Read-ahead material ===

We will assume everyone has watched the following 15 minute video before attending the workshop:
* Z. Z. Sun, C. A. Hayes, J. Shin, F. Caschera, R. M. Murray, V. Noireaux, [http://www.jove.com/video/50762 Protocols for Implementing an Escherichia Coli Based TX-TL Cell-Free Expression System for Synthetic Biology]. ''Journal. of Visualized Experiments'' (JoVE), e50762, doi:10.3791/50762 (2013).

If you have time, we also encourage you to take a look at the following material before arriving:
* J. Shin and V. Noireaux, [http://pubs.acs.org/doi/abs/10.1021/sb200016s An ''E. coli'' cell-free expression toolbox: application to synthetic gene circuits and artificial cells]. ''ACS Synthetic Biology'', 1(1):29–41, 2012.

* Z. Z. Sun, E. Yeung, C. A. Hayes, V. Noireaux and Richard M. Murray, [http://www.cds.caltech.edu/~murray/papers/sun+13-acs_synbio.html Linear DNA for rapid prototyping of synthetic biological circuits in an ''Escherichia coli'' based TX-TL cell-free system]. ''ACS Synthetic Biology'', 2014.

* [http://openwetware.org/wiki/Biomolecular_Breadboards Biomolecular Breadboards pages on OpenWetWare]
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Models Modeling overview] - setting up simulations using MATLAB-based TX-TL toolbox
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Preliminary_Data Preliminary data] - includes linear DNA protection, protein degradation
** [http://openwetware.org/wiki/Biomolecular_Breadboards:More_Info More info] - additional references and presentations on TX-TL

=== Software ===
We will make use of the following software as part of the workshop:
* Microsoft Excel (or Numbers)
* [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE] (free), [http://www.geneious.com Geneious] (free trial)
* [http://www.mathworks.com MATLAB], [http://www.mathworks.com/products/simbiology/ Simbiology]
* [http://sourceforge.net/projects/txtl/ TX-TL modeling toolbox] (requires MATLAB 2010+ and SimBiology]
Participants are encouraged to install this software on their laptops prior to the workshop, but version of the software will also be available on lab computers.

TX-TL Bootcamp, Jun 2015

2015-06-04T23:38:15Z

Chayes: /* Thu evening */

Caltech will be hosting a hands-on "bootcamp" on cell-free prototyping and debugging of biological circuits. This page contains information for the TX-TL workshop, which will take place at Caltech on 16-18 Jun 2015. This workshop is by invitation only. __NOTOC__

=== Workshop goals ===
The purpose of the workshop is to provide participants with a working knowledge of cell-free methods for design of biomolecular circuits, using the TX-TL system developed by Vincent Noireaux at U. Minnesota. By the end of the workshop, participants will be able to:

* Build models and simulate circuits using the TX-TL modeling toolbox (MATLAB-based)
* Assemble and test genetic circuits using linear DNA assembly in a single day
* Test and characterize circuits that are part of our current research activities

=== Summary Schedule ===

The schedule below gives an overview of the activities during the workshop.

{| width=100% border=1
|- valign=top
| width=25% |
==== Tue morning ====
9-11 am: Optional tutorials (details below):
* Lab basics - meet in 111 Keck
| width=25% |

==== Wed morning ====
9-12 pm: Meet in 111 Keck
* Analyzing TX-TL results (from overnight run)
* TX-TL using linear DNA
* Lab (136 Keck): Set up Golden Gate reactions

Group lunch at Chandler (when done)
| width= 25% |

==== Thu morning ====
9:00a - Analyze TX-TL results from previous day [111 Keck]
10:00a - Plan out circuits designs to build and test (with mentors)

| width=25% |
==== Fri morning ====

|- valign=top
| width= 25% |
==== Tue afternoon ====
11 am: '''Bootcamp starts''', 111 Keck (lunch will be provided)
* Overview of workshop and TX-TL system (Richard)
* Lab safety briefing (Clare)

1:45-5 pm: SURF check-in and orientation
* 1:45-3 pm: SURF checkin
* 1:45-3:45 pm: Housing move in
* 3:45-5 pm: SURF orientation
| width= 25% |

==== Wed afternoon ====
1:30 - 2:30 pm - SURF safety meeting (mandatory)

2:30 pm: Set up PCR reactions for GGA linear DNAs (Clare)

3 pm - Project discussions (with co-mentors) at CDS tea and/or initial experiments

| width= 25% |

==== Thu afternoon ====
Set up characterization runs

| width=25% |
==== Fri afternoon ====

Adjourn by 4 pm
|- valign=top
|

==== Tue evening ====
5-7 pm: SURF BBQ

Lab session: 7-9 pm
* Set up and run first TX-TL reactions

| width=25% |
==== Wed evening ====
5-8 pm - Set up FFL runs from GGA assembly

| width=25% |
==== Thu evening ====
Group dinner?

| width=25% |

Description of tutorials:
* Lab basics - this tutorial is intended for participants who have not had any experience in a molecular biology lab. You will learn how to pipette small volumes of clear fluids, run PCR reactions and run gels. If you have had an undergraduate lab class in biology in the last 10 years, you probably don't need to come.

* MATLAB basics - this tutorial is for participants who have never used the MATLAB program. You will learn how to load and plot data in MATLAB and how to use the SimBiology toolbox for setting up very simple reactions.

* Sequence editing - this tutorial will show how to use a DNA sequence editing program such as Geneious or ApE (we mainly use Geneious). You'll learn how to annotate a sequence, simulate PCR reactions and other similar techniques.

=== Read-ahead material ===

We will assume everyone has watched the following 15 minute video before attending the workshop:
* Z. Z. Sun, C. A. Hayes, J. Shin, F. Caschera, R. M. Murray, V. Noireaux, [http://www.jove.com/video/50762 Protocols for Implementing an Escherichia Coli Based TX-TL Cell-Free Expression System for Synthetic Biology]. ''Journal. of Visualized Experiments'' (JoVE), e50762, doi:10.3791/50762 (2013).

If you have time, we also encourage you to take a look at the following material before arriving:
* J. Shin and V. Noireaux, [http://pubs.acs.org/doi/abs/10.1021/sb200016s An ''E. coli'' cell-free expression toolbox: application to synthetic gene circuits and artificial cells]. ''ACS Synthetic Biology'', 1(1):29–41, 2012.

* Z. Z. Sun, E. Yeung, C. A. Hayes, V. Noireaux and Richard M. Murray, [http://www.cds.caltech.edu/~murray/papers/sun+13-acs_synbio.html Linear DNA for rapid prototyping of synthetic biological circuits in an ''Escherichia coli'' based TX-TL cell-free system]. ''ACS Synthetic Biology'', 2014.

* [http://openwetware.org/wiki/Biomolecular_Breadboards Biomolecular Breadboards pages on OpenWetWare]
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Models Modeling overview] - setting up simulations using MATLAB-based TX-TL toolbox
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Preliminary_Data Preliminary data] - includes linear DNA protection, protein degradation
** [http://openwetware.org/wiki/Biomolecular_Breadboards:More_Info More info] - additional references and presentations on TX-TL

=== Software ===
We will make use of the following software as part of the workshop:
* Microsoft Excel (or Numbers)
* [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE] (free), [http://www.geneious.com Geneious] (free trial)
* [http://www.mathworks.com MATLAB], [http://www.mathworks.com/products/simbiology/ Simbiology]
* [http://sourceforge.net/projects/txtl/ TX-TL modeling toolbox] (requires MATLAB 2010+ and SimBiology]
Participants are encouraged to install this software on their laptops prior to the workshop, but version of the software will also be available on lab computers.

TX-TL Bootcamp, Jun 2015

2015-06-04T23:36:37Z

Chayes: /* Summary Schedule */

Caltech will be hosting a hands-on "bootcamp" on cell-free prototyping and debugging of biological circuits. This page contains information for the TX-TL workshop, which will take place at Caltech on 16-18 Jun 2015. This workshop is by invitation only. __NOTOC__

=== Workshop goals ===
The purpose of the workshop is to provide participants with a working knowledge of cell-free methods for design of biomolecular circuits, using the TX-TL system developed by Vincent Noireaux at U. Minnesota. By the end of the workshop, participants will be able to:

* Build models and simulate circuits using the TX-TL modeling toolbox (MATLAB-based)
* Assemble and test genetic circuits using linear DNA assembly in a single day
* Test and characterize circuits that are part of our current research activities

=== Summary Schedule ===

The schedule below gives an overview of the activities during the workshop.

{| width=100% border=1
|- valign=top
| width=25% |
==== Tue morning ====
9-11 am: Optional tutorials (details below):
* Lab basics - meet in 111 Keck
| width=25% |

==== Wed morning ====
9-12 pm: Meet in 111 Keck
* Analyzing TX-TL results (from overnight run)
* TX-TL using linear DNA
* Lab (136 Keck): Set up Golden Gate reactions

Group lunch at Chandler (when done)
| width= 25% |

==== Thu morning ====
9:00a - Analyze TX-TL results from previous day [111 Keck]
10:00a - Plan out circuits designs to build and test (with mentors)

| width=25% |
==== Fri morning ====

|- valign=top
| width= 25% |
==== Tue afternoon ====
11 am: '''Bootcamp starts''', 111 Keck (lunch will be provided)
* Overview of workshop and TX-TL system (Richard)
* Lab safety briefing (Clare)

1:45-5 pm: SURF check-in and orientation
* 1:45-3 pm: SURF checkin
* 1:45-3:45 pm: Housing move in
* 3:45-5 pm: SURF orientation
| width= 25% |

==== Wed afternoon ====
1:30 - 2:30 pm - SURF safety meeting (mandatory)

2:30 pm: Set up PCR reactions for GGA linear DNAs (Clare)

3 pm - Project discussions (with co-mentors) at CDS tea and/or initial experiments

| width= 25% |

==== Thu afternoon ====
Set up characterization runs

| width=25% |
==== Fri afternoon ====

Adjourn by 4 pm
|- valign=top
|

==== Tue evening ====
5-7 pm: SURF BBQ

Lab session: 7-9 pm
* Set up and run first TX-TL reactions

| width=25% |
==== Wed evening ====
5-8 pm - Set up FFL runs from GGA assembly

| width=25% |
==== Thu evening ====
| width=25% |
|}

Description of tutorials:
* Lab basics - this tutorial is intended for participants who have not had any experience in a molecular biology lab. You will learn how to pipette small volumes of clear fluids, run PCR reactions and run gels. If you have had an undergraduate lab class in biology in the last 10 years, you probably don't need to come.

* MATLAB basics - this tutorial is for participants who have never used the MATLAB program. You will learn how to load and plot data in MATLAB and how to use the SimBiology toolbox for setting up very simple reactions.

* Sequence editing - this tutorial will show how to use a DNA sequence editing program such as Geneious or ApE (we mainly use Geneious). You'll learn how to annotate a sequence, simulate PCR reactions and other similar techniques.

=== Read-ahead material ===

We will assume everyone has watched the following 15 minute video before attending the workshop:
* Z. Z. Sun, C. A. Hayes, J. Shin, F. Caschera, R. M. Murray, V. Noireaux, [http://www.jove.com/video/50762 Protocols for Implementing an Escherichia Coli Based TX-TL Cell-Free Expression System for Synthetic Biology]. ''Journal. of Visualized Experiments'' (JoVE), e50762, doi:10.3791/50762 (2013).

If you have time, we also encourage you to take a look at the following material before arriving:
* J. Shin and V. Noireaux, [http://pubs.acs.org/doi/abs/10.1021/sb200016s An ''E. coli'' cell-free expression toolbox: application to synthetic gene circuits and artificial cells]. ''ACS Synthetic Biology'', 1(1):29–41, 2012.

* Z. Z. Sun, E. Yeung, C. A. Hayes, V. Noireaux and Richard M. Murray, [http://www.cds.caltech.edu/~murray/papers/sun+13-acs_synbio.html Linear DNA for rapid prototyping of synthetic biological circuits in an ''Escherichia coli'' based TX-TL cell-free system]. ''ACS Synthetic Biology'', 2014.

* [http://openwetware.org/wiki/Biomolecular_Breadboards Biomolecular Breadboards pages on OpenWetWare]
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Models Modeling overview] - setting up simulations using MATLAB-based TX-TL toolbox
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Preliminary_Data Preliminary data] - includes linear DNA protection, protein degradation
** [http://openwetware.org/wiki/Biomolecular_Breadboards:More_Info More info] - additional references and presentations on TX-TL

=== Software ===
We will make use of the following software as part of the workshop:
* Microsoft Excel (or Numbers)
* [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE] (free), [http://www.geneious.com Geneious] (free trial)
* [http://www.mathworks.com MATLAB], [http://www.mathworks.com/products/simbiology/ Simbiology]
* [http://sourceforge.net/projects/txtl/ TX-TL modeling toolbox] (requires MATLAB 2010+ and SimBiology]
Participants are encouraged to install this software on their laptops prior to the workshop, but version of the software will also be available on lab computers.

TX-TL Bootcamp, Jun 2015

2015-06-04T23:34:22Z

Chayes: /* Wed evening */

Caltech will be hosting a hands-on "bootcamp" on cell-free prototyping and debugging of biological circuits. This page contains information for the TX-TL workshop, which will take place at Caltech on 16-18 Jun 2015. This workshop is by invitation only. __NOTOC__

=== Workshop goals ===
The purpose of the workshop is to provide participants with a working knowledge of cell-free methods for design of biomolecular circuits, using the TX-TL system developed by Vincent Noireaux at U. Minnesota. By the end of the workshop, participants will be able to:

* Build models and simulate circuits using the TX-TL modeling toolbox (MATLAB-based)
* Assemble and test genetic circuits using linear DNA assembly in a single day
* Test and characterize circuits that are part of our current research activities

=== Summary Schedule ===

The schedule below gives an overview of the activities during the workshop.

{| width=100% border=1
|- valign=top
| width=25% |
==== Tue morning ====
9-11 am: Optional tutorials (details below):
* Lab basics - meet in 111 Keck
| width=25% |

==== Wed morning ====
9-12 pm: Meet in 111 Keck
* Analyzing TX-TL results (from overnight run)
* TX-TL using linear DNA
* Lab (136 Keck): Set up Golden Gate reactions

Group lunch at Chandler (when done)
| width= 25% |

==== Thu morning ====
9:00a - Analyze TX-TL results from previous day [111 Keck]
10:00a - Plan out circuits designs to build and test (with mentors)

| width=25% |
==== Fri morning ====

|- valign=top
| width= 25% |
==== Tue afternoon ====
11 am: '''Bootcamp starts''', 111 Keck (lunch will be provided)
* Overview of workshop and TX-TL system (Richard)
* Lab safety briefing (Clare)

1:45-5 pm: SURF check-in and orientation
* 1:45-3 pm: SURF checkin
* 1:45-3:45 pm: Housing move in
* 3:45-5 pm: SURF orientation
| width= 25% |

==== Wed afternoon ====
1:30 - 2:30 pm - SURF safety meeting (mandatory)

2:30 pm: Set up PCR reactions for GGA linear DNAs (Clare)

3 pm - Project discussions (with co-mentors) at CDS tea and/or initial experiments

| width= 25% |

==== Thu afternoon ====
Set up characterization runs

| width=25% |
==== Fri afternoon ====

Adjourn by 4 pm
|- valign=top
|

==== Tue evening ====
5-7 pm: SURF BBQ

Lab session: 7-9 pm
* Set up and run first TX-TL reactions

| width=25% |
==== Wed evening ====
5-8 pm - Set up FFL runs from GGA assembly

==== Thu evening ====
| width=25% |
|}

Description of tutorials:
* Lab basics - this tutorial is intended for participants who have not had any experience in a molecular biology lab. You will learn how to pipette small volumes of clear fluids, run PCR reactions and run gels. If you have had an undergraduate lab class in biology in the last 10 years, you probably don't need to come.

* MATLAB basics - this tutorial is for participants who have never used the MATLAB program. You will learn how to load and plot data in MATLAB and how to use the SimBiology toolbox for setting up very simple reactions.

* Sequence editing - this tutorial will show how to use a DNA sequence editing program such as Geneious or ApE (we mainly use Geneious). You'll learn how to annotate a sequence, simulate PCR reactions and other similar techniques.

=== Read-ahead material ===

We will assume everyone has watched the following 15 minute video before attending the workshop:
* Z. Z. Sun, C. A. Hayes, J. Shin, F. Caschera, R. M. Murray, V. Noireaux, [http://www.jove.com/video/50762 Protocols for Implementing an Escherichia Coli Based TX-TL Cell-Free Expression System for Synthetic Biology]. ''Journal. of Visualized Experiments'' (JoVE), e50762, doi:10.3791/50762 (2013).

If you have time, we also encourage you to take a look at the following material before arriving:
* J. Shin and V. Noireaux, [http://pubs.acs.org/doi/abs/10.1021/sb200016s An ''E. coli'' cell-free expression toolbox: application to synthetic gene circuits and artificial cells]. ''ACS Synthetic Biology'', 1(1):29–41, 2012.

* Z. Z. Sun, E. Yeung, C. A. Hayes, V. Noireaux and Richard M. Murray, [http://www.cds.caltech.edu/~murray/papers/sun+13-acs_synbio.html Linear DNA for rapid prototyping of synthetic biological circuits in an ''Escherichia coli'' based TX-TL cell-free system]. ''ACS Synthetic Biology'', 2014.

* [http://openwetware.org/wiki/Biomolecular_Breadboards Biomolecular Breadboards pages on OpenWetWare]
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Models Modeling overview] - setting up simulations using MATLAB-based TX-TL toolbox
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Preliminary_Data Preliminary data] - includes linear DNA protection, protein degradation
** [http://openwetware.org/wiki/Biomolecular_Breadboards:More_Info More info] - additional references and presentations on TX-TL

=== Software ===
We will make use of the following software as part of the workshop:
* Microsoft Excel (or Numbers)
* [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE] (free), [http://www.geneious.com Geneious] (free trial)
* [http://www.mathworks.com MATLAB], [http://www.mathworks.com/products/simbiology/ Simbiology]
* [http://sourceforge.net/projects/txtl/ TX-TL modeling toolbox] (requires MATLAB 2010+ and SimBiology]
Participants are encouraged to install this software on their laptops prior to the workshop, but version of the software will also be available on lab computers.

TX-TL Bootcamp, Jun 2015

2015-06-04T23:34:13Z

Chayes: /* Wed afternoon */

Caltech will be hosting a hands-on "bootcamp" on cell-free prototyping and debugging of biological circuits. This page contains information for the TX-TL workshop, which will take place at Caltech on 16-18 Jun 2015. This workshop is by invitation only. __NOTOC__

=== Workshop goals ===
The purpose of the workshop is to provide participants with a working knowledge of cell-free methods for design of biomolecular circuits, using the TX-TL system developed by Vincent Noireaux at U. Minnesota. By the end of the workshop, participants will be able to:

* Build models and simulate circuits using the TX-TL modeling toolbox (MATLAB-based)
* Assemble and test genetic circuits using linear DNA assembly in a single day
* Test and characterize circuits that are part of our current research activities

=== Summary Schedule ===

The schedule below gives an overview of the activities during the workshop.

{| width=100% border=1
|- valign=top
| width=25% |
==== Tue morning ====
9-11 am: Optional tutorials (details below):
* Lab basics - meet in 111 Keck
| width=25% |

==== Wed morning ====
9-12 pm: Meet in 111 Keck
* Analyzing TX-TL results (from overnight run)
* TX-TL using linear DNA
* Lab (136 Keck): Set up Golden Gate reactions

Group lunch at Chandler (when done)
| width= 25% |

==== Thu morning ====
9:00a - Analyze TX-TL results from previous day [111 Keck]
10:00a - Plan out circuits designs to build and test (with mentors)

| width=25% |
==== Fri morning ====

|- valign=top
| width= 25% |
==== Tue afternoon ====
11 am: '''Bootcamp starts''', 111 Keck (lunch will be provided)
* Overview of workshop and TX-TL system (Richard)
* Lab safety briefing (Clare)

1:45-5 pm: SURF check-in and orientation
* 1:45-3 pm: SURF checkin
* 1:45-3:45 pm: Housing move in
* 3:45-5 pm: SURF orientation
| width= 25% |

==== Wed afternoon ====
1:30 - 2:30 pm - SURF safety meeting (mandatory)

2:30 pm: Set up PCR reactions for GGA linear DNAs (Clare)

3 pm - Project discussions (with co-mentors) at CDS tea and/or initial experiments

| width= 25% |

==== Thu afternoon ====
Set up characterization runs

| width=25% |
==== Fri afternoon ====

Adjourn by 4 pm
|- valign=top
|

==== Tue evening ====
5-7 pm: SURF BBQ

Lab session: 7-9 pm
* Set up and run first TX-TL reactions

| width=25% |
==== Wed evening ====

==== Thu evening ====
| width=25% |
|}

Description of tutorials:
* Lab basics - this tutorial is intended for participants who have not had any experience in a molecular biology lab. You will learn how to pipette small volumes of clear fluids, run PCR reactions and run gels. If you have had an undergraduate lab class in biology in the last 10 years, you probably don't need to come.

* MATLAB basics - this tutorial is for participants who have never used the MATLAB program. You will learn how to load and plot data in MATLAB and how to use the SimBiology toolbox for setting up very simple reactions.

* Sequence editing - this tutorial will show how to use a DNA sequence editing program such as Geneious or ApE (we mainly use Geneious). You'll learn how to annotate a sequence, simulate PCR reactions and other similar techniques.

=== Read-ahead material ===

We will assume everyone has watched the following 15 minute video before attending the workshop:
* Z. Z. Sun, C. A. Hayes, J. Shin, F. Caschera, R. M. Murray, V. Noireaux, [http://www.jove.com/video/50762 Protocols for Implementing an Escherichia Coli Based TX-TL Cell-Free Expression System for Synthetic Biology]. ''Journal. of Visualized Experiments'' (JoVE), e50762, doi:10.3791/50762 (2013).

If you have time, we also encourage you to take a look at the following material before arriving:
* J. Shin and V. Noireaux, [http://pubs.acs.org/doi/abs/10.1021/sb200016s An ''E. coli'' cell-free expression toolbox: application to synthetic gene circuits and artificial cells]. ''ACS Synthetic Biology'', 1(1):29–41, 2012.

* Z. Z. Sun, E. Yeung, C. A. Hayes, V. Noireaux and Richard M. Murray, [http://www.cds.caltech.edu/~murray/papers/sun+13-acs_synbio.html Linear DNA for rapid prototyping of synthetic biological circuits in an ''Escherichia coli'' based TX-TL cell-free system]. ''ACS Synthetic Biology'', 2014.

* [http://openwetware.org/wiki/Biomolecular_Breadboards Biomolecular Breadboards pages on OpenWetWare]
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Models Modeling overview] - setting up simulations using MATLAB-based TX-TL toolbox
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Preliminary_Data Preliminary data] - includes linear DNA protection, protein degradation
** [http://openwetware.org/wiki/Biomolecular_Breadboards:More_Info More info] - additional references and presentations on TX-TL

=== Software ===
We will make use of the following software as part of the workshop:
* Microsoft Excel (or Numbers)
* [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE] (free), [http://www.geneious.com Geneious] (free trial)
* [http://www.mathworks.com MATLAB], [http://www.mathworks.com/products/simbiology/ Simbiology]
* [http://sourceforge.net/projects/txtl/ TX-TL modeling toolbox] (requires MATLAB 2010+ and SimBiology]
Participants are encouraged to install this software on their laptops prior to the workshop, but version of the software will also be available on lab computers.

TX-TL Bootcamp, Jun 2015

2015-06-04T23:33:58Z

Chayes: /* Wed evening */

Caltech will be hosting a hands-on "bootcamp" on cell-free prototyping and debugging of biological circuits. This page contains information for the TX-TL workshop, which will take place at Caltech on 16-18 Jun 2015. This workshop is by invitation only. __NOTOC__

=== Workshop goals ===
The purpose of the workshop is to provide participants with a working knowledge of cell-free methods for design of biomolecular circuits, using the TX-TL system developed by Vincent Noireaux at U. Minnesota. By the end of the workshop, participants will be able to:

* Build models and simulate circuits using the TX-TL modeling toolbox (MATLAB-based)
* Assemble and test genetic circuits using linear DNA assembly in a single day
* Test and characterize circuits that are part of our current research activities

=== Summary Schedule ===

The schedule below gives an overview of the activities during the workshop.

{| width=100% border=1
|- valign=top
| width=25% |
==== Tue morning ====
9-11 am: Optional tutorials (details below):
* Lab basics - meet in 111 Keck
| width=25% |

==== Wed morning ====
9-12 pm: Meet in 111 Keck
* Analyzing TX-TL results (from overnight run)
* TX-TL using linear DNA
* Lab (136 Keck): Set up Golden Gate reactions

Group lunch at Chandler (when done)
| width= 25% |

==== Thu morning ====
9:00a - Analyze TX-TL results from previous day [111 Keck]
10:00a - Plan out circuits designs to build and test (with mentors)

| width=25% |
==== Fri morning ====

|- valign=top
| width= 25% |
==== Tue afternoon ====
11 am: '''Bootcamp starts''', 111 Keck (lunch will be provided)
* Overview of workshop and TX-TL system (Richard)
* Lab safety briefing (Clare)

1:45-5 pm: SURF check-in and orientation
* 1:45-3 pm: SURF checkin
* 1:45-3:45 pm: Housing move in
* 3:45-5 pm: SURF orientation
| width= 25% |

==== Wed afternoon ====
1:30 - 2:30 pm - SURF safety meeting (mandatory)

2:30 pm: Set up PCR reactions for GGA linear DNAs (Clare)

3 pm - Project discussions (with co-mentors) at CDS tea and/or initial experiments

5-8 pm - Set up FFL runs from GGA assembly

| width= 25% |

==== Thu afternoon ====
Set up characterization runs

| width=25% |
==== Fri afternoon ====

Adjourn by 4 pm
|- valign=top
|

==== Tue evening ====
5-7 pm: SURF BBQ

Lab session: 7-9 pm
* Set up and run first TX-TL reactions

| width=25% |
==== Wed evening ====

==== Thu evening ====
| width=25% |
|}

Description of tutorials:
* Lab basics - this tutorial is intended for participants who have not had any experience in a molecular biology lab. You will learn how to pipette small volumes of clear fluids, run PCR reactions and run gels. If you have had an undergraduate lab class in biology in the last 10 years, you probably don't need to come.

* MATLAB basics - this tutorial is for participants who have never used the MATLAB program. You will learn how to load and plot data in MATLAB and how to use the SimBiology toolbox for setting up very simple reactions.

* Sequence editing - this tutorial will show how to use a DNA sequence editing program such as Geneious or ApE (we mainly use Geneious). You'll learn how to annotate a sequence, simulate PCR reactions and other similar techniques.

=== Read-ahead material ===

We will assume everyone has watched the following 15 minute video before attending the workshop:
* Z. Z. Sun, C. A. Hayes, J. Shin, F. Caschera, R. M. Murray, V. Noireaux, [http://www.jove.com/video/50762 Protocols for Implementing an Escherichia Coli Based TX-TL Cell-Free Expression System for Synthetic Biology]. ''Journal. of Visualized Experiments'' (JoVE), e50762, doi:10.3791/50762 (2013).

If you have time, we also encourage you to take a look at the following material before arriving:
* J. Shin and V. Noireaux, [http://pubs.acs.org/doi/abs/10.1021/sb200016s An ''E. coli'' cell-free expression toolbox: application to synthetic gene circuits and artificial cells]. ''ACS Synthetic Biology'', 1(1):29–41, 2012.

* Z. Z. Sun, E. Yeung, C. A. Hayes, V. Noireaux and Richard M. Murray, [http://www.cds.caltech.edu/~murray/papers/sun+13-acs_synbio.html Linear DNA for rapid prototyping of synthetic biological circuits in an ''Escherichia coli'' based TX-TL cell-free system]. ''ACS Synthetic Biology'', 2014.

* [http://openwetware.org/wiki/Biomolecular_Breadboards Biomolecular Breadboards pages on OpenWetWare]
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Models Modeling overview] - setting up simulations using MATLAB-based TX-TL toolbox
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Preliminary_Data Preliminary data] - includes linear DNA protection, protein degradation
** [http://openwetware.org/wiki/Biomolecular_Breadboards:More_Info More info] - additional references and presentations on TX-TL

=== Software ===
We will make use of the following software as part of the workshop:
* Microsoft Excel (or Numbers)
* [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE] (free), [http://www.geneious.com Geneious] (free trial)
* [http://www.mathworks.com MATLAB], [http://www.mathworks.com/products/simbiology/ Simbiology]
* [http://sourceforge.net/projects/txtl/ TX-TL modeling toolbox] (requires MATLAB 2010+ and SimBiology]
Participants are encouraged to install this software on their laptops prior to the workshop, but version of the software will also be available on lab computers.

TX-TL Bootcamp, Jun 2015

2015-06-04T23:31:45Z

Chayes: /* Wed afternoon */

Caltech will be hosting a hands-on "bootcamp" on cell-free prototyping and debugging of biological circuits. This page contains information for the TX-TL workshop, which will take place at Caltech on 16-18 Jun 2015. This workshop is by invitation only. __NOTOC__

=== Workshop goals ===
The purpose of the workshop is to provide participants with a working knowledge of cell-free methods for design of biomolecular circuits, using the TX-TL system developed by Vincent Noireaux at U. Minnesota. By the end of the workshop, participants will be able to:

* Build models and simulate circuits using the TX-TL modeling toolbox (MATLAB-based)
* Assemble and test genetic circuits using linear DNA assembly in a single day
* Test and characterize circuits that are part of our current research activities

=== Summary Schedule ===

The schedule below gives an overview of the activities during the workshop.

{| width=100% border=1
|- valign=top
| width=25% |
==== Tue morning ====
9-11 am: Optional tutorials (details below):
* Lab basics - meet in 111 Keck
| width=25% |

==== Wed morning ====
9-12 pm: Meet in 111 Keck
* Analyzing TX-TL results (from overnight run)
* TX-TL using linear DNA
* Lab (136 Keck): Set up Golden Gate reactions

Group lunch at Chandler (when done)
| width= 25% |

==== Thu morning ====
9:00a - Analyze TX-TL results from previous day [111 Keck]
10:00a - Plan out circuits designs to build and test (with mentors)

| width=25% |
==== Fri morning ====

|- valign=top
| width= 25% |
==== Tue afternoon ====
11 am: '''Bootcamp starts''', 111 Keck (lunch will be provided)
* Overview of workshop and TX-TL system (Richard)
* Lab safety briefing (Clare)

1:45-5 pm: SURF check-in and orientation
* 1:45-3 pm: SURF checkin
* 1:45-3:45 pm: Housing move in
* 3:45-5 pm: SURF orientation
| width= 25% |

==== Wed afternoon ====
1:30 - 2:30 pm - SURF safety meeting (mandatory)

2:30 pm: Set up PCR reactions for GGA linear DNAs (Clare)

3 pm - Project discussions (with co-mentors) at CDS tea and/or initial experiments

5-8 pm - Set up FFL runs from GGA assembly

| width= 25% |

==== Thu afternoon ====
Set up characterization runs

| width=25% |
==== Fri afternoon ====

Adjourn by 4 pm
|- valign=top
|

==== Tue evening ====
5-7 pm: SURF BBQ

Lab session: 7-9 pm
* Set up and run first TX-TL reactions

| width=25% |
==== Wed evening ====
6:30-8 pm: Group dinner on S. Lake (participants and mentors)

Lab session: 8-10 pm
* Set up TX-TL runs

| width=25% |
==== Thu evening ====
| width=25% |
|}

Description of tutorials:
* Lab basics - this tutorial is intended for participants who have not had any experience in a molecular biology lab. You will learn how to pipette small volumes of clear fluids, run PCR reactions and run gels. If you have had an undergraduate lab class in biology in the last 10 years, you probably don't need to come.

* MATLAB basics - this tutorial is for participants who have never used the MATLAB program. You will learn how to load and plot data in MATLAB and how to use the SimBiology toolbox for setting up very simple reactions.

* Sequence editing - this tutorial will show how to use a DNA sequence editing program such as Geneious or ApE (we mainly use Geneious). You'll learn how to annotate a sequence, simulate PCR reactions and other similar techniques.

=== Read-ahead material ===

We will assume everyone has watched the following 15 minute video before attending the workshop:
* Z. Z. Sun, C. A. Hayes, J. Shin, F. Caschera, R. M. Murray, V. Noireaux, [http://www.jove.com/video/50762 Protocols for Implementing an Escherichia Coli Based TX-TL Cell-Free Expression System for Synthetic Biology]. ''Journal. of Visualized Experiments'' (JoVE), e50762, doi:10.3791/50762 (2013).

If you have time, we also encourage you to take a look at the following material before arriving:
* J. Shin and V. Noireaux, [http://pubs.acs.org/doi/abs/10.1021/sb200016s An ''E. coli'' cell-free expression toolbox: application to synthetic gene circuits and artificial cells]. ''ACS Synthetic Biology'', 1(1):29–41, 2012.

* Z. Z. Sun, E. Yeung, C. A. Hayes, V. Noireaux and Richard M. Murray, [http://www.cds.caltech.edu/~murray/papers/sun+13-acs_synbio.html Linear DNA for rapid prototyping of synthetic biological circuits in an ''Escherichia coli'' based TX-TL cell-free system]. ''ACS Synthetic Biology'', 2014.

* [http://openwetware.org/wiki/Biomolecular_Breadboards Biomolecular Breadboards pages on OpenWetWare]
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Models Modeling overview] - setting up simulations using MATLAB-based TX-TL toolbox
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Preliminary_Data Preliminary data] - includes linear DNA protection, protein degradation
** [http://openwetware.org/wiki/Biomolecular_Breadboards:More_Info More info] - additional references and presentations on TX-TL

=== Software ===
We will make use of the following software as part of the workshop:
* Microsoft Excel (or Numbers)
* [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE] (free), [http://www.geneious.com Geneious] (free trial)
* [http://www.mathworks.com MATLAB], [http://www.mathworks.com/products/simbiology/ Simbiology]
* [http://sourceforge.net/projects/txtl/ TX-TL modeling toolbox] (requires MATLAB 2010+ and SimBiology]
Participants are encouraged to install this software on their laptops prior to the workshop, but version of the software will also be available on lab computers.

TX-TL Bootcamp, Jun 2015

2015-06-04T23:31:22Z

Chayes: /* Wed afternoon */

Caltech will be hosting a hands-on "bootcamp" on cell-free prototyping and debugging of biological circuits. This page contains information for the TX-TL workshop, which will take place at Caltech on 16-18 Jun 2015. This workshop is by invitation only. __NOTOC__

=== Workshop goals ===
The purpose of the workshop is to provide participants with a working knowledge of cell-free methods for design of biomolecular circuits, using the TX-TL system developed by Vincent Noireaux at U. Minnesota. By the end of the workshop, participants will be able to:

* Build models and simulate circuits using the TX-TL modeling toolbox (MATLAB-based)
* Assemble and test genetic circuits using linear DNA assembly in a single day
* Test and characterize circuits that are part of our current research activities

=== Summary Schedule ===

The schedule below gives an overview of the activities during the workshop.

{| width=100% border=1
|- valign=top
| width=25% |
==== Tue morning ====
9-11 am: Optional tutorials (details below):
* Lab basics - meet in 111 Keck
| width=25% |

==== Wed morning ====
9-12 pm: Meet in 111 Keck
* Analyzing TX-TL results (from overnight run)
* TX-TL using linear DNA
* Lab (136 Keck): Set up Golden Gate reactions

Group lunch at Chandler (when done)
| width= 25% |

==== Thu morning ====
9:00a - Analyze TX-TL results from previous day [111 Keck]
10:00a - Plan out circuits designs to build and test (with mentors)

| width=25% |
==== Fri morning ====

|- valign=top
| width= 25% |
==== Tue afternoon ====
11 am: '''Bootcamp starts''', 111 Keck (lunch will be provided)
* Overview of workshop and TX-TL system (Richard)
* Lab safety briefing (Clare)

1:45-5 pm: SURF check-in and orientation
* 1:45-3 pm: SURF checkin
* 1:45-3:45 pm: Housing move in
* 3:45-5 pm: SURF orientation
| width= 25% |

==== Wed afternoon ====
1:30 - 2:30 pm - SURF safety meeting (mandatory)

2:30 pm: Set up PCR reactions for GGA linear DNAs (Clare)

3 pm - Project discussions (with co-mentors) at CDS tea and initial experiments

5-8 pm - Set up FFL runs from GGA assembly

| width= 25% |

==== Thu afternoon ====
Set up characterization runs

| width=25% |
==== Fri afternoon ====

Adjourn by 4 pm
|- valign=top
|

==== Tue evening ====
5-7 pm: SURF BBQ

Lab session: 7-9 pm
* Set up and run first TX-TL reactions

| width=25% |
==== Wed evening ====
6:30-8 pm: Group dinner on S. Lake (participants and mentors)

Lab session: 8-10 pm
* Set up TX-TL runs

| width=25% |
==== Thu evening ====
| width=25% |
|}

Description of tutorials:
* Lab basics - this tutorial is intended for participants who have not had any experience in a molecular biology lab. You will learn how to pipette small volumes of clear fluids, run PCR reactions and run gels. If you have had an undergraduate lab class in biology in the last 10 years, you probably don't need to come.

* MATLAB basics - this tutorial is for participants who have never used the MATLAB program. You will learn how to load and plot data in MATLAB and how to use the SimBiology toolbox for setting up very simple reactions.

* Sequence editing - this tutorial will show how to use a DNA sequence editing program such as Geneious or ApE (we mainly use Geneious). You'll learn how to annotate a sequence, simulate PCR reactions and other similar techniques.

=== Read-ahead material ===

We will assume everyone has watched the following 15 minute video before attending the workshop:
* Z. Z. Sun, C. A. Hayes, J. Shin, F. Caschera, R. M. Murray, V. Noireaux, [http://www.jove.com/video/50762 Protocols for Implementing an Escherichia Coli Based TX-TL Cell-Free Expression System for Synthetic Biology]. ''Journal. of Visualized Experiments'' (JoVE), e50762, doi:10.3791/50762 (2013).

If you have time, we also encourage you to take a look at the following material before arriving:
* J. Shin and V. Noireaux, [http://pubs.acs.org/doi/abs/10.1021/sb200016s An ''E. coli'' cell-free expression toolbox: application to synthetic gene circuits and artificial cells]. ''ACS Synthetic Biology'', 1(1):29–41, 2012.

* Z. Z. Sun, E. Yeung, C. A. Hayes, V. Noireaux and Richard M. Murray, [http://www.cds.caltech.edu/~murray/papers/sun+13-acs_synbio.html Linear DNA for rapid prototyping of synthetic biological circuits in an ''Escherichia coli'' based TX-TL cell-free system]. ''ACS Synthetic Biology'', 2014.

* [http://openwetware.org/wiki/Biomolecular_Breadboards Biomolecular Breadboards pages on OpenWetWare]
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Models Modeling overview] - setting up simulations using MATLAB-based TX-TL toolbox
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Preliminary_Data Preliminary data] - includes linear DNA protection, protein degradation
** [http://openwetware.org/wiki/Biomolecular_Breadboards:More_Info More info] - additional references and presentations on TX-TL

=== Software ===
We will make use of the following software as part of the workshop:
* Microsoft Excel (or Numbers)
* [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE] (free), [http://www.geneious.com Geneious] (free trial)
* [http://www.mathworks.com MATLAB], [http://www.mathworks.com/products/simbiology/ Simbiology]
* [http://sourceforge.net/projects/txtl/ TX-TL modeling toolbox] (requires MATLAB 2010+ and SimBiology]
Participants are encouraged to install this software on their laptops prior to the workshop, but version of the software will also be available on lab computers.

TX-TL Bootcamp, Jun 2015

2015-06-04T23:31:04Z

Chayes: /* Wed afternoon */

Caltech will be hosting a hands-on "bootcamp" on cell-free prototyping and debugging of biological circuits. This page contains information for the TX-TL workshop, which will take place at Caltech on 16-18 Jun 2015. This workshop is by invitation only. __NOTOC__

=== Workshop goals ===
The purpose of the workshop is to provide participants with a working knowledge of cell-free methods for design of biomolecular circuits, using the TX-TL system developed by Vincent Noireaux at U. Minnesota. By the end of the workshop, participants will be able to:

* Build models and simulate circuits using the TX-TL modeling toolbox (MATLAB-based)
* Assemble and test genetic circuits using linear DNA assembly in a single day
* Test and characterize circuits that are part of our current research activities

=== Summary Schedule ===

The schedule below gives an overview of the activities during the workshop.

{| width=100% border=1
|- valign=top
| width=25% |
==== Tue morning ====
9-11 am: Optional tutorials (details below):
* Lab basics - meet in 111 Keck
| width=25% |

==== Wed morning ====
9-12 pm: Meet in 111 Keck
* Analyzing TX-TL results (from overnight run)
* TX-TL using linear DNA
* Lab (136 Keck): Set up Golden Gate reactions

Group lunch at Chandler (when done)
| width= 25% |

==== Thu morning ====
9:00a - Analyze TX-TL results from previous day [111 Keck]
10:00a - Plan out circuits designs to build and test (with mentors)

| width=25% |
==== Fri morning ====

|- valign=top
| width= 25% |
==== Tue afternoon ====
11 am: '''Bootcamp starts''', 111 Keck (lunch will be provided)
* Overview of workshop and TX-TL system (Richard)
* Lab safety briefing (Clare)

1:45-5 pm: SURF check-in and orientation
* 1:45-3 pm: SURF checkin
* 1:45-3:45 pm: Housing move in
* 3:45-5 pm: SURF orientation
| width= 25% |

==== Wed afternoon ====
1:30 - 2:30 pm - SURF safety meeting (mandatory)

2:30 pm: Set up PCR reactions for GGA linear DNAs (Clare)

3:00p - Project discussions (with co-mentors) at CDS tea and initial experiments

5-8 pm - Set up FFL runs from GGA assembly

| width= 25% |

==== Thu afternoon ====
Set up characterization runs

| width=25% |
==== Fri afternoon ====

Adjourn by 4 pm
|- valign=top
|

==== Tue evening ====
5-7 pm: SURF BBQ

Lab session: 7-9 pm
* Set up and run first TX-TL reactions

| width=25% |
==== Wed evening ====
6:30-8 pm: Group dinner on S. Lake (participants and mentors)

Lab session: 8-10 pm
* Set up TX-TL runs

| width=25% |
==== Thu evening ====
| width=25% |
|}

Description of tutorials:
* Lab basics - this tutorial is intended for participants who have not had any experience in a molecular biology lab. You will learn how to pipette small volumes of clear fluids, run PCR reactions and run gels. If you have had an undergraduate lab class in biology in the last 10 years, you probably don't need to come.

* MATLAB basics - this tutorial is for participants who have never used the MATLAB program. You will learn how to load and plot data in MATLAB and how to use the SimBiology toolbox for setting up very simple reactions.

* Sequence editing - this tutorial will show how to use a DNA sequence editing program such as Geneious or ApE (we mainly use Geneious). You'll learn how to annotate a sequence, simulate PCR reactions and other similar techniques.

=== Read-ahead material ===

We will assume everyone has watched the following 15 minute video before attending the workshop:
* Z. Z. Sun, C. A. Hayes, J. Shin, F. Caschera, R. M. Murray, V. Noireaux, [http://www.jove.com/video/50762 Protocols for Implementing an Escherichia Coli Based TX-TL Cell-Free Expression System for Synthetic Biology]. ''Journal. of Visualized Experiments'' (JoVE), e50762, doi:10.3791/50762 (2013).

If you have time, we also encourage you to take a look at the following material before arriving:
* J. Shin and V. Noireaux, [http://pubs.acs.org/doi/abs/10.1021/sb200016s An ''E. coli'' cell-free expression toolbox: application to synthetic gene circuits and artificial cells]. ''ACS Synthetic Biology'', 1(1):29–41, 2012.

* Z. Z. Sun, E. Yeung, C. A. Hayes, V. Noireaux and Richard M. Murray, [http://www.cds.caltech.edu/~murray/papers/sun+13-acs_synbio.html Linear DNA for rapid prototyping of synthetic biological circuits in an ''Escherichia coli'' based TX-TL cell-free system]. ''ACS Synthetic Biology'', 2014.

* [http://openwetware.org/wiki/Biomolecular_Breadboards Biomolecular Breadboards pages on OpenWetWare]
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Models Modeling overview] - setting up simulations using MATLAB-based TX-TL toolbox
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Preliminary_Data Preliminary data] - includes linear DNA protection, protein degradation
** [http://openwetware.org/wiki/Biomolecular_Breadboards:More_Info More info] - additional references and presentations on TX-TL

=== Software ===
We will make use of the following software as part of the workshop:
* Microsoft Excel (or Numbers)
* [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE] (free), [http://www.geneious.com Geneious] (free trial)
* [http://www.mathworks.com MATLAB], [http://www.mathworks.com/products/simbiology/ Simbiology]
* [http://sourceforge.net/projects/txtl/ TX-TL modeling toolbox] (requires MATLAB 2010+ and SimBiology]
Participants are encouraged to install this software on their laptops prior to the workshop, but version of the software will also be available on lab computers.

TX-TL Bootcamp, Jun 2015

2015-06-04T23:30:42Z

Chayes: /* Wed afternoon */

Caltech will be hosting a hands-on "bootcamp" on cell-free prototyping and debugging of biological circuits. This page contains information for the TX-TL workshop, which will take place at Caltech on 16-18 Jun 2015. This workshop is by invitation only. __NOTOC__

=== Workshop goals ===
The purpose of the workshop is to provide participants with a working knowledge of cell-free methods for design of biomolecular circuits, using the TX-TL system developed by Vincent Noireaux at U. Minnesota. By the end of the workshop, participants will be able to:

* Build models and simulate circuits using the TX-TL modeling toolbox (MATLAB-based)
* Assemble and test genetic circuits using linear DNA assembly in a single day
* Test and characterize circuits that are part of our current research activities

=== Summary Schedule ===

The schedule below gives an overview of the activities during the workshop.

{| width=100% border=1
|- valign=top
| width=25% |
==== Tue morning ====
9-11 am: Optional tutorials (details below):
* Lab basics - meet in 111 Keck
| width=25% |

==== Wed morning ====
9-12 pm: Meet in 111 Keck
* Analyzing TX-TL results (from overnight run)
* TX-TL using linear DNA
* Lab (136 Keck): Set up Golden Gate reactions

Group lunch at Chandler (when done)
| width= 25% |

==== Thu morning ====
9:00a - Analyze TX-TL results from previous day [111 Keck]
10:00a - Plan out circuits designs to build and test (with mentors)

| width=25% |
==== Fri morning ====

|- valign=top
| width= 25% |
==== Tue afternoon ====
11 am: '''Bootcamp starts''', 111 Keck (lunch will be provided)
* Overview of workshop and TX-TL system (Richard)
* Lab safety briefing (Clare)

1:45-5 pm: SURF check-in and orientation
* 1:45-3 pm: SURF checkin
* 1:45-3:45 pm: Housing move in
* 3:45-5 pm: SURF orientation
| width= 25% |

==== Wed afternoon ====
1:30 - 2:30 pm - SURF safety meeting (mandatory)

2:30 pm: Set up PCR reactions for GGA linear DNAs (Clare)

3:00p - Project discussions (with co-mentors) at CDS tea and initial experiments

5:00 - 8:00 pm - Set up FFL runs from GGA assembly

| width= 25% |

==== Thu afternoon ====
Set up characterization runs

| width=25% |
==== Fri afternoon ====

Adjourn by 4 pm
|- valign=top
|

==== Tue evening ====
5-7 pm: SURF BBQ

Lab session: 7-9 pm
* Set up and run first TX-TL reactions

| width=25% |
==== Wed evening ====
6:30-8 pm: Group dinner on S. Lake (participants and mentors)

Lab session: 8-10 pm
* Set up TX-TL runs

| width=25% |
==== Thu evening ====
| width=25% |
|}

Description of tutorials:
* Lab basics - this tutorial is intended for participants who have not had any experience in a molecular biology lab. You will learn how to pipette small volumes of clear fluids, run PCR reactions and run gels. If you have had an undergraduate lab class in biology in the last 10 years, you probably don't need to come.

* MATLAB basics - this tutorial is for participants who have never used the MATLAB program. You will learn how to load and plot data in MATLAB and how to use the SimBiology toolbox for setting up very simple reactions.

* Sequence editing - this tutorial will show how to use a DNA sequence editing program such as Geneious or ApE (we mainly use Geneious). You'll learn how to annotate a sequence, simulate PCR reactions and other similar techniques.

=== Read-ahead material ===

We will assume everyone has watched the following 15 minute video before attending the workshop:
* Z. Z. Sun, C. A. Hayes, J. Shin, F. Caschera, R. M. Murray, V. Noireaux, [http://www.jove.com/video/50762 Protocols for Implementing an Escherichia Coli Based TX-TL Cell-Free Expression System for Synthetic Biology]. ''Journal. of Visualized Experiments'' (JoVE), e50762, doi:10.3791/50762 (2013).

If you have time, we also encourage you to take a look at the following material before arriving:
* J. Shin and V. Noireaux, [http://pubs.acs.org/doi/abs/10.1021/sb200016s An ''E. coli'' cell-free expression toolbox: application to synthetic gene circuits and artificial cells]. ''ACS Synthetic Biology'', 1(1):29–41, 2012.

* Z. Z. Sun, E. Yeung, C. A. Hayes, V. Noireaux and Richard M. Murray, [http://www.cds.caltech.edu/~murray/papers/sun+13-acs_synbio.html Linear DNA for rapid prototyping of synthetic biological circuits in an ''Escherichia coli'' based TX-TL cell-free system]. ''ACS Synthetic Biology'', 2014.

* [http://openwetware.org/wiki/Biomolecular_Breadboards Biomolecular Breadboards pages on OpenWetWare]
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Models Modeling overview] - setting up simulations using MATLAB-based TX-TL toolbox
** [http://openwetware.org/wiki/Biomolecular_Breadboards:Preliminary_Data Preliminary data] - includes linear DNA protection, protein degradation
** [http://openwetware.org/wiki/Biomolecular_Breadboards:More_Info More info] - additional references and presentations on TX-TL

=== Software ===
We will make use of the following software as part of the workshop:
* Microsoft Excel (or Numbers)
* [http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE] (free), [http://www.geneious.com Geneious] (free trial)
* [http://www.mathworks.com MATLAB], [http://www.mathworks.com/products/simbiology/ Simbiology]
* [http://sourceforge.net/projects/txtl/ TX-TL modeling toolbox] (requires MATLAB 2010+ and SimBiology]
Participants are encouraged to install this software on their laptops prior to the workshop, but version of the software will also be available on lab computers.