Murray Wiki - User contributions [en]

Soheil Feizi, Oct 2015

2015-10-08T16:41:14Z

Ehyeung: /* Schedule */

* Visitor: Soheil Feizi (MIT)
* Date: October 19th (Mon)
=== Schedule ===
* 9:15 am - Yutaka Hori (218 ANB; ex 3552)
* 10:15 am -
* 11 am -
* 11:45 am - seminar set up
* 12-1:15 pm - seminar (121 ANB)
* 1:30 pm -
* 2:15 pm - Anandh Swaminathan (Steele 103)
* 3 pm - Enoch Yeung (Keck 139)
* 4 pm - Richard Murray (Steele 109)
* 4:45 pm - Done

=== Seminar ===
Title: Learning (from) networks: fundamental limits, algorithms, and applications

Abstract: Network models provide a unifying framework for understanding dependencies among variables in medical, biological, and other sciences. Networks can be used to reveal underlying data structures, infer functional modules, and facilitate experiment design. In practice, however, size, uncertainty and complexity of the underlying associations render these applications challenging.

In this talk, we illustrate the use of spectral, combinatorial, and statistical inference techniques in several significant network science problems. First, we consider the problem of network alignment where the goal is to find a bijective mapping between nodes of two networks to maximize their overlapping edges while minimizing mismatches. To solve this combinatorial problem, we present a new scalable spectral algorithm, and establish its efficiency theoretically and experimentally over several synthetic and real networks. Next, we introduce network maximal correlation (NMC) as an essential measure to capture nonlinear associations in networks. We characterize NMC using geometric properties of Hilbert spaces and illustrate its application in learning network topology when variables have unknown nonlinear dependencies. Finally, we discuss the problem of learning low dimensional structures (such as clusters) in large networks, where we introduce logistic Random Dot Product Graphs, a new class of networks which includes most stochastic block models as well as other low dimensional structures. Using this model, we propose a spectral network clustering algorithm that possesses robust performance under different clustering setups. In all of these problems, we examine underlying fundamental limits and present efficient algorithms for solving them. We also highlight applications of the proposed algorithms to data-driven problems such as functional and regulatory genomics of human diseases, and cancer.

Group Schedule, Spring 2015

2015-04-13T20:09:59Z

Ehyeung: /* Week 7: 11 May - 15 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 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=33% |
* Group meetings - 213 ANB
| width=33% |
* Biocircuits subgroup - 111 Keck
| width=33% |
* NCS subgroup - 243 ANB
|}

{| width=100% border=1

|- valign=top
| width=33% |
=== Week 1: 30 Mar - 3 Apr ===

'''Biocircuits: 1 Apr (Wed), 10a-12p 114 Steele'''
* Lab safety (Clare, Richard)
* Ania Baetica (short)

'''NCS: 1 Apr (Wed), 4p-5:30p'''
* Anthony Fragoso (main)
* Open (short)

| width=33% |

=== Week 2: 6 Apr - 10 Apr ===
'''NCS: 6 Apr (Mon), 2:30p-4p'''
* Catharine McGhan (main)
* Scott (short)
'''Biocircuits: 8 Apr (Wed), 10a-12p 114 Steele'''
* Emzo de los Santos (long)
* Yutaka Hori (short)
| width=33% |

=== Week 3: 13 Apr - 17 Apr ===
* Richard out of town, Mon-Thu
* Biocircuits lab cleanup, Wed @ 10 am
|- valign=top
| width=33% |

=== Week 4: 20 Apr - 24 Apr ===
'''NCS: 22 Apr (Wed), 12:30p-2p
* Scott Livingston (main)
* Open (short)
'''Biocircuits: 22 Apr (Wed), 10a-12p 114 Steele
* Anandh Saminathan (long)
* Victoria Hsiao (short)
| width=33% |

=== Week 5: 27 Apr - 1 May ===
'''Biocircuits: 29 Apr (Wed), 10a-12p 114 Steele'''
* Anu Thubagere (long)
* Dan Siegal (short)
<hr>
* NASA Formal Methods Symposium, Mon-Wed

| width=33% |

=== Week 6: 4 May - 8 May ===
'''NCS: 5 May (Tue), 2:30p-4p
* Ivan Papusha (main)
* Benson Christalin (short)
'''Biocircuits: 6 May (Wed), 10a-12p 114 Steele'''
* Clare Hayes (long)
* Vipul Singhal (short)
|- valign=top
| width=33% |

=== Week 7: 11 May - 15 May ===
'''NCS: 11 May (Mon), 2:30p-4p
* Ioannis Filippidis (main)
* Open (short)
'''Biocircuits: 13 May (Wed), 10a-12p 114 Steele'''
* Shaobin Guo (long)
* Enoch Yeung (short)

| width=33% |

=== Week 8: 18 May - 22 May ===
'''Biocircuits: 20 May (Wed), 10a-12p 114 Steele'''
* Zach Sun (long)
*Yong Wu (short)
'''NCS: 20 May (Wed), 4-5:30p
* Samira Farahani (main)
* Open (short)

| width=33% |

=== Week 9: 25 May - 29 May ===
'''NCS: 25 May (Mon), 2:30p-4p
* Yilin Mo (main)
* Open (short)
'''Biocircuits: 27 May (Wed), 10a-12p 114 Steele'''
* Rotation student (long)
* Sean Sanchez (short)

|- valign=top
| width=33% |

=== Week 10: 1 Jun - 5 Jun ===
'''NCS: 1 Jun (Mon), 2:30p-4p
* Vasu Raman (main)
* Open (short)
'''Biocircuits: 4 Jun (Thu), 10a-12p'''
* Rotation student (long)
* Tiffany Zhou (short)

| width=33% |

=== Week 11: 8 Jun - 12 Jun ===
'''NCS: 8 Jun (Mon), 2:30p-4p
* Benson Christalin (short)
* Daniel Naftalovich (short)
<hr>
* SEED: Wed-Sat in Boston
| width=33% |

|}

Group Schedule, Spring 2015

2015-04-13T20:09:41Z

Ehyeung: /* Week 8: 18 May - 22 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 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=33% |
* Group meetings - 213 ANB
| width=33% |
* Biocircuits subgroup - 111 Keck
| width=33% |
* NCS subgroup - 243 ANB
|}

{| width=100% border=1

|- valign=top
| width=33% |
=== Week 1: 30 Mar - 3 Apr ===

'''Biocircuits: 1 Apr (Wed), 10a-12p 114 Steele'''
* Lab safety (Clare, Richard)
* Ania Baetica (short)

'''NCS: 1 Apr (Wed), 4p-5:30p'''
* Anthony Fragoso (main)
* Open (short)

| width=33% |

=== Week 2: 6 Apr - 10 Apr ===
'''NCS: 6 Apr (Mon), 2:30p-4p'''
* Catharine McGhan (main)
* Scott (short)
'''Biocircuits: 8 Apr (Wed), 10a-12p 114 Steele'''
* Emzo de los Santos (long)
* Yutaka Hori (short)
| width=33% |

=== Week 3: 13 Apr - 17 Apr ===
* Richard out of town, Mon-Thu
* Biocircuits lab cleanup, Wed @ 10 am
|- valign=top
| width=33% |

=== Week 4: 20 Apr - 24 Apr ===
'''NCS: 22 Apr (Wed), 12:30p-2p
* Scott Livingston (main)
* Open (short)
'''Biocircuits: 22 Apr (Wed), 10a-12p 114 Steele
* Anandh Saminathan (long)
* Victoria Hsiao (short)
| width=33% |

=== Week 5: 27 Apr - 1 May ===
'''Biocircuits: 29 Apr (Wed), 10a-12p 114 Steele'''
* Anu Thubagere (long)
* Dan Siegal (short)
<hr>
* NASA Formal Methods Symposium, Mon-Wed

| width=33% |

=== Week 6: 4 May - 8 May ===
'''NCS: 5 May (Tue), 2:30p-4p
* Ivan Papusha (main)
* Benson Christalin (short)
'''Biocircuits: 6 May (Wed), 10a-12p 114 Steele'''
* Clare Hayes (long)
* Vipul Singhal (short)
|- valign=top
| width=33% |

=== Week 7: 11 May - 15 May ===
'''NCS: 11 May (Mon), 2:30p-4p
* Ioannis Filippidis (main)
* Open (short)
'''Biocircuits: 13 May (Wed), 10a-12p 114 Steele'''
* Shaobin Guo (long)
* Yong Wu (short)

| width=33% |

=== Week 8: 18 May - 22 May ===
'''Biocircuits: 20 May (Wed), 10a-12p 114 Steele'''
* Zach Sun (long)
*Yong Wu (short)
'''NCS: 20 May (Wed), 4-5:30p
* Samira Farahani (main)
* Open (short)

| width=33% |

=== Week 9: 25 May - 29 May ===
'''NCS: 25 May (Mon), 2:30p-4p
* Yilin Mo (main)
* Open (short)
'''Biocircuits: 27 May (Wed), 10a-12p 114 Steele'''
* Rotation student (long)
* Sean Sanchez (short)

|- valign=top
| width=33% |

=== Week 10: 1 Jun - 5 Jun ===
'''NCS: 1 Jun (Mon), 2:30p-4p
* Vasu Raman (main)
* Open (short)
'''Biocircuits: 4 Jun (Thu), 10a-12p'''
* Rotation student (long)
* Tiffany Zhou (short)

| width=33% |

=== Week 11: 8 Jun - 12 Jun ===
'''NCS: 8 Jun (Mon), 2:30p-4p
* Benson Christalin (short)
* Daniel Naftalovich (short)
<hr>
* SEED: Wed-Sat in Boston
| width=33% |

|}

SURF 2015

2014-12-16T19:02:04Z

Ehyeung: /* List of available projects */

{{righttoc}}
This page is intended for students interested in working on SURF projects in the Summer of 2015. It contains information about how to apply for a SURF project in my group along with a list of project areas.

=== Applying for a SURF project ===

Because I get many students interested in doing SURFs in my group and because we have several projects available, we use the first few weeks in January to sort out who we will work with in writing proposals. We only submit one proposal per project area and so we often can't accommodate everyone who wants to work in my group over the summer.

# A list of SURF project descriptions is given in the table below. Due to the number of SURF projects that we support, we are only able to support students who select from among these projects. Please make sure to read the project descriptions, required skills (if any) and skim a few of the listed references before contacting me about doing a SURF project.
# Students interested in writing proposals for SURF projects should contact me via e-mail by 9 Jan (Fri) and provide the following information:
#* A list of up to three SURF projects from the list below that you are interested in working on
#* A one page resume listing relevant experience and coursework
#* If you are not a Caltech student, I will also need the following additional information:
#** An unofficial copy of your academic transcript
#** Names of two faculty members at your current institution that I can contact for a reference
# Starting on 10 January, I will go through all applications and work with my group to identify who is a possible fit for each project. We will then contact you and ask for you to meet (or talk with) possible co-mentors so that we can eventually work out who we will work with in writing up a proposal.
# We hope to make final decisions on projects by about 20 Jan, at which point we will start working with students on writing up proposals.
# All applications should go through the normal SURF application process, described at www.surf.caltech.edu. SURF applications are due on ~21 Feb 2015.
# If you are selected for a SURF, please be aware of the following information
#* All SURF projects in my group will start on 16 Jun (Tue). If you can't start on that date, please make sure that you indicate this when you contact me
#* All SURF projects are for a minimum of 10 weeks, although I usually recommend that you try to stay for 12 weeks if possible (at no additional pay). It's hard to complete a project in just 10 weeks and spending a few extra weeks can greatly improve the project.
#* All SURF students in my group will be expected to devote full-time effort to their SURF project, so you cannot have a second job in addition to your SURF.

=== List of available projects ===

Projects will be posted as they come available. I recommend waiting until near the deadline submission before submitting your project preferences.

{| border=1 width=100%
|-
| '''Title''' || '''Grant/Project''' || '''Co-Mentors''' || '''Comments'''



|-
| {{SURF entry|2015|Correct-by-Construction Control of UAVs Under Environmental Uncertainty}}
| NGC
| [http://directory.caltech.edu/personnel/farahani Samira Farahani]
|
|}

SURF 2015

2014-12-16T19:01:16Z

Ehyeung: /* List of available projects */

{{righttoc}}
This page is intended for students interested in working on SURF projects in the Summer of 2015. It contains information about how to apply for a SURF project in my group along with a list of project areas.

=== Applying for a SURF project ===

Because I get many students interested in doing SURFs in my group and because we have several projects available, we use the first few weeks in January to sort out who we will work with in writing proposals. We only submit one proposal per project area and so we often can't accommodate everyone who wants to work in my group over the summer.

# A list of SURF project descriptions is given in the table below. Due to the number of SURF projects that we support, we are only able to support students who select from among these projects. Please make sure to read the project descriptions, required skills (if any) and skim a few of the listed references before contacting me about doing a SURF project.
# Students interested in writing proposals for SURF projects should contact me via e-mail by 9 Jan (Fri) and provide the following information:
#* A list of up to three SURF projects from the list below that you are interested in working on
#* A one page resume listing relevant experience and coursework
#* If you are not a Caltech student, I will also need the following additional information:
#** An unofficial copy of your academic transcript
#** Names of two faculty members at your current institution that I can contact for a reference
# Starting on 10 January, I will go through all applications and work with my group to identify who is a possible fit for each project. We will then contact you and ask for you to meet (or talk with) possible co-mentors so that we can eventually work out who we will work with in writing up a proposal.
# We hope to make final decisions on projects by about 20 Jan, at which point we will start working with students on writing up proposals.
# All applications should go through the normal SURF application process, described at www.surf.caltech.edu. SURF applications are due on ~21 Feb 2015.
# If you are selected for a SURF, please be aware of the following information
#* All SURF projects in my group will start on 16 Jun (Tue). If you can't start on that date, please make sure that you indicate this when you contact me
#* All SURF projects are for a minimum of 10 weeks, although I usually recommend that you try to stay for 12 weeks if possible (at no additional pay). It's hard to complete a project in just 10 weeks and spending a few extra weeks can greatly improve the project.
#* All SURF students in my group will be expected to devote full-time effort to their SURF project, so you cannot have a second job in addition to your SURF.

=== List of available projects ===

Projects will be posted as they come available. I recommend waiting until near the deadline submission before submitting your project preferences.

{| border=1 width=100%
|-
| '''Title''' || '''Grant/Project''' || '''Co-Mentors''' || '''Comments'''



|-
| {{SURF entry|2015|Correct-by-Construction Control of UAVs Under Environmental Uncertainty}}
| NGC
| [http://directory.caltech.edu/personnel/farahani Samira Farahani]
|
|}

SURF 2015: Quantitating Differences in Gene Expresion in Linear and Plasmid DNA in a Cell-Free Expression (TXTL) System

2014-12-16T19:00:38Z

Ehyeung: Created page with "Website under construction."

Website under construction.

SURF 2015

2014-12-16T19:00:26Z

Ehyeung: /* List of available projects */

{{righttoc}}
This page is intended for students interested in working on SURF projects in the Summer of 2015. It contains information about how to apply for a SURF project in my group along with a list of project areas.

=== Applying for a SURF project ===

Because I get many students interested in doing SURFs in my group and because we have several projects available, we use the first few weeks in January to sort out who we will work with in writing proposals. We only submit one proposal per project area and so we often can't accommodate everyone who wants to work in my group over the summer.

# A list of SURF project descriptions is given in the table below. Due to the number of SURF projects that we support, we are only able to support students who select from among these projects. Please make sure to read the project descriptions, required skills (if any) and skim a few of the listed references before contacting me about doing a SURF project.
# Students interested in writing proposals for SURF projects should contact me via e-mail by 9 Jan (Fri) and provide the following information:
#* A list of up to three SURF projects from the list below that you are interested in working on
#* A one page resume listing relevant experience and coursework
#* If you are not a Caltech student, I will also need the following additional information:
#** An unofficial copy of your academic transcript
#** Names of two faculty members at your current institution that I can contact for a reference
# Starting on 10 January, I will go through all applications and work with my group to identify who is a possible fit for each project. We will then contact you and ask for you to meet (or talk with) possible co-mentors so that we can eventually work out who we will work with in writing up a proposal.
# We hope to make final decisions on projects by about 20 Jan, at which point we will start working with students on writing up proposals.
# All applications should go through the normal SURF application process, described at www.surf.caltech.edu. SURF applications are due on ~21 Feb 2015.
# If you are selected for a SURF, please be aware of the following information
#* All SURF projects in my group will start on 16 Jun (Tue). If you can't start on that date, please make sure that you indicate this when you contact me
#* All SURF projects are for a minimum of 10 weeks, although I usually recommend that you try to stay for 12 weeks if possible (at no additional pay). It's hard to complete a project in just 10 weeks and spending a few extra weeks can greatly improve the project.
#* All SURF students in my group will be expected to devote full-time effort to their SURF project, so you cannot have a second job in addition to your SURF.

=== List of available projects ===

Projects will be posted as they come available. I recommend waiting until near the deadline submission before submitting your project preferences.

{| border=1 width=100%
|-
| '''Title''' || '''Grant/Project''' || '''Co-Mentors''' || '''Comments'''

|-
| {{SURF entry|2015|Quantitating Differences in Gene Expresion in Linear and Plasmid DNA in a Cell-Free Expression (TXTL) System }}
| Keywords: in vitro synthetic biology, nonlinear modeling, model prediction and validation
| [https://www.cds.caltech.edu/~eyeung/ Enoch Yeung]
|
|-
| {{SURF entry|2015|Correct-by-Construction Control of UAVs Under Environmental Uncertainty}}
| NGC
| [http://directory.caltech.edu/personnel/farahani Samira Farahani]
|
|}

SURF 2015

2014-12-16T19:00:07Z

Ehyeung: /* List of available projects */

{{righttoc}}
This page is intended for students interested in working on SURF projects in the Summer of 2015. It contains information about how to apply for a SURF project in my group along with a list of project areas.

=== Applying for a SURF project ===

Because I get many students interested in doing SURFs in my group and because we have several projects available, we use the first few weeks in January to sort out who we will work with in writing proposals. We only submit one proposal per project area and so we often can't accommodate everyone who wants to work in my group over the summer.

# A list of SURF project descriptions is given in the table below. Due to the number of SURF projects that we support, we are only able to support students who select from among these projects. Please make sure to read the project descriptions, required skills (if any) and skim a few of the listed references before contacting me about doing a SURF project.
# Students interested in writing proposals for SURF projects should contact me via e-mail by 9 Jan (Fri) and provide the following information:
#* A list of up to three SURF projects from the list below that you are interested in working on
#* A one page resume listing relevant experience and coursework
#* If you are not a Caltech student, I will also need the following additional information:
#** An unofficial copy of your academic transcript
#** Names of two faculty members at your current institution that I can contact for a reference
# Starting on 10 January, I will go through all applications and work with my group to identify who is a possible fit for each project. We will then contact you and ask for you to meet (or talk with) possible co-mentors so that we can eventually work out who we will work with in writing up a proposal.
# We hope to make final decisions on projects by about 20 Jan, at which point we will start working with students on writing up proposals.
# All applications should go through the normal SURF application process, described at www.surf.caltech.edu. SURF applications are due on ~21 Feb 2015.
# If you are selected for a SURF, please be aware of the following information
#* All SURF projects in my group will start on 16 Jun (Tue). If you can't start on that date, please make sure that you indicate this when you contact me
#* All SURF projects are for a minimum of 10 weeks, although I usually recommend that you try to stay for 12 weeks if possible (at no additional pay). It's hard to complete a project in just 10 weeks and spending a few extra weeks can greatly improve the project.
#* All SURF students in my group will be expected to devote full-time effort to their SURF project, so you cannot have a second job in addition to your SURF.

=== List of available projects ===

Projects will be posted as they come available. I recommend waiting until near the deadline submission before submitting your project preferences.

{| border=1 width=100%
|-
| '''Title''' || '''Grant/Project''' || '''Co-Mentors''' || '''Comments'''


|-
| {{SURF entry|2015|Correct-by-Construction Control of UAVs Under Environmental Uncertainty}}
| NGC
| [http://directory.caltech.edu/personnel/farahani Samira Farahani]
|
|}

Group Schedule, Fall 2013

2013-12-06T22:33:32Z

Ehyeung: /* Week 10: 2 Dec - 6 Dec */

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, Summer 2013]]
|}

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=30% |
=== Week 1: 30 Sep - 4 Oct ===
'''Biocircuits: 1 Oct (Tue), 10a-noon''' - 114 Steele
* Zoltan Tuza
* Project/lab planning (Richard)
'''NCS: 2 Oct (Wed), 10:30a-12:30p''' - 110 Steele 
* Ivan Papusha
* Stephanie Tsuei
'''Group meeting: 3 Oct (Thu), 12:15-1:30p'''
* Yutaka Hori
| width=30% |

=== Week 2: 7 Oct - 11 Oct ===
'''NCS: 9 Oct (Wed), 10a-noon'''
* Vasu Raman
* Scott Livingston
'''Biocircuits: 10 Oct (Thu), 10a-noon''' - 114 Steele
* Victoria Hsiao
* Vipul Singhal
'''Group meeting: 10 Oct (Thu), 12:15-1:30p'''
* Subramanian Bose
| width=30% |

=== Week 3: 14 Oct - 18 Oct ===
'''Biocircuits: 17 Oct (Thu), 10a-noon'''
* <s>Anu Thubagere</s>
* Anandh Swaminathan
'''Group meeting: 17 Oct (Thu), 12:15-1:30p'''
* Dan Siegal-Gaskins
'''NCS: 17 Oct (Thu), 3-5p'''
* Yilin Mo
* Eric Wolff
|- valign=top
| width=30% |

=== Week 4: 21 Oct - 25 Oct ===
* Richard out of town, Mon-Fri
* Biocircuits lab cleanup, Tue @ 10 am
| width=30% |

=== Week 5: 28 Oct - 1 Nov ===
'''NCS: 30 Oct (Wed), 10a-noon'''
* TuLiP planning (Richard)
'''Biocircuits: 31 Oct (Thu), 11a-1p'''
* Anu Thubagere
* Zach Sun
| width=30% |

=== Week 6: 4 Nov - 8 Nov ===
'''Biocircuits: 4 Nov (Mon), 10a-noon'''
* Jongmin Kim
* Vanessa Jonsson
'''NCS: 7 Nov (Thu), 10a-noon'''
* Matanya Horowitz
'''Group meeting: 7 Nov (Thu), 12:15-1:30p'''
* Joe Levine
|- valign=top
| width=30% |

=== Week 7: 11 Nov - 15 Nov ===
* Richard out of town, Mon-Fri
| width=30% |

=== Week 8: 18 Nov - 22 Nov ===
'''NCS: 20 Nov (Wed), 10a-noon'''
* Rangoli Sharan
* Ioannis Filippidis
'''Biocircuits: 21 Nov (Thu), 10a-noon'''
* Shaobin Guo
* Emzo de los Santos
'''Group meeting: 21 Nov (Thu), 12:15-1:30p'''
* Chris Kempes
| width=30% |
=== Week 9: 25 Nov - 29 Nov ===
'''NCS: 25 Nov (Mon), 10a-noon'''
* Nikolai Matni
* Jean-Maurice Leonetti
'''Biocircuits: 26 Nov (Tue), 10a-noon'''
* Yong Wu
* Clare Hayes
'''Group meeting: 26 Nov (Tue), 12:15-1:30p'''
* Alex Mauroy (UCSB)
|- valign=top
| width=30% |

=== Week 10: 2 Dec - 6 Dec ===
'''NCS: 5 Dec (Thu), 3-5p'''
* Marcella Gomez
* TuLiP planning (Richard)
'''Biocircuits: 6 Dec (Fri), 10a-noon'''
* [[File:EYDec6-13.pdf | Enoch Yeung]]
* Joe Meyerowitz
| width=30% |

=== Week 12: 9 Dec - 13 Dec ===
* Richard out of town, Mon-Fri
* Biocircuits lab cleanup, Tue @ 10 am
| width=30% |

=== Week 13: 16 Dec - 20 Dec ===
'''Biocircuits: 17 Dec (Tue), 10a-noon'''
* TBD
'''NCS: 17 Dec (Wed), 10a-noon'''
* TBD

|}

Group Schedule, Fall 2013

2013-12-06T22:33:16Z

Ehyeung:

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, Summer 2013]]
|}

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=30% |
=== Week 1: 30 Sep - 4 Oct ===
'''Biocircuits: 1 Oct (Tue), 10a-noon''' - 114 Steele
* Zoltan Tuza
* Project/lab planning (Richard)
'''NCS: 2 Oct (Wed), 10:30a-12:30p''' - 110 Steele 
* Ivan Papusha
* Stephanie Tsuei
'''Group meeting: 3 Oct (Thu), 12:15-1:30p'''
* Yutaka Hori
| width=30% |

=== Week 2: 7 Oct - 11 Oct ===
'''NCS: 9 Oct (Wed), 10a-noon'''
* Vasu Raman
* Scott Livingston
'''Biocircuits: 10 Oct (Thu), 10a-noon''' - 114 Steele
* Victoria Hsiao
* Vipul Singhal
'''Group meeting: 10 Oct (Thu), 12:15-1:30p'''
* Subramanian Bose
| width=30% |

=== Week 3: 14 Oct - 18 Oct ===
'''Biocircuits: 17 Oct (Thu), 10a-noon'''
* <s>Anu Thubagere</s>
* Anandh Swaminathan
'''Group meeting: 17 Oct (Thu), 12:15-1:30p'''
* Dan Siegal-Gaskins
'''NCS: 17 Oct (Thu), 3-5p'''
* Yilin Mo
* Eric Wolff
|- valign=top
| width=30% |

=== Week 4: 21 Oct - 25 Oct ===
* Richard out of town, Mon-Fri
* Biocircuits lab cleanup, Tue @ 10 am
| width=30% |

=== Week 5: 28 Oct - 1 Nov ===
'''NCS: 30 Oct (Wed), 10a-noon'''
* TuLiP planning (Richard)
'''Biocircuits: 31 Oct (Thu), 11a-1p'''
* Anu Thubagere
* Zach Sun
| width=30% |

=== Week 6: 4 Nov - 8 Nov ===
'''Biocircuits: 4 Nov (Mon), 10a-noon'''
* Jongmin Kim
* Vanessa Jonsson
'''NCS: 7 Nov (Thu), 10a-noon'''
* Matanya Horowitz
'''Group meeting: 7 Nov (Thu), 12:15-1:30p'''
* Joe Levine
|- valign=top
| width=30% |

=== Week 7: 11 Nov - 15 Nov ===
* Richard out of town, Mon-Fri
| width=30% |

=== Week 8: 18 Nov - 22 Nov ===
'''NCS: 20 Nov (Wed), 10a-noon'''
* Rangoli Sharan
* Ioannis Filippidis
'''Biocircuits: 21 Nov (Thu), 10a-noon'''
* Shaobin Guo
* Emzo de los Santos
'''Group meeting: 21 Nov (Thu), 12:15-1:30p'''
* Chris Kempes
| width=30% |
=== Week 9: 25 Nov - 29 Nov ===
'''NCS: 25 Nov (Mon), 10a-noon'''
* Nikolai Matni
* Jean-Maurice Leonetti
'''Biocircuits: 26 Nov (Tue), 10a-noon'''
* Yong Wu
* Clare Hayes
'''Group meeting: 26 Nov (Tue), 12:15-1:30p'''
* Alex Mauroy (UCSB)
|- valign=top
| width=30% |

=== Week 10: 2 Dec - 6 Dec ===
'''NCS: 5 Dec (Thu), 3-5p'''
* Marcella Gomez
* TuLiP planning (Richard)
'''Biocircuits: 6 Dec (Fri), 10a-noon'''
* [[File:EYDec6-13.pdf Enoch Yeung]]
* Joe Meyerowitz
| width=30% |

=== Week 12: 9 Dec - 13 Dec ===
* Richard out of town, Mon-Fri
* Biocircuits lab cleanup, Tue @ 10 am
| width=30% |

=== Week 13: 16 Dec - 20 Dec ===
'''Biocircuits: 17 Dec (Tue), 10a-noon'''
* TBD
'''NCS: 17 Dec (Wed), 10a-noon'''
* TBD

|}

Group Schedule, Fall 2013

2013-09-16T21:17:01Z

Ehyeung: /* Week 10: 2 Dec - 6 Dec */

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 2013]]
|}

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=30% |
=== Week 1: 30 Sep - 4 Oct ===
'''Biocircuits: 1 Oct (Tue), 10a-noon'''
* Zoltan Tuza
* Project/lab planning (Richard)
'''NCS: 2 Oct (Wed), 10a-noon'''
* Note: this meeting may shift to 11a-1p
* Ivan Papusha
* Stephanie Tsuei
'''Group meeting: 3 Oct (Thu), 12:15-1:30p'''
* Yutaka Hori
| width=30% |

=== Week 2: 7 Oct - 11 Oct ===
'''NCS: 9 Oct (Wed), 10a-noon'''
* Vasu Raman
* Scott Livingston
'''Biocircuits: 10 Oct (Thu), 10a-noon'''
* Victoria Hsiao
* Vipul Singhal
'''Group meeting: 10 Oct (Thu), 12:15-1:30p'''
* Subramanian Bose
| width=30% |
=== Week 3: 14 Oct - 18 Oct ===
'''Biocircuits: 17 Oct (Thu), 10a-noon'''
* Anu Thubagere
* Anandh Swaminathan
'''Group meeting: 17 Oct (Thu), 12:15-1:30p'''
* Dan Siegal-Gaskins
'''NCS: 17 Oct (Thu), 3-5p'''
* Yilin Mo
* Eric Wolff
|- valign=top
| width=30% |
=== Week 4: 21 Oct - 25 Oct ===
* Richard out of town, Mon-Fri
* Biocircuits lab cleanup, Tue @ 10 am
| width=30% |

=== Week 5: 28 Oct - 1 Nov ===
'''Biocircuits: 29 Oct (Tue), 10a-noon'''
* Note: this meeting may shift to 31 Oct (Thu), 11a-1p
* TBD
* Zach Sun
'''NCS: 30 Oct (Wed), 10a-noon'''
* TuLiP planning (Richard)
'''Group meeting: 31 Oct (Thu), 12:15-1:30p'''
* TBD (may be cancelled)
| width=30% |

=== Week 6: 4 Nov - 8 Nov ===
'''Biocircuits: 4 Nov (Mon), 10a-noon'''
* Jongmin Kim
* Vanessa Jonsson
'''NCS: 7 Nov (Thu), 10a-noon'''
* Note: this meeting may shift to 9a-11a
* Matanya Horowitz
* Anandh Swaminathan?
'''Group meeting: 7 Nov (Thu), 12:15-1:30p'''
* Joe Levine
|- valign=top
| width=30% |

=== Week 7: 11 Nov - 15 Nov ===
* Richard out of town, Mon-Fri
| width=30% |

=== Week 8: 18 Nov - 22 Nov ===
'''NCS: 20 Nov (Wed), 10a-noon'''
* Rangoli Sharan
* Ioannis Filippidis
'''Biocircuits: 21 Nov (Thu), 10a-noon'''
* Shaobin Guo
* Emzo de los Santos
'''Group meeting: 21 Nov (Thu), 12:15-1:30p'''
* Chris Kempes
| width=30% |
=== Week 9: 25 Nov - 29 Nov ===
'''NCS: 25 Nov (Mon), 10a-noon'''
* Nikolai Matni
* Jean-Maurice Leonetti
'''Biocircuits: 26 Nov (Tue), 10a-noon'''
* Yong Wu
* Joe Meyerowitz
'''Group meeting: 26 Nov (Tue), 12:15-1:30p'''
* TBD
|- valign=top
| width=30% |

=== Week 10: 2 Dec - 6 Dec ===
'''NCS: 5 Dec (Thu), 3-5p'''
* Marcella Gomez
* TuLiP planning (Richard)
'''Biocircuits: 6 Dec (Fri), 10a-noon'''
* [http://www.cds.caltech.edu/~eyeung Enoch Yeung]
* Open
| width=30% |

=== Week 12: 9 Dec - 13 Dec ===
* Richard out of town, Mon-Fri
* Biocircuits lab cleanup, Tue @ 10 am
| width=30% |

=== Week 13: 16 Dec - 20 Dec ===
'''Biocircuits: 17 Dec (Tue), 10a-noon'''
* TBD
'''NCS: 17 Dec (Wed), 10a-noon'''
* TBD

|}

Group Schedule, Fall 2013

2013-09-16T21:16:32Z

Ehyeung: /* Week 10: 2 Dec - 6 Dec */

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 2013]]
|}

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=30% |
=== Week 1: 30 Sep - 4 Oct ===
'''Biocircuits: 1 Oct (Tue), 10a-noon'''
* Zoltan Tuza
* Project/lab planning (Richard)
'''NCS: 2 Oct (Wed), 10a-noon'''
* Note: this meeting may shift to 11a-1p
* Ivan Papusha
* Stephanie Tsuei
'''Group meeting: 3 Oct (Thu), 12:15-1:30p'''
* Yutaka Hori
| width=30% |

=== Week 2: 7 Oct - 11 Oct ===
'''NCS: 9 Oct (Wed), 10a-noon'''
* Vasu Raman
* Scott Livingston
'''Biocircuits: 10 Oct (Thu), 10a-noon'''
* Victoria Hsiao
* Vipul Singhal
'''Group meeting: 10 Oct (Thu), 12:15-1:30p'''
* Subramanian Bose
| width=30% |
=== Week 3: 14 Oct - 18 Oct ===
'''Biocircuits: 17 Oct (Thu), 10a-noon'''
* Anu Thubagere
* Anandh Swaminathan
'''Group meeting: 17 Oct (Thu), 12:15-1:30p'''
* Dan Siegal-Gaskins
'''NCS: 17 Oct (Thu), 3-5p'''
* Yilin Mo
* Eric Wolff
|- valign=top
| width=30% |
=== Week 4: 21 Oct - 25 Oct ===
* Richard out of town, Mon-Fri
* Biocircuits lab cleanup, Tue @ 10 am
| width=30% |

=== Week 5: 28 Oct - 1 Nov ===
'''Biocircuits: 29 Oct (Tue), 10a-noon'''
* Note: this meeting may shift to 31 Oct (Thu), 11a-1p
* TBD
* Zach Sun
'''NCS: 30 Oct (Wed), 10a-noon'''
* TuLiP planning (Richard)
'''Group meeting: 31 Oct (Thu), 12:15-1:30p'''
* TBD (may be cancelled)
| width=30% |

=== Week 6: 4 Nov - 8 Nov ===
'''Biocircuits: 4 Nov (Mon), 10a-noon'''
* Jongmin Kim
* Vanessa Jonsson
'''NCS: 7 Nov (Thu), 10a-noon'''
* Note: this meeting may shift to 9a-11a
* Matanya Horowitz
* Anandh Swaminathan?
'''Group meeting: 7 Nov (Thu), 12:15-1:30p'''
* Joe Levine
|- valign=top
| width=30% |

=== Week 7: 11 Nov - 15 Nov ===
* Richard out of town, Mon-Fri
| width=30% |

=== Week 8: 18 Nov - 22 Nov ===
'''NCS: 20 Nov (Wed), 10a-noon'''
* Rangoli Sharan
* Ioannis Filippidis
'''Biocircuits: 21 Nov (Thu), 10a-noon'''
* Shaobin Guo
* Emzo de los Santos
'''Group meeting: 21 Nov (Thu), 12:15-1:30p'''
* Chris Kempes
| width=30% |
=== Week 9: 25 Nov - 29 Nov ===
'''NCS: 25 Nov (Mon), 10a-noon'''
* Nikolai Matni
* Jean-Maurice Leonetti
'''Biocircuits: 26 Nov (Tue), 10a-noon'''
* Yong Wu
* Joe Meyerowitz
'''Group meeting: 26 Nov (Tue), 12:15-1:30p'''
* TBD
|- valign=top
| width=30% |

=== Week 10: 2 Dec - 6 Dec ===
'''NCS: 5 Dec (Thu), 3-5p'''
* Marcella Gomez
* TuLiP planning (Richard)
'''Biocircuits: 6 Dec (Fri), 10a-noon'''
* [www.cds.caltech.edu/~eyeung Enoch Yeung]
* Open
| width=30% |

=== Week 12: 9 Dec - 13 Dec ===
* Richard out of town, Mon-Fri
* Biocircuits lab cleanup, Tue @ 10 am
| width=30% |

=== Week 13: 16 Dec - 20 Dec ===
'''Biocircuits: 17 Dec (Tue), 10a-noon'''
* TBD
'''NCS: 17 Dec (Wed), 10a-noon'''
* TBD

|}

Group Schedule, Fall 2013

2013-09-16T21:16:19Z

Ehyeung: /* Week 10: 2 Dec - 6 Dec */

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 2013]]
|}

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=30% |
=== Week 1: 30 Sep - 4 Oct ===
'''Biocircuits: 1 Oct (Tue), 10a-noon'''
* Zoltan Tuza
* Project/lab planning (Richard)
'''NCS: 2 Oct (Wed), 10a-noon'''
* Note: this meeting may shift to 11a-1p
* Ivan Papusha
* Stephanie Tsuei
'''Group meeting: 3 Oct (Thu), 12:15-1:30p'''
* Yutaka Hori
| width=30% |

=== Week 2: 7 Oct - 11 Oct ===
'''NCS: 9 Oct (Wed), 10a-noon'''
* Vasu Raman
* Scott Livingston
'''Biocircuits: 10 Oct (Thu), 10a-noon'''
* Victoria Hsiao
* Vipul Singhal
'''Group meeting: 10 Oct (Thu), 12:15-1:30p'''
* Subramanian Bose
| width=30% |
=== Week 3: 14 Oct - 18 Oct ===
'''Biocircuits: 17 Oct (Thu), 10a-noon'''
* Anu Thubagere
* Anandh Swaminathan
'''Group meeting: 17 Oct (Thu), 12:15-1:30p'''
* Dan Siegal-Gaskins
'''NCS: 17 Oct (Thu), 3-5p'''
* Yilin Mo
* Eric Wolff
|- valign=top
| width=30% |
=== Week 4: 21 Oct - 25 Oct ===
* Richard out of town, Mon-Fri
* Biocircuits lab cleanup, Tue @ 10 am
| width=30% |

=== Week 5: 28 Oct - 1 Nov ===
'''Biocircuits: 29 Oct (Tue), 10a-noon'''
* Note: this meeting may shift to 31 Oct (Thu), 11a-1p
* TBD
* Zach Sun
'''NCS: 30 Oct (Wed), 10a-noon'''
* TuLiP planning (Richard)
'''Group meeting: 31 Oct (Thu), 12:15-1:30p'''
* TBD (may be cancelled)
| width=30% |

=== Week 6: 4 Nov - 8 Nov ===
'''Biocircuits: 4 Nov (Mon), 10a-noon'''
* Jongmin Kim
* Vanessa Jonsson
'''NCS: 7 Nov (Thu), 10a-noon'''
* Note: this meeting may shift to 9a-11a
* Matanya Horowitz
* Anandh Swaminathan?
'''Group meeting: 7 Nov (Thu), 12:15-1:30p'''
* Joe Levine
|- valign=top
| width=30% |

=== Week 7: 11 Nov - 15 Nov ===
* Richard out of town, Mon-Fri
| width=30% |

=== Week 8: 18 Nov - 22 Nov ===
'''NCS: 20 Nov (Wed), 10a-noon'''
* Rangoli Sharan
* Ioannis Filippidis
'''Biocircuits: 21 Nov (Thu), 10a-noon'''
* Shaobin Guo
* Emzo de los Santos
'''Group meeting: 21 Nov (Thu), 12:15-1:30p'''
* Chris Kempes
| width=30% |
=== Week 9: 25 Nov - 29 Nov ===
'''NCS: 25 Nov (Mon), 10a-noon'''
* Nikolai Matni
* Jean-Maurice Leonetti
'''Biocircuits: 26 Nov (Tue), 10a-noon'''
* Yong Wu
* Joe Meyerowitz
'''Group meeting: 26 Nov (Tue), 12:15-1:30p'''
* TBD
|- valign=top
| width=30% |

=== Week 10: 2 Dec - 6 Dec ===
'''NCS: 5 Dec (Thu), 3-5p'''
* Marcella Gomez
* TuLiP planning (Richard)
'''Biocircuits: 6 Dec (Fri), 10a-noon'''
* [[www.cds.caltech.edu/~eyeung Enoch Yeung]]
* Open
| width=30% |

=== Week 12: 9 Dec - 13 Dec ===
* Richard out of town, Mon-Fri
* Biocircuits lab cleanup, Tue @ 10 am
| width=30% |

=== Week 13: 16 Dec - 20 Dec ===
'''Biocircuits: 17 Dec (Tue), 10a-noon'''
* TBD
'''NCS: 17 Dec (Wed), 10a-noon'''
* TBD

|}

Group Schedule, Fall 2013

2013-09-16T21:13:40Z

Ehyeung: /* Week 5: 28 Oct - 1 Nov */

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 2013]]
|}

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=30% |
=== Week 1: 30 Sep - 4 Oct ===
'''Biocircuits: 1 Oct (Tue), 10a-noon'''
* Zoltan Tuza
* Project/lab planning (Richard)
'''NCS: 2 Oct (Wed), 10a-noon'''
* Note: this meeting may shift to 11a-1p
* Ivan Papusha
* Stephanie Tsuei
'''Group meeting: 3 Oct (Thu), 12:15-1:30p'''
* Yutaka Hori
| width=30% |

=== Week 2: 7 Oct - 11 Oct ===
'''NCS: 9 Oct (Wed), 10a-noon'''
* Vasu Raman
* Scott Livingston
'''Biocircuits: 10 Oct (Thu), 10a-noon'''
* Victoria Hsiao
* Vipul Singhal
'''Group meeting: 10 Oct (Thu), 12:15-1:30p'''
* Subramanian Bose
| width=30% |
=== Week 3: 14 Oct - 18 Oct ===
'''Biocircuits: 17 Oct (Thu), 10a-noon'''
* Anu Thubagere
* Anandh Swaminathan
'''Group meeting: 17 Oct (Thu), 12:15-1:30p'''
* Dan Siegal-Gaskins
'''NCS: 17 Oct (Thu), 3-5p'''
* Yilin Mo
* Eric Wolff
|- valign=top
| width=30% |
=== Week 4: 21 Oct - 25 Oct ===
* Richard out of town, Mon-Fri
* Biocircuits lab cleanup, Tue @ 10 am
| width=30% |

=== Week 5: 28 Oct - 1 Nov ===
'''Biocircuits: 29 Oct (Tue), 10a-noon'''
* Note: this meeting may shift to 31 Oct (Thu), 11a-1p
* TBD
* Zach Sun
'''NCS: 30 Oct (Wed), 10a-noon'''
* TuLiP planning (Richard)
'''Group meeting: 31 Oct (Thu), 12:15-1:30p'''
* TBD (may be cancelled)
| width=30% |

=== Week 6: 4 Nov - 8 Nov ===
'''Biocircuits: 4 Nov (Mon), 10a-noon'''
* Jongmin Kim
* Vanessa Jonsson
'''NCS: 7 Nov (Thu), 10a-noon'''
* Note: this meeting may shift to 9a-11a
* Matanya Horowitz
* Anandh Swaminathan?
'''Group meeting: 7 Nov (Thu), 12:15-1:30p'''
* Joe Levine
|- valign=top
| width=30% |

=== Week 7: 11 Nov - 15 Nov ===
* Richard out of town, Mon-Fri
| width=30% |

=== Week 8: 18 Nov - 22 Nov ===
'''NCS: 20 Nov (Wed), 10a-noon'''
* Rangoli Sharan
* Ioannis Filippidis
'''Biocircuits: 21 Nov (Thu), 10a-noon'''
* Shaobin Guo
* Emzo de los Santos
'''Group meeting: 21 Nov (Thu), 12:15-1:30p'''
* Chris Kempes
| width=30% |
=== Week 9: 25 Nov - 29 Nov ===
'''NCS: 25 Nov (Mon), 10a-noon'''
* Nikolai Matni
* Jean-Maurice Leonetti
'''Biocircuits: 26 Nov (Tue), 10a-noon'''
* Yong Wu
* Joe Meyerowitz
'''Group meeting: 26 Nov (Tue), 12:15-1:30p'''
* TBD
|- valign=top
| width=30% |

=== Week 10: 2 Dec - 6 Dec ===
'''NCS: 5 Dec (Thu), 3-5p'''
* Marcella Gomez
* TuLiP planning (Richard)
'''Biocircuits: 6 Dec (Fri), 10a-noon'''
* Enoch
* Open
| width=30% |

=== Week 12: 9 Dec - 13 Dec ===
* Richard out of town, Mon-Fri
* Biocircuits lab cleanup, Tue @ 10 am
| width=30% |

=== Week 13: 16 Dec - 20 Dec ===
'''Biocircuits: 17 Dec (Tue), 10a-noon'''
* TBD
'''NCS: 17 Dec (Wed), 10a-noon'''
* TBD

|}

Group Schedule, Fall 2013

2013-09-16T21:13:29Z

Ehyeung: /* Week 10: 2 Dec - 6 Dec */

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 2013]]
|}

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=30% |
=== Week 1: 30 Sep - 4 Oct ===
'''Biocircuits: 1 Oct (Tue), 10a-noon'''
* Zoltan Tuza
* Project/lab planning (Richard)
'''NCS: 2 Oct (Wed), 10a-noon'''
* Note: this meeting may shift to 11a-1p
* Ivan Papusha
* Stephanie Tsuei
'''Group meeting: 3 Oct (Thu), 12:15-1:30p'''
* Yutaka Hori
| width=30% |

=== Week 2: 7 Oct - 11 Oct ===
'''NCS: 9 Oct (Wed), 10a-noon'''
* Vasu Raman
* Scott Livingston
'''Biocircuits: 10 Oct (Thu), 10a-noon'''
* Victoria Hsiao
* Vipul Singhal
'''Group meeting: 10 Oct (Thu), 12:15-1:30p'''
* Subramanian Bose
| width=30% |
=== Week 3: 14 Oct - 18 Oct ===
'''Biocircuits: 17 Oct (Thu), 10a-noon'''
* Anu Thubagere
* Anandh Swaminathan
'''Group meeting: 17 Oct (Thu), 12:15-1:30p'''
* Dan Siegal-Gaskins
'''NCS: 17 Oct (Thu), 3-5p'''
* Yilin Mo
* Eric Wolff
|- valign=top
| width=30% |
=== Week 4: 21 Oct - 25 Oct ===
* Richard out of town, Mon-Fri
* Biocircuits lab cleanup, Tue @ 10 am
| width=30% |

=== Week 5: 28 Oct - 1 Nov ===
'''Biocircuits: 29 Oct (Tue), 10a-noon'''
* Note: this meeting may shift to 31 Oct (Thu), 11a-1p
* Enoch Yeung
* Zach Sun
'''NCS: 30 Oct (Wed), 10a-noon'''
* TuLiP planning (Richard)
'''Group meeting: 31 Oct (Thu), 12:15-1:30p'''
* TBD (may be cancelled)
| width=30% |

=== Week 6: 4 Nov - 8 Nov ===
'''Biocircuits: 4 Nov (Mon), 10a-noon'''
* Jongmin Kim
* Vanessa Jonsson
'''NCS: 7 Nov (Thu), 10a-noon'''
* Note: this meeting may shift to 9a-11a
* Matanya Horowitz
* Anandh Swaminathan?
'''Group meeting: 7 Nov (Thu), 12:15-1:30p'''
* Joe Levine
|- valign=top
| width=30% |

=== Week 7: 11 Nov - 15 Nov ===
* Richard out of town, Mon-Fri
| width=30% |

=== Week 8: 18 Nov - 22 Nov ===
'''NCS: 20 Nov (Wed), 10a-noon'''
* Rangoli Sharan
* Ioannis Filippidis
'''Biocircuits: 21 Nov (Thu), 10a-noon'''
* Shaobin Guo
* Emzo de los Santos
'''Group meeting: 21 Nov (Thu), 12:15-1:30p'''
* Chris Kempes
| width=30% |
=== Week 9: 25 Nov - 29 Nov ===
'''NCS: 25 Nov (Mon), 10a-noon'''
* Nikolai Matni
* Jean-Maurice Leonetti
'''Biocircuits: 26 Nov (Tue), 10a-noon'''
* Yong Wu
* Joe Meyerowitz
'''Group meeting: 26 Nov (Tue), 12:15-1:30p'''
* TBD
|- valign=top
| width=30% |

=== Week 10: 2 Dec - 6 Dec ===
'''NCS: 5 Dec (Thu), 3-5p'''
* Marcella Gomez
* TuLiP planning (Richard)
'''Biocircuits: 6 Dec (Fri), 10a-noon'''
* Enoch
* Open
| width=30% |

=== Week 12: 9 Dec - 13 Dec ===
* Richard out of town, Mon-Fri
* Biocircuits lab cleanup, Tue @ 10 am
| width=30% |

=== Week 13: 16 Dec - 20 Dec ===
'''Biocircuits: 17 Dec (Tue), 10a-noon'''
* TBD
'''NCS: 17 Dec (Wed), 10a-noon'''
* TBD

|}

September 2013 Meetings

2013-08-27T07:18:37Z

Ehyeung: /* Thu, 12 Sep */

The list below has times that I am available to meet between 3 and 13 September. Please pick a time that works and fill in your name. If none of the times work, send me e-mail (or find someone else who has a slot that does work and figure out how much of a bribe is required to get them to switch). __NOTOC__

{| border=1 width=100%
|- valign=top
| width=20% |
2 Sep - Labor Day
| width=20% |
==== Tue, 3 Sep ====
{{agenda begin}}
{{agenda item|2:00p|Emzo}}
{{agenda item|3:00p|Joe Levine}}
{{agenda item| | }}
{{agenda item|4:30|Enoch}}
{{agenda item|5:30|Zach}}
{{agenda end}}
| width=20% |

==== Wed, 4 Sep ====
{{agenda begin}}
{{agenda item| | }}
{{agenda item| | }}
{{agenda item| | }}
{{agenda item|4:30|Joe}}
{{agenda item|5:30|Jongmin}}
{{agenda end}}
| width=20% |

==== Thu, 5 Sep ====
{{agenda begin}}
{{agenda item|2:00p|Open}}
{{agenda item|3:00p|Open}}
{{agenda item| | }}
{{agenda item|4:30|Open}}
{{agenda item|5:30|Ioannis}}
{{agenda end}}
| width=20% |
6 Sep - Richard out of town
|- valign=top
| colspan=2 width=40% |

==== Mon, 9 Sep / Tue, 10 Sep ====
{| cellspacing=0 cellpadding=0
|- valign=top
| width=50% |
{{agenda begin}}
{{agenda item|2:00p|dsg}}
{{agenda item|3:00p|Scott Livingston}}
{{agenda item| | }}
{{agenda item|4:30|Ivan Papusha}}
{{agenda item|5:30|Zoltan}}
{{agenda end}}
| width=50% |
Note: I may need to travel on either Mon or Tue {{implies}} please only sign up for a slot if you can make that time on both days.
|}
| width=20% |

==== Wed, 11 Sep ====
{{agenda begin}}
{{agenda item|1:00p|Clare}}
{{agenda item|2:00p|Yong}}
{{agenda item| | }}
{{agenda item|4:00|Anandh}}
{{agenda item|5:00|Anu}}
{{agenda end}}
| width=20% |

==== Thu, 12 Sep ====
{{agenda begin}}
{{agenda item|2:00p|Stephanie}}
{{agenda item|3:00p|Victoria}}
{{agenda item| | }}
{{agenda item|4:30|Shaobin}}
{{agenda item|5:30|Enoch}}
{{agenda end}}
| width=20% |

==== Fri, 13 Sep ====
{{agenda begin}}
{{agenda item|1:00p|Vanessa}}
{{agenda item|2:00p|Open}}
{{agenda end}}
|}

March 2013 meeting schedule

2013-03-04T15:48:37Z

Ehyeung: /* 12 Mar (Tue) */

The list below has times that I am available to meet between 4 March and 13 March. Please pick a time that works and fill in your name. If none of the times work, send me e-mail (or find someone else who has a slot that does work and figure out how much of a bribe is required to get them to switch). Please only sign up for one time slot. __NOTOC__

{| width=100% border=1
|- valign=top
| width=30% |
==== 6 Mar (Wed) ====
{{agenda begin}}
{{agenda item|8:45-9:45|Ophelia}}
{{agenda item||}}
{{agenda item|1:15-2:00|Stephanie}}
{{agenda item||}}
{{agenda item|5:00-5:45|Shuo}}
{{agenda item|5:45-6:00|UG advisee}}
{{agenda item|6:00-6:45|Jongmin}}
{{agenda item|6:45-7:30|Zoltan}}
{{agenda end}}
| width=30% |

==== 7 Mar (Thu) ====
{{agenda begin}}
{{agenda item|2:00-3:30|DARPA breadboards}}
{{agenda item|4:00-4:15|UG advisee}}
{{agenda item|4:15-5:00|Open}}
{{agenda item|5:00-5:45|Chris Kempes}}
{{agenda item|5:45-6:00|UG advisee}}
{{agenda item|6:00-6:45|Anandh}}
{{agenda item|6:45-7:30|Open}}
{{agenda end}}
| width=30% |

==== 8 Mar (Fri) ====
{{agenda begin}}
{{agenda item|8:45-9:30|}} (no longer available)
{{agenda item||}}
{{agenda item|11:00-11:45|ALL telecon (Enoch, Joe M)}}
{{agenda item||}}
{{agenda item|12:00-1:15|NCS group meeting}}
{{agenda item|1:15-2:00|Nadine (might get shortened)}}
{{agenda item||}}
{{agenda item|5:00-5:45|Eric}}
{{agenda item|5:45-6:30|Scott Livingston}}
{{agenda end}}

|- valign=top
|

==== 10 Mar (Sun) ====
{{agenda begin}}
{{agenda item|2:30-2:45|UG advisee}}
{{agenda item|2:45-3:00|UG advisee}}
{{agenda item|3:00-4:00|dan}}
{{agenda item|4:00-5:00|Open}}
{{agenda item|5:00-6:00|Open}}
{{agenda item|6:00-6:15|UG advisee}}
{{agenda item|6:15-6:30|UG advisee}}
{{agenda end}}
|

==== 11 Mar (Mon) ====
{{agenda begin}}
{{agenda item|3:30-4:15|Mumu}}
{{agenda item|4:15-5:00|Shaobin}}
{{agenda item|5:00-5:15|UG advisee}}
{{agenda item|5:15-6:00|Marcella}}
{{agenda item|6:00-6:45|Victoria}}
{{agenda item|6:45-7:30|Open}}
{{agenda end}}
|

==== 12 Mar (Tue) ====
{{agenda begin}}
{{agenda item|11:00-11:45|Emzo}}
{{agenda item||}}
{{agenda item|1:00-3:00|Biocircuits meeting}}
{{agenda item||}}
{{agenda item|3:30-4:15|Nathan Belliveau}}
{{agenda item|4:15-5:00|Vipul}}
{{agenda item|5:00-5:15|UG advisee}}
{{agenda item|5:15-6:00|Enoch}}
{{agenda item|6:00-6:45|Open}}
{{agenda item|6:45-7:30|Open}}
{{agenda end}}
|}

March 2013 meeting schedule

2013-03-04T15:46:38Z

Ehyeung: /* 8 Mar (Fri) */

The list below has times that I am available to meet between 4 March and 13 March. Please pick a time that works and fill in your name. If none of the times work, send me e-mail (or find someone else who has a slot that does work and figure out how much of a bribe is required to get them to switch). Please only sign up for one time slot. __NOTOC__

{| width=100% border=1
|- valign=top
| width=30% |
==== 6 Mar (Wed) ====
{{agenda begin}}
{{agenda item|8:45-9:45|Ophelia}}
{{agenda item||}}
{{agenda item|1:15-2:00|Stephanie}}
{{agenda item||}}
{{agenda item|5:00-5:45|Shuo}}
{{agenda item|5:45-6:00|UG advisee}}
{{agenda item|6:00-6:45|Jongmin}}
{{agenda item|6:45-7:30|Zoltan}}
{{agenda end}}
| width=30% |

==== 7 Mar (Thu) ====
{{agenda begin}}
{{agenda item|2:00-3:30|DARPA breadboards}}
{{agenda item|4:00-4:15|UG advisee}}
{{agenda item|4:15-5:00|Open}}
{{agenda item|5:00-5:45|Chris Kempes}}
{{agenda item|5:45-6:00|UG advisee}}
{{agenda item|6:00-6:45|Anandh}}
{{agenda item|6:45-7:30|Open}}
{{agenda end}}
| width=30% |

==== 8 Mar (Fri) ====
{{agenda begin}}
{{agenda item|8:45-9:30|}} (no longer available)
{{agenda item||}}
{{agenda item|11:00-11:45|ALL telecon (Enoch, Joe M)}}
{{agenda item||}}
{{agenda item|12:00-1:15|NCS group meeting}}
{{agenda item|1:15-2:00|Nadine (might get shortened)}}
{{agenda item||}}
{{agenda item|5:00-5:45|Eric}}
{{agenda item|5:45-6:30|Scott Livingston}}
{{agenda end}}

|- valign=top
|

==== 10 Mar (Sun) ====
{{agenda begin}}
{{agenda item|2:30-2:45|UG advisee}}
{{agenda item|2:45-3:00|UG advisee}}
{{agenda item|3:00-4:00|dan}}
{{agenda item|4:00-5:00|Open}}
{{agenda item|5:00-6:00|Open}}
{{agenda item|6:00-6:15|UG advisee}}
{{agenda item|6:15-6:30|UG advisee}}
{{agenda end}}
|

==== 11 Mar (Mon) ====
{{agenda begin}}
{{agenda item|3:30-4:15|Mumu}}
{{agenda item|4:15-5:00|Shaobin}}
{{agenda item|5:00-5:15|UG advisee}}
{{agenda item|5:15-6:00|Marcella}}
{{agenda item|6:00-6:45|Victoria}}
{{agenda item|6:45-7:30|Open}}
{{agenda end}}
|

==== 12 Mar (Tue) ====
{{agenda begin}}
{{agenda item|11:00-11:45|Emzo}}
{{agenda item||}}
{{agenda item|1:00-3:00|Biocircuits meeting}}
{{agenda item||}}
{{agenda item|3:30-4:15|Nathan Belliveau}}
{{agenda item|4:15-5:00|Vipul}}
{{agenda item|5:00-5:15|UG advisee}}
{{agenda item|5:15-6:00|Open}}
{{agenda item|6:00-6:45|Open}}
{{agenda item|6:45-7:30|Open}}
{{agenda end}}
|}

March 2013 meeting schedule

2013-03-03T09:10:18Z

Ehyeung: /* 8 Mar (Fri) */

The list below has times that I am available to meet between 4 March and 13 March. Please pick a time that works and fill in your name. If none of the times work, send me e-mail (or find someone else who has a slot that does work and figure out how much of a bribe is required to get them to switch). Please only sign up for one time slot. __NOTOC__

{| width=100% border=1
|- valign=top
| width=30% |
==== 6 Mar (Wed) ====
{{agenda begin}}
{{agenda item|8:45-9:45|Ophelia}}
{{agenda item||}}
{{agenda item|1:15-2:00|Stephanie}}
{{agenda item||}}
{{agenda item|5:00-5:45|Shuo}}
{{agenda item|5:45-6:00|UG advisee}}
{{agenda item|6:00-6:45|Jongmin}}
{{agenda item|6:45-7:30|Zoltan}}
{{agenda end}}
| width=30% |

==== 7 Mar (Thu) ====
{{agenda begin}}
{{agenda item|2:00-3:30|DARPA breadboards}}
{{agenda item|4:00-4:15|UG advisee}}
{{agenda item|4:15-5:00|Open}}
{{agenda item|5:00-5:45|Open}}
{{agenda item|5:45-6:00|UG advisee}}
{{agenda item|6:00-6:45|Anandh}}
{{agenda item|6:45-7:30|Open}}
{{agenda end}}
| width=30% |

==== 8 Mar (Fri) ====
{{agenda begin}}
{{agenda item|8:45-9:30|Enoch}}
{{agenda item||}}
{{agenda item|11:00-11:45|ALL telecon (Enoch, Joe M)}}
{{agenda item||}}
{{agenda item|12:00-1:15|NCS group meeting}}
{{agenda item|1:15-2:00|Open (might get shortened)}}
{{agenda item||}}
{{agenda item|5:00-5:45|Eric}}
{{agenda item|5:45-6:30|Scott Livingston}}
{{agenda end}}

|- valign=top
|

==== 10 Mar (Sun) ====
{{agenda begin}}
{{agenda item|2:30-2:45|UG advisee}}
{{agenda item|2:45-3:00|UG advisee}}
{{agenda item|3:00-4:00|Open}}
{{agenda item|4:00-5:00|Open}}
{{agenda item|5:00-6:00|Open}}
{{agenda item|6:00-6:15|UG advisee}}
{{agenda item|6:15-6:30|UG advisee}}
{{agenda end}}
|
==== 11 Mar (Mon) ====
{{agenda begin}}
{{agenda item|3:30-4:15|Mumu}}
{{agenda item|4:15-5:00|Shaobin}}
{{agenda item|5:00-5:15|UG advisee}}
{{agenda item|5:15-6:00|Marcella}}
{{agenda item|6:00-6:45|Victoria}}
{{agenda item|6:45-7:30|Open}}
{{agenda end}}
|

==== 12 Mar (Tue) ====
{{agenda begin}}
{{agenda item|11:00-11:45|Emzo}}
{{agenda item||}}
{{agenda item|1:00-3:00|Biocircuits meeting}}
{{agenda item||}}
{{agenda item|3:30-4:15|Nathan Belliveau}}
{{agenda item|4:15-5:00|Vipul}}
{{agenda item|5:00-5:15|UG advisee}}
{{agenda item|5:15-6:00|Open}}
{{agenda item|6:00-6:45|Open}}
{{agenda item|6:45-7:30|Open}}
{{agenda end}}
|}

SURF discussions, Jan 2013

2013-01-24T19:55:48Z

Ehyeung: /* 28 Jan (Mon) */

Slots for talking with applicants and co-mentors about SURF projects. Please sign up for one of the slots below. All times are PST.

{| width=100% border=1
|- valign=top
|
==== 28 Jan (Mon) ====
* 9:00: Anu/ Monica
* 9:20: Andrew + Enoch
* 9:40: James + Eric
|

==== 30 Jan (Wed) ====
* 14:00: Open
* 14:20: Open
* 14:40: Open
|
==== 31 Jan (Thu) ====
* 10:30: Open
* 10:50: Open
* 11:10: Open
|}

The agenda for the phone call is (roughly):

# Description of the basic idea behind the project (based on applicant's understanding)
# Discussion about approaches, things to read, variations to consider, etc
# Discussion of the format of the proposal
# Questions and discussion about the process

SURF 2013

2013-01-04T02:39:32Z

Ehyeung: /* List of available projects */

{{righttoc}}
This page is intended for students interested in working on SURF projects in the Summer of 2013. It contains a list of project areas where I will be supervising projects this year along with information about how to apply for a SURF project in my group.

=== Applying for a SURF project ===

Because I get many students interested in doing SURFs in my group and because we have several projects available, we use the first few weeks in January to sort out who we will work with in writing proposals. We only submit one proposal per project area and so we often can't accommodate everyone who wants to work in my group over the summer.

# A list of SURF project descriptions is given in the table below. Due to the number of SURF projects that we support, we are only able to support students who select from among these projects. Please make sure to read the project descriptions, required skills (if any) and skim a few of the listed references before contacting me about doing a SURF project.
# Students interested in writing proposals for SURF projects should contact me via e-mail by 11 Jan (Fri) and provide the following information:
#* A list of up to three SURF projects from the list below that you are interested in working on
#* A one page resume listing relevant experience and coursework
#* If you are not a Caltech student or part of one of our CDS exchange programs (Lund, KTH), I will also need the following additional information:
#** An unofficial copy of your academic transcript
#** Names of two faculty members at your current institution that I can contact for a reference
# Starting on 12 January, I will go through all applications and work with my group to identify who is a possible fit for each project. We will then contact you and ask for you to meet (or talk with) possible co-mentors so that we can eventually work out who we will work with in writing up a proposal.
# We hope to make final decisions on projects by about 20 Jan, at which point we will start working with students on writing up proposals.
# All applications should go through the normal SURF application process, described at www.surf.caltech.edu. SURF applications are due on 22 Feb 2013.
# If you are selected for a SURF, please be aware of the following information
#* All SURF projects in my group will start on 18 Jun (Tue). If you can't start on that date, please make sure that you indicate this when you contact me
#* All SURF projects are for a minimum of 10 weeks, although I usually recommend that you try to stay for 12 weeks if possible (at no additional pay). It's hard to complete a project in just 10 weeks and spending a few extra weeks can greatly improve the project.
#* All SURF students in my group will be expected to devote full-time effort to their SURF project, so you cannot have a second job in addition to your SURF.

=== List of available projects ===

{| border=1 width=100%
|-
| '''Title''' || '''Grant/Project''' || '''Co-Mentors''' || '''Comments'''
|-
| {{SURF entry|2013|The costs and benefits of various designs of biochemical 'decision engines'}}
| [[Molecular Programming Project|MPP]]
| Dan Siegal-Gaskins
|
|-
| {{SURF entry|2013|Robot Motion Planning with Complex Tasks}}
| [[Correct-by-Construction Synthesis of Control Protocols for Aerospace Systems|Boeing]]
| Eric Wolff
|
|-
| {{SURF entry|2013|Experiments with dynamic obstacles and correct-by-construction controllers}}
| [[Correct-by-Construction Synthesis of Control Protocols for Aerospace Systems|Boeing]]
| [http://scottman.net Scott C. Livingston]
|
|-
| {{SURF entry|2013|Synthetic logic circuits using RNA aptamers}}
| [[Molecular Programming Project|MPP]]
| Jongmin Kim
|
|-
| {{SURF entry|2013|Role of Delays in Biological Processes}}
| [[Molecular Programming Project|MPP]]
| Marcella Gomez
|
|-
| {{SURF entry|2013|Designing phosphorylation sensitive protein domains for use in synthetic circuits}}
| [[Molecular Programming Project|MPP]]
| Emzo de los Santos
|
|-
| {{SURF entry|2013|Synthetic biological circuit design implementing protein degradation in-vitro}}
| [[Molecular Programming Project|MPP]]
| Zach Sun
|
|-
|{{SURF entry|2013|Understanding the Effect of Compositional Context on Biocircuit Performance}}
| [[Molecular Programming Project|MPP]]
| [http://www.cds.caltech.edu/~eyeung Enoch Yeung]
|
|}

SURF 2013

2013-01-04T02:19:42Z

Ehyeung: /* List of available projects */

{{righttoc}}
This page is intended for students interested in working on SURF projects in the Summer of 2013. It contains a list of project areas where I will be supervising projects this year along with information about how to apply for a SURF project in my group.

=== Applying for a SURF project ===

Because I get many students interested in doing SURFs in my group and because we have several projects available, we use the first few weeks in January to sort out who we will work with in writing proposals. We only submit one proposal per project area and so we often can't accommodate everyone who wants to work in my group over the summer.

# A list of SURF project descriptions is given in the table below. Due to the number of SURF projects that we support, we are only able to support students who select from among these projects. Please make sure to read the project descriptions, required skills (if any) and skim a few of the listed references before contacting me about doing a SURF project.
# Students interested in writing proposals for SURF projects should contact me via e-mail by 11 Jan (Fri) and provide the following information:
#* A list of up to three SURF projects from the list below that you are interested in working on
#* A one page resume listing relevant experience and coursework
#* If you are not a Caltech student or part of one of our CDS exchange programs (Lund, KTH), I will also need the following additional information:
#** An unofficial copy of your academic transcript
#** Names of two faculty members at your current institution that I can contact for a reference
# Starting on 12 January, I will go through all applications and work with my group to identify who is a possible fit for each project. We will then contact you and ask for you to meet (or talk with) possible co-mentors so that we can eventually work out who we will work with in writing up a proposal.
# We hope to make final decisions on projects by about 20 Jan, at which point we will start working with students on writing up proposals.
# All applications should go through the normal SURF application process, described at www.surf.caltech.edu. SURF applications are due on 22 Feb 2013.
# If you are selected for a SURF, please be aware of the following information
#* All SURF projects in my group will start on 18 Jun (Tue). If you can't start on that date, please make sure that you indicate this when you contact me
#* All SURF projects are for a minimum of 10 weeks, although I usually recommend that you try to stay for 12 weeks if possible (at no additional pay). It's hard to complete a project in just 10 weeks and spending a few extra weeks can greatly improve the project.
#* All SURF students in my group will be expected to devote full-time effort to their SURF project, so you cannot have a second job in addition to your SURF.

=== List of available projects ===

{| border=1 width=100%
|-
| '''Title''' || '''Grant/Project''' || '''Co-Mentors''' || '''Comments'''
|-
| {{SURF entry|2013|The costs and benefits of various designs of biochemical 'decision engines'}}
| [[Molecular Programming Project|MPP]]
| Dan Siegal-Gaskins
|
|-
| {{SURF entry|2013|Robot Motion Planning with Complex Tasks}}
| [[Correct-by-Construction Synthesis of Control Protocols for Aerospace Systems|Boeing]]
| Eric Wolff
|
|-
| {{SURF entry|2013|Experiments with dynamic obstacles and correct-by-construction controllers}}
| [[Correct-by-Construction Synthesis of Control Protocols for Aerospace Systems|Boeing]]
| [http://scottman.net Scott C. Livingston]
|
|-
| {{SURF entry|2013|Synthetic logic circuits using RNA aptamers}}
| [[Molecular Programming Project|MPP]]
| Jongmin Kim
|
|-
| {{SURF entry|2013|Role of Delays in Biological Processes}}
| [[Molecular Programming Project|MPP]]
| Marcella Gomez
|
|-
| {{SURF entry|2013|Designing phosphorylation sensitive protein domains for use in synthetic circuits}}
| [[Molecular Programming Project|MPP]]
| Emzo de los Santos
|
|-
| {{SURF entry|2013|Synthetic biological circuit design implementing protein degradation in-vitro}}
| [[Molecular Programming Project|MPP]]
| Zach Sun
|
|-
|{{SURF entry|2013|Understanding the Effect of Compositional Context on Biocircuit_Performance}}
| [[Molecular Programming Project|MPP]]
| [http://www.cds.caltech.edu/~eyeung Enoch Yeung]
|
|}

SURF 2013: Understanding the Effect of Compositional Context on Biocircuit Performance

2013-01-04T02:18:59Z

Ehyeung:

'''[[SURF 2013|2013 SURF]] project description'''
* Mentor: Richard Murray
* Co-mentor: Enoch Yeung

Synthetic biocircuits often involve multiple components --- different genes that work together to achieve a desired function. For example, the repressilator employs three distinct genes that are designed to inhibit each other with a cyclic structure to produce oscillation. The toggle switch uses two genes, both repressing each other as they compete to be the dominant active gene. A signal cascade involves a sequence of genes where the arrival of a chemical signal triggers the first gene to activate a second (downstream) gene, which in turn activates a third gene, and so forth. Each of these example circuits as well as a host of others have been implemented in a variety of ways. The increasing number of biocircuits fuels hope for the assembly of complex synthetic systems constructed from multiple biocircuits. However, a major challenge to reliably implementing biocircuits within a more complex synthetic system is understanding the effects of biocircuit context. Biocircuit context can be classified roughly into three categories: compositional context, host context, and environmental context (Cardinale and Arkin, 2012).

The goal of this project is to understand the effect of compositional context on biocircuit performance. Compositional context refers to the effects arising from coupling multiple genes or undesigned interactions between genes located on the same molecule. We will explore how spatial composition, or layout, of different genes can impact performance of one or more biocircuits. To understand how these factors will affect circuit operation, we will take (or build) a simple genetic circuit consisting of 2 or more genes and implement it in multiple ways, varying the orientation and relative location of the genes to each other. The dynamic response of the circuit will be measured, including cell-to-cell variability (via flow cytometry or microscopy). The circuit that we test could be a genetic switch, repressilator, incoherent feedforward loop, etc. The project could involve both simulations of circuit dynamics and experimental quantification of circuit dynamics, with comparisons between the two. This would likely involve intensive cloning, measuring using flow cytometer and/or microscope, modeling using stochastic simulation and (possibly) differential equations.

Possible SURF Activities:
* Construct multiple versions of that simple circuit to systematically explore the compositional context space.
* Characterize the mean expression dynamics (using a plate reader) and expression distribution (using flow cytometry or fluorescence microscopy) of each version of the circuit.
* Quantify differences in mean and distributional expression (if any) between the versions of the circuit.
* Build a simulation for each version of the circuit dynamics using a stochastic simulation or differential equations.
* Develop design strategies to attenuate or insulate against the effects of compositional context (in simulation or experimentally)

===References===
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3440575/ Stefano Cardinale and Adam Arkin (2012) Contextualizing context for synthetic biology -- identifying causes of failure of synthetic biological systems, Journal of Biotechnology 7(7):856-866.]

*[http://ec.asm.org/content/10/1/43.short James Arnone and Michael McAlear (2011), Adjacent Gene Pairing Plays a Role in the Coordinated Expression of Ribosome Biogenesis Genes MPP10 and YJR003C in Saccharomyces cerevisiae, Eukaryotic Cell 10(1):43-53.]

*[http://www.sciencemag.org/content/307/5717/1965 Juan Pedraza, Alexander van Oudenaarden (2005), Noise Propagation in Gene Networks, Science 307 (5717):1965-1969.]

*[http://www.nature.com/nbt/journal/v22/n7/abs/nbt988.html Jan Korbel, Lars Jensen, Christian von Mering, Peer Bork (2004) Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs, Nature Biotechnology 22:911-917.]

SURF 2013: Understanding the Effect of Compositional Context on Biocircuit Performance

2013-01-04T02:18:26Z

Ehyeung: Created page with "'''2013 SURF project description''' * Mentor: Richard Murray * Co-mentor: Enoch Yeung Synthetic biocircuits often involve multiple components --- different gene..."

'''[[SURF 2013|2013 SURF]] project description'''
* Mentor: Richard Murray
* Co-mentor: Enoch Yeung

Synthetic biocircuits often involve multiple components --- different genes that work together to achieve a desired function. For example, the repressilator employs three distinct genes that are designed to inhibit each other with a cyclic structure to produce oscillation. The toggle switch uses two genes, both repressing each other as they compete to be the dominant active gene. A signal cascade involves a sequence of genes where the arrival of a chemical signal triggers the first gene to activate a second (downstream) gene, which in turn activates a third gene, and so forth. Each of these example circuits as well as a host of others have been implemented in a variety of ways. The increasing number of biocircuits fuels hope for the assembly of complex synthetic systems constructed from multiple biocircuits. However, a major challenge to reliably implementing biocircuits within a more complex synthetic system is understanding the effects of biocircuit context. Biocircuit context can be classified roughly into three categories: compositional context, host context, and environmental context (Cardinale and Arkin, 2012).

The goal of this project is to understand the effect of compositional context on biocircuit performance. Compositional context refers to the effects arising from coupling multiple genes or undesigned interactions between genes located on the same molecule. We will explore how spatial composition, or layout, of different genes can impact performance of one or more biocircuits. To understand how these factors will affect circuit operation, we will take (or build) a simple genetic circuit consisting of 2 or more genes and implement it in multiple ways, varying the orientation and relative location of the genes to each other. The dynamic response of the circuit will be measured, including cell-to-cell variability (via flow cytometry or microscopy). The circuit that we test could be a genetic switch, repressilator, incoherent feedforward loop, etc. The project could involve both simulations of circuit dynamics and experimental quantification of circuit dynamics, with comparisons between the two. This would likely involve intensive cloning, measuring using flow cytometer and/or microscope, modeling using stochastic simulation and (possibly) differential equations.

Possible SURF Activities:
* Construct multiple versions of that simple circuit to systematically explore the compositional context space.
* Characterize the mean expression dynamics (using a plate reader) and expression distribution (using flow cytometry or fluorescence microscopy) of each version of the circuit.
* Quantify differences in mean and distributional expression (if any) between the versions of the circuit.
* Build a simulation for each version of the circuit dynamics using a stochastic simulation or differential equations.
* Develop design strategies to attenuate or insulate against the effects of compositional context (in simulation or experimentally)

===References===
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3440575/ Stefano Cardinale and Adam Arkin (2012) Contextualizing context for synthetic biology -- identifying causes of failure of synthetic biological systems, Journal of Biotechnology 7(7):856-866.]

*[http://ec.asm.org/content/10/1/43.short James Arnone and Michael McAlear (2011), Adjacent Gene Pairing Plays a Role in the Coordinated Expression of Ribosome Biogenesis Genes MPP10 and YJR003C in Saccharomyces cerevisiae, Eukaryotic Cell 10(1):43-53.]

*[http://www.jbioleng.org/content/3/1/4 Jason Kelly et al (2009) Measuring the activity of Biobrick promoters using an in vivo reference standard, Journal of Biological Engineering 3:4.]

*[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.0020074 Yuan-Yuan Li, Hui Yu, Zong-Ming Guo, Ting-Qing Guo, Kang Tu, Yi-Xue Li (2006) Systematic Analysis of Head-to-Head Gene Organization: Evolutionary Conservation and Potential Biological Relevance, PLoS Computational Biology 2(7):e74.]

*[http://www.sciencemag.org/content/307/5717/1965 Juan Pedraza, Alexander van Oudenaarden (2005), Noise Propagation in Gene Networks, Science 307 (5717):1965-1969.]

*[http://www.nature.com/nbt/journal/v22/n7/abs/nbt988.html Jan Korbel, Lars Jensen, Christian von Mering, Peer Bork (2004) Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs, Nature Biotechnology 22:911-917.]

*[http://www.sciencemag.org/content/297/5584/1183.full Michael Elowitz, Alan Levine, Eric Siggia, Peter.Swain (2002) Stochastic Gene Expression in a Single Cell, Science 297: 1183-1186.]

SURF 2013

2013-01-04T02:18:02Z

Ehyeung: /* List of available projects */

{{righttoc}}
This page is intended for students interested in working on SURF projects in the Summer of 2013. It contains a list of project areas where I will be supervising projects this year along with information about how to apply for a SURF project in my group.

=== Applying for a SURF project ===

Because I get many students interested in doing SURFs in my group and because we have several projects available, we use the first few weeks in January to sort out who we will work with in writing proposals. We only submit one proposal per project area and so we often can't accommodate everyone who wants to work in my group over the summer.

# A list of SURF project descriptions is given in the table below. Due to the number of SURF projects that we support, we are only able to support students who select from among these projects. Please make sure to read the project descriptions, required skills (if any) and skim a few of the listed references before contacting me about doing a SURF project.
# Students interested in writing proposals for SURF projects should contact me via e-mail by 11 Jan (Fri) and provide the following information:
#* A list of up to three SURF projects from the list below that you are interested in working on
#* A one page resume listing relevant experience and coursework
#* If you are not a Caltech student or part of one of our CDS exchange programs (Lund, KTH), I will also need the following additional information:
#** An unofficial copy of your academic transcript
#** Names of two faculty members at your current institution that I can contact for a reference
# Starting on 12 January, I will go through all applications and work with my group to identify who is a possible fit for each project. We will then contact you and ask for you to meet (or talk with) possible co-mentors so that we can eventually work out who we will work with in writing up a proposal.
# We hope to make final decisions on projects by about 20 Jan, at which point we will start working with students on writing up proposals.
# All applications should go through the normal SURF application process, described at www.surf.caltech.edu. SURF applications are due on 22 Feb 2013.
# If you are selected for a SURF, please be aware of the following information
#* All SURF projects in my group will start on 18 Jun (Tue). If you can't start on that date, please make sure that you indicate this when you contact me
#* All SURF projects are for a minimum of 10 weeks, although I usually recommend that you try to stay for 12 weeks if possible (at no additional pay). It's hard to complete a project in just 10 weeks and spending a few extra weeks can greatly improve the project.
#* All SURF students in my group will be expected to devote full-time effort to their SURF project, so you cannot have a second job in addition to your SURF.

=== List of available projects ===

{| border=1 width=100%
|-
| '''Title''' || '''Grant/Project''' || '''Co-Mentors''' || '''Comments'''
|-
| {{SURF entry|2013|The costs and benefits of various designs of biochemical 'decision engines'}}
| [[Molecular Programming Project|MPP]]
| Dan Siegal-Gaskins
|
|-
| {{SURF entry|2013|Robot Motion Planning with Complex Tasks}}
| [[Correct-by-Construction Synthesis of Control Protocols for Aerospace Systems|Boeing]]
| Eric Wolff
|
|-
| {{SURF entry|2013|Experiments with dynamic obstacles and correct-by-construction controllers}}
| [[Correct-by-Construction Synthesis of Control Protocols for Aerospace Systems|Boeing]]
| [http://scottman.net Scott C. Livingston]
|
|-
| {{SURF entry|2013|Synthetic logic circuits using RNA aptamers}}
| [[Molecular Programming Project|MPP]]
| Jongmin Kim
|
|-
| {{SURF entry|2013|Role of Delays in Biological Processes}}
| [[Molecular Programming Project|MPP]]
| Marcella Gomez
|
|-
| {{SURF entry|2013|Designing phosphorylation sensitive protein domains for use in synthetic circuits}}
| [[Molecular Programming Project|MPP]]
| Emzo de los Santos
|
|-
| {{SURF entry|2013|Synthetic biological circuit design implementing protein degradation in-vitro}}
| [[Molecular Programming Project|MPP]]
| Zach Sun
|
|-
|{{SURF entry|2013|Understanding the Effect of Compositional Context on Biocircuit_Performance}}
| [[Molecular Programming Project|MPP]]
| [http://www.cds.caltech.edu/~eyeung Enoch Yeung]
|}

Understanding the Effect of Compositional Context on Biocircuit Performance

2013-01-04T02:15:16Z

Ehyeung:

'''[[SURF 2013|2013 SURF]] project description'''
* Mentor: Richard Murray
* Co-mentor: Enoch Yeung

Synthetic biocircuits often involve multiple components --- different genes that work together to achieve a desired function. For example, the repressilator employs three distinct genes that are designed to inhibit each other with a cyclic structure to produce oscillation. The toggle switch uses two genes, both repressing each other as they compete to be the dominant active gene. A signal cascade involves a sequence of genes where the arrival of a chemical signal triggers the first gene to activate a second (downstream) gene, which in turn activates a third gene, and so forth. Each of these example circuits as well as a host of others have been implemented in a variety of ways. The increasing number of biocircuits fuels hope for the assembly of complex synthetic systems constructed from multiple biocircuits. However, a major challenge to reliably implementing biocircuits within a more complex synthetic system is understanding the effects of biocircuit context. Biocircuit context can be classified roughly into three categories: compositional context, host context, and environmental context (Cardinale and Arkin, 2012).

The goal of this project is to understand the effect of compositional context on biocircuit performance. Compositional context refers to the effects arising from coupling multiple genes or undesigned interactions between genes located on the same molecule. We will explore how spatial composition, or layout, of different genes can impact performance of one or more biocircuits. To understand how these factors will affect circuit operation, we will take (or build) a simple genetic circuit consisting of 2 or more genes and implement it in multiple ways, varying the orientation and relative location of the genes to each other. The dynamic response of the circuit will be measured, including cell-to-cell variability (via flow cytometry or microscopy). The circuit that we test could be a genetic switch, repressilator, incoherent feedforward loop, etc. The project could involve both simulations of circuit dynamics and experimental quantification of circuit dynamics, with comparisons between the two. This would likely involve intensive cloning, measuring using flow cytometer and/or microscope, modeling using stochastic simulation and (possibly) differential equations.

Possible SURF Activities:
* Construct multiple versions of that simple circuit to systematically explore the compositional context space.
* Characterize the mean expression dynamics (using a plate reader) and expression distribution (using flow cytometry or fluorescence microscopy) of each version of the circuit.
* Quantify differences in mean and distributional expression (if any) between the versions of the circuit.
* Build a simulation for each version of the circuit dynamics using a stochastic simulation or differential equations.
* Develop design strategies to attenuate or insulate against the effects of compositional context (in simulation or experimentally)

===References===
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3440575/ Stefano Cardinale and Adam Arkin (2012) Contextualizing context for synthetic biology -- identifying causes of failure of synthetic biological systems, Journal of Biotechnology 7(7):856-866.]

*[http://ec.asm.org/content/10/1/43.short James Arnone and Michael McAlear (2011), Adjacent Gene Pairing Plays a Role in the Coordinated Expression of Ribosome Biogenesis Genes MPP10 and YJR003C in Saccharomyces cerevisiae, Eukaryotic Cell 10(1):43-53.]

*[http://www.jbioleng.org/content/3/1/4 Jason Kelly et al (2009) Measuring the activity of Biobrick promoters using an in vivo reference standard, Journal of Biological Engineering 3:4.]

*[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.0020074 Yuan-Yuan Li, Hui Yu, Zong-Ming Guo, Ting-Qing Guo, Kang Tu, Yi-Xue Li (2006) Systematic Analysis of Head-to-Head Gene Organization: Evolutionary Conservation and Potential Biological Relevance, PLoS Computational Biology 2(7):e74.]

*[http://www.sciencemag.org/content/307/5717/1965 Juan Pedraza, Alexander van Oudenaarden (2005), Noise Propagation in Gene Networks, Science 307 (5717):1965-1969.]

*[http://www.nature.com/nbt/journal/v22/n7/abs/nbt988.html Jan Korbel, Lars Jensen, Christian von Mering, Peer Bork (2004) Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs, Nature Biotechnology 22:911-917.]

*[http://www.sciencemag.org/content/297/5584/1183.full Michael Elowitz, Alan Levine, Eric Siggia, Peter.Swain (2002) Stochastic Gene Expression in a Single Cell, Science 297: 1183-1186.]

Understanding the Effect of Compositional Context on Biocircuit Performance

2013-01-04T02:13:11Z

Ehyeung:

'''[[SURF 2013|2013 SURF]] project description'''
* Mentor: Richard Murray
* Co-mentor: Enoch Yeung

Synthetic biocircuits often involve multiple components --- different genes that work together to achieve a desired function. For example, the repressilator employs three distinct genes that are designed to inhibit each other with a cyclic structure to produce oscillation. The toggle switch uses two genes, both repressing each other as they compete to be the dominant active gene. A signal cascade involves a sequence of genes where the arrival of a chemical signal triggers the first gene to activate a second (downstream) gene, which in turn activates a third gene, and so forth. Each of these example circuits as well as a host of others have been implemented in a variety of ways. The increasing number of biocircuits fuels hope for the assembly of complex synthetic systems constructed from multiple biocircuits. However, a major challenge to reliably implementing biocircuits in more complex synthetic systems is understanding the effects of biocircuit context. Biocircuit context can be classified roughly into three categories: compositional context, host context, and environmental context (Cardinale and Arkin, 2012).

The goal of this project is to understand the effect of compositional context on biocircuit performance. Compositional context refers to the effects arising from coupling multiple genes or undesigned interactions between genes located on the same molecule. We will explore how spatial composition, or layout, of different genes can impact performance of one or more biocircuits. To understand how these factors will affect circuit operation, we will take (or build) a simple genetic circuit consisting of 2 or more genes and implement it in multiple ways, varying the orientation and relative location of the genes to each other. The dynamic response of the circuit will be measured, including cell-to-cell variability (via flow cytometry or microscopy). The circuit that we test could be a genetic switch, repressilator, incoherent feedforward loop, etc. The project could involve both simulations of circuit dynamics and experimental quantification of circuit dynamics, with comparisons between the two. This would likely involve intensive cloning, measuring using flow cytometer and/or microscope, modeling using stochastic simulation and (possibly) differential equations.

Possible SURF Activities:
* Construct multiple versions of that simple circuit to systematically explore the compositional context space.
* Characterize the mean expression dynamics (using a plate reader) and expression distribution (using flow cytometry or fluorescence microscopy) of each version of the circuit.
* Quantify differences in mean and distributional expression (if any) between the versions of the circuit.
* Build a simulation for each version of the circuit dynamics using a stochastic simulation or differential equations.
* Develop design strategies to attenuate or insulate against the effects of compositional context (in simulation or experimentally)

===References===
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3440575/ Stefano Cardinale and Adam Arkin (2012) Contextualizing context for synthetic biology -- identifying causes of failure of synthetic biological systems, Journal of Biotechnology 7(7):856-866.]

*[http://ec.asm.org/content/10/1/43.short James Arnone and Michael McAlear (2011), Adjacent Gene Pairing Plays a Role in the Coordinated Expression of Ribosome Biogenesis Genes MPP10 and YJR003C in Saccharomyces cerevisiae, Eukaryotic Cell 10(1):43-53.]

*[http://www.jbioleng.org/content/3/1/4 Jason Kelly et al (2009) Measuring the activity of Biobrick promoters using an in vivo reference standard, Journal of Biological Engineering 3:4.]

*[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.0020074 Yuan-Yuan Li, Hui Yu, Zong-Ming Guo, Ting-Qing Guo, Kang Tu, Yi-Xue Li (2006) Systematic Analysis of Head-to-Head Gene Organization: Evolutionary Conservation and Potential Biological Relevance, PLoS Computational Biology 2(7):e74.]

*[http://www.sciencemag.org/content/307/5717/1965 Juan Pedraza, Alexander van Oudenaarden (2005), Noise Propagation in Gene Networks, Science 307 (5717):1965-1969.]

*[http://www.nature.com/nbt/journal/v22/n7/abs/nbt988.html Jan Korbel, Lars Jensen, Christian von Mering, Peer Bork (2004) Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs, Nature Biotechnology 22:911-917.]

*[http://www.sciencemag.org/content/297/5584/1183.full Michael Elowitz, Alan Levine, Eric Siggia, Peter.Swain (2002) Stochastic Gene Expression in a Single Cell, Science 297: 1183-1186.]

Understanding the Effect of Compositional Context on Biocircuit Performance

2013-01-04T02:11:31Z

Ehyeung:

'''[[SURF 2013|2013 SURF]] project description'''
* Mentor: Richard Murray
* Co-mentor: Enoch Yeung

Synthetic biocircuits often involve multiple components --- different genes that work together to achieve a desired function. For example, the repressilator employs three distinct genes that are designed to inhibit each other with a cyclic structure to produce oscillation. The toggle switch uses two genes, both repressing each other as they compete to be the dominant active gene. A signal cascade involves a sequence of genes where the arrival of a chemical signal triggers the first gene to activate a second (downstream) gene, which in turn activates a third gene, and so forth. Each of these example circuits as well as a host of others have been implemented in a variety of ways. The increasing number of biocircuits fuels hope for the assembly of complex synthetic systems constructed from multiple biocircuits. However, a major challenge in modular assembly of biocircuits as well as the reliable implementation of a single biocircuit are the poorly understood effects of biocircuit context. Biocircuit context can be classified roughly into three categories: compositional context, host context, and environmental context (Cardinale and Arkin, 2012).

The goal of this project is to understand the effect of compositional context on biocircuit performance. Compositional context refers to the effects arising from coupling multiple genes or undesigned interactions between genes located on the same molecule. We will explore how spatial composition, or layout, of different genes can impact performance of one or more biocircuits. To understand how these factors will affect circuit operation, we will take (or build) a simple genetic circuit consisting of 2 or more genes and implement it in multiple ways, varying the orientation and relative location of the genes to each other. The dynamic response of the circuit will be measured, including cell-to-cell variability (via flow cytometry or microscopy). The circuit that we test could be a genetic switch, repressilator, incoherent feedforward loop, etc. The project could involve both simulations of circuit dynamics and experimental quantification of circuit dynamics, with comparisons between the two. This would likely involve intensive cloning, measuring using flow cytometer and/or microscope, modeling using stochastic simulation and (possibly) differential equations.

Possible SURF Activities:
* Construct multiple versions of that simple circuit to systematically explore the compositional context space.
* Characterize the mean expression dynamics (using a plate reader) and expression distribution (using flow cytometry or fluorescence microscopy) of each version of the circuit.
* Quantify differences in mean and distributional expression (if any) between the versions of the circuit.
* Build a simulation for each version of the circuit dynamics using a stochastic simulation or differential equations.
* Develop design strategies to attenuate or insulate against the effects of compositional context (in simulation or experimentally)

===References===
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3440575/ Stefano Cardinale and Adam Arkin (2012) Contextualizing context for synthetic biology -- identifying causes of failure of synthetic biological systems, Journal of Biotechnology 7(7):856-866.]

*[http://ec.asm.org/content/10/1/43.short James Arnone and Michael McAlear (2011), Adjacent Gene Pairing Plays a Role in the Coordinated Expression of Ribosome Biogenesis Genes MPP10 and YJR003C in Saccharomyces cerevisiae, Eukaryotic Cell 10(1):43-53.]

*[http://www.jbioleng.org/content/3/1/4 Jason Kelly et al (2009) Measuring the activity of Biobrick promoters using an in vivo reference standard, Journal of Biological Engineering 3:4.]

*[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.0020074 Yuan-Yuan Li, Hui Yu, Zong-Ming Guo, Ting-Qing Guo, Kang Tu, Yi-Xue Li (2006) Systematic Analysis of Head-to-Head Gene Organization: Evolutionary Conservation and Potential Biological Relevance, PLoS Computational Biology 2(7):e74.]

*[http://www.sciencemag.org/content/307/5717/1965 Juan Pedraza, Alexander van Oudenaarden (2005), Noise Propagation in Gene Networks, Science 307 (5717):1965-1969.]

*[http://www.nature.com/nbt/journal/v22/n7/abs/nbt988.html Jan Korbel, Lars Jensen, Christian von Mering, Peer Bork (2004) Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs, Nature Biotechnology 22:911-917.]

*[http://www.sciencemag.org/content/297/5584/1183.full Michael Elowitz, Alan Levine, Eric Siggia, Peter.Swain (2002) Stochastic Gene Expression in a Single Cell, Science 297: 1183-1186.]

Understanding the Effect of Compositional Context on Biocircuit Performance

2013-01-04T02:09:19Z

Ehyeung:

'''[[SURF 2013|2013 SURF]] project description'''
* Mentor: Richard Murray
* Co-mentor: Enoch Yeung

Synthetic biocircuits often involve multiple components --- different genes that work together to achieve a desired function. For example, the repressilator employs three distinct genes that are designed to inhibit each other with a cyclic structure to produce oscillation. The toggle switch uses two genes, both repressing each other as they compete to be the dominant active gene. A signal cascade involves a sequence of genes where the arrival of a chemical signal triggers the first gene to activate a second (downstream) gene, which in turn activates a third gene, and so forth. Each of these example circuits as well as a host of others have been implemented in a variety of ways. The increasing number of biocircuits fuels hope for the assembly of complex synthetic systems constructed from multiple biocircuits. However, synthetic biologists and engineers are finding that biocircuit context can impact system performance. Biocircuit context can be classified roughly into three categories: compositional context, host context, and environmental context (Cardinale and Arkin, 2012).

The goal of this project is to understand the effect of compositional context on biocircuit performance. Compositional context refers to the effects arising from coupling multiple genes or undesigned interactions between genes located on the same molecule. We will explore how spatial composition, or layout, of different genes can impact performance of one or more biocircuits. To understand how these factors will affect circuit operation, we will take (or build) a simple genetic circuit consisting of 2 or more genes and implement it in multiple ways, varying the orientation and relative location of the genes to each other. The dynamic response of the circuit will be measured, including cell-to-cell variability (via flow cytometry or microscopy). The circuit that we test could be a genetic switch, repressilator, incoherent feedforward loop, etc. The project could involve both simulations of circuit dynamics and experimental quantification of circuit dynamics, with comparisons between the two. This would likely involve intensive cloning, measuring using flow cytometer and/or microscope, modeling using stochastic simulation and (possibly) differential equations.

Possible SURF Activities:
* Construct multiple versions of that simple circuit to systematically explore the compositional context space.
* Characterize the mean expression dynamics (using a plate reader) and expression distribution (using flow cytometry or fluorescence microscopy) of each version of the circuit.
* Quantify differences in mean and distributional expression (if any) between the versions of the circuit.
* Build a simulation for each version of the circuit dynamics using a stochastic simulation or differential equations.
* Develop design strategies to attenuate or insulate against the effects of compositional context (in simulation or experimentally)

===References===
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3440575/ Stefano Cardinale and Adam Arkin (2012) Contextualizing context for synthetic biology -- identifying causes of failure of synthetic biological systems, Journal of Biotechnology 7(7):856-866.]

*[http://ec.asm.org/content/10/1/43.short James Arnone and Michael McAlear (2011), Adjacent Gene Pairing Plays a Role in the Coordinated Expression of Ribosome Biogenesis Genes MPP10 and YJR003C in Saccharomyces cerevisiae, Eukaryotic Cell 10(1):43-53.]

*[http://www.jbioleng.org/content/3/1/4 Jason Kelly et al (2009) Measuring the activity of Biobrick promoters using an in vivo reference standard, Journal of Biological Engineering 3:4.]

*[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.0020074 Yuan-Yuan Li, Hui Yu, Zong-Ming Guo, Ting-Qing Guo, Kang Tu, Yi-Xue Li (2006) Systematic Analysis of Head-to-Head Gene Organization: Evolutionary Conservation and Potential Biological Relevance, PLoS Computational Biology 2(7):e74.]

*[http://www.sciencemag.org/content/307/5717/1965 Juan Pedraza, Alexander van Oudenaarden (2005), Noise Propagation in Gene Networks, Science 307 (5717):1965-1969.]

*[http://www.nature.com/nbt/journal/v22/n7/abs/nbt988.html Jan Korbel, Lars Jensen, Christian von Mering, Peer Bork (2004) Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs, Nature Biotechnology 22:911-917.]

*[http://www.sciencemag.org/content/297/5584/1183.full Michael Elowitz, Alan Levine, Eric Siggia, Peter.Swain (2002) Stochastic Gene Expression in a Single Cell, Science 297: 1183-1186.]

Understanding the Effect of Compositional Context on Biocircuit Performance

2013-01-04T02:04:45Z

Ehyeung:

'''[[SURF 2013|2013 SURF]] project description'''
* Mentor: Richard Murray
* Co-mentor: Enoch Yeung

Synthetic biocircuits often involve multiple components --- different genes that work together to achieve a desired function. For example, the repressilator employs three distinct genes that are designed to inhibit each other with a cyclic structure to produce oscillation. The toggle switch uses two genes, both repressing each other as they compete to be the dominant active gene. A signal cascade involves a sequence of genes where the arrival of a chemical signal triggers the first gene to activate a second (downstream) gene, which in turn activates a third gene, and so forth. The increasing number of biocircuits fuels hope for the assembly of complex synthetic systems constructed from multiple biocircuits. However, synthetic biologists and engineers are finding that biocircuit context can impact system performance. Biocircuit context can be classified roughly into three categories: compositional context, host context, and environmental context (Cardinale and Arkin, 2012).

The goal of this project is to understand the effect of compositional context on biocircuit performance. Compositional context refers to the effects arising from coupling multiple genes or undesigned interactions between genes located on the same molecule. We will explore how spatial composition, or layout, of different genes can impact performance of one or more biocircuits. To understand how these factors will affect circuit operation, we will take (or build) a simple genetic circuit consisting of 2 or more genes and implement it in multiple ways, varying the orientation and relative location of the genes to each other. The dynamic response of the circuit will be measured, including cell-to-cell variability (via flow cytometry or microscopy). The circuit that we test could be a genetic switch, repressilator, incoherent feedforward loop, etc. The project could involve both simulations of circuit dynamics and experimental quantification of circuit dynamics, with comparisons between the two. This would likely involve intensive cloning, measuring using flow cytometer and/or microscope, modeling using stochastic simulation and (possibly) differential equations.

Possible SURF Activities:
* Construct multiple versions of that simple circuit to systematically explore the compositional context space.
* Characterize the mean expression dynamics (using a plate reader) and expression distribution (using flow cytometry or fluorescence microscopy) of each version of the circuit.
* Quantify differences in mean and distributional expression (if any) between the versions of the circuit.
* Build a simulation for each version of the circuit dynamics using a stochastic simulation or differential equations.
* Develop design strategies to attenuate or insulate against the effects of compositional context (in simulation or experimentally)

===References===
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3440575/ Stefano Cardinale and Adam Arkin (2012) Contextualizing context for synthetic biology -- identifying causes of failure of synthetic biological systems, Journal of Biotechnology 7(7):856-866.]

*[http://ec.asm.org/content/10/1/43.short James Arnone and Michael McAlear (2011), Adjacent Gene Pairing Plays a Role in the Coordinated Expression of Ribosome Biogenesis Genes MPP10 and YJR003C in Saccharomyces cerevisiae, Eukaryotic Cell 10(1):43-53.]

*[http://www.jbioleng.org/content/3/1/4 Jason Kelly et al (2009) Measuring the activity of Biobrick promoters using an in vivo reference standard, Journal of Biological Engineering 3:4.]

*[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.0020074 Yuan-Yuan Li, Hui Yu, Zong-Ming Guo, Ting-Qing Guo, Kang Tu, Yi-Xue Li (2006) Systematic Analysis of Head-to-Head Gene Organization: Evolutionary Conservation and Potential Biological Relevance, PLoS Computational Biology 2(7):e74.]

*[http://www.sciencemag.org/content/307/5717/1965 Juan Pedraza, Alexander van Oudenaarden (2005), Noise Propagation in Gene Networks, Science 307 (5717):1965-1969.]

*[http://www.nature.com/nbt/journal/v22/n7/abs/nbt988.html Jan Korbel, Lars Jensen, Christian von Mering, Peer Bork (2004) Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs, Nature Biotechnology 22:911-917.]

*[http://www.sciencemag.org/content/297/5584/1183.full Michael Elowitz, Alan Levine, Eric Siggia, Peter.Swain (2002) Stochastic Gene Expression in a Single Cell, Science 297: 1183-1186.]

Understanding the Effect of Compositional Context on Biocircuit Performance

2013-01-04T02:03:47Z

Ehyeung:

'''[[SURF 2013|2013 SURF]] project description'''
* Mentor: Richard Murray
* Co-mentor: Enoch Yeung

Synthetic biocircuits often involve multiple components --- different genes that work together to achieve a desired function. For example, the repressilator employs three distinct genes that are designed to inhibit each other with a cyclic structure to produce oscillation. The toggle switch uses two genes, both repressing each other as they compete to be the dominant active gene. A signal cascade involves a sequence of genes where the arrival of a chemical signal triggers the first gene to activate a second (downstream) gene, which in turn activates a third gene, and so forth. The increasing number of biocircuits fuels hope for the assembly of complex synthetic systems constructed from multiple biocircuits. However, synthetic biologists and engineers are finding that biocircuit context can impact system performance. Biocircuit context can be classified roughly into three categories: compositional context, host context, and environmental context.

The goal of this project is to understand the effect of compositional context on biocircuit performance. Compositional context refers to the effects arising from coupling multiple genes or undesigned interactions between genes located on the same molecule. We will explore how spatial composition, or layout, of different genes can impact performance of one or more biocircuits. To understand how these factors will affect circuit operation, we will take (or build) a simple genetic circuit consisting of 2 or more genes and implement it in multiple ways, varying the orientation and relative location of the genes to each other. The dynamic response of the circuit will be measured, including cell-to-cell variability (via flow cytometry or microscopy). The circuit that we test could be a genetic switch, repressilator, incoherent feedforward loop, etc. The project could involve both simulations of circuit dynamics and experimental quantification of circuit dynamics, with comparisons between the two. This would likely involve intensive cloning, measuring using flow cytometer and/or microscope, modeling using stochastic simulation and (possibly) differential equations.

Possible SURF Activities:
* Construct multiple versions of that simple circuit to systematically explore the compositional context space.
* Characterize the mean expression dynamics (using a plate reader) and expression distribution (using flow cytometry or fluorescence microscopy) of each version of the circuit.
* Quantify differences in mean and distributional expression (if any) between the versions of the circuit.
* Build a simulation for each version of the circuit dynamics using a stochastic simulation or differential equations.
* Develop design strategies to attenuate or insulate against the effects of compositional context (in simulation or experimentally)

===References===
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3440575/ Stefano Cardinale and Adam Arkin (2012) Contextualizing context for synthetic biology -- identifying causes of failure of synthetic biological systems, Journal of Biotechnology 7(7):856-866.]

*[http://ec.asm.org/content/10/1/43.short James Arnone and Michael McAlear (2011), Adjacent Gene Pairing Plays a Role in the Coordinated Expression of Ribosome Biogenesis Genes MPP10 and YJR003C in Saccharomyces cerevisiae, Eukaryotic Cell 10(1):43-53.]

*[http://www.jbioleng.org/content/3/1/4 Jason Kelly et al (2009) Measuring the activity of Biobrick promoters using an in vivo reference standard, Journal of Biological Engineering 3:4.]

*[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.0020074 Yuan-Yuan Li, Hui Yu, Zong-Ming Guo, Ting-Qing Guo, Kang Tu, Yi-Xue Li (2006) Systematic Analysis of Head-to-Head Gene Organization: Evolutionary Conservation and Potential Biological Relevance, PLoS Computational Biology 2(7):e74.]

*[http://www.sciencemag.org/content/307/5717/1965 Juan Pedraza, Alexander van Oudenaarden (2005), Noise Propagation in Gene Networks, Science 307 (5717):1965-1969.]

*[http://www.nature.com/nbt/journal/v22/n7/abs/nbt988.html Jan Korbel, Lars Jensen, Christian von Mering, Peer Bork (2004) Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs, Nature Biotechnology 22:911-917.]

*[http://www.sciencemag.org/content/297/5584/1183.full Michael Elowitz, Alan Levine, Eric Siggia, Peter.Swain (2002) Stochastic Gene Expression in a Single Cell, Science 297: 1183-1186.]

Understanding the Effect of Compositional Context on Biocircuit Performance

2013-01-04T01:53:41Z

Ehyeung: /* Supplementary Resources */

'''[[SURF 2013|2013 SURF]] project description'''
* Mentor: Richard Murray
* Co-mentor: Enoch Yeung

Synthetic biocircuits often involve multiple components --- different genes that work together to achieve a desired function. For example, the repressilator employs three distinct genes that are designed to inhibit each other with a cyclic structure to produce oscillation. The toggle switch uses two genes, both repressing each other as they compete to be the dominant active gene. A signal cascade involves a sequence of genes where the arrival of a chemical signal triggers the first gene to activate a second (downstream) gene, which in turn activates a third gene, and so forth. The increasing number of biocircuits fuels hope for the assembly of complex synthetic systems constructed from multiple biocircuits. However, synthetic biologists and engineers are finding that biocircuit context can impact system performance. Biocircuit context can be classified roughly into three categories: compositional context, host context, and environmental context.

The goal of this project is to understand the effect of compositional context on biocircuit performance. Compositional context refers to the effects arising from coupling multiple genes or undesigned interactions between genes located on the same molecule. We will explore how spatial composition, or layout, of different genes can impact performance of one or more biocircuits. To understand how these factors will affect circuit operation, we will take a simple genetic circuit consisting of 2 or more genes and implement it in multiple ways, varying the orientation and relative location of the genes to each other. The dynamic response of the circuit will be measured, including cell-to-cell variability (via flow cytometry or microscopy). The circuit that we test could be a genetic switch, repressilator, incoherent feedforward loop, etc. The project could involve both simulations of circuit dynamics and experimental quantification of circuit dynamics, with comparisons between the two. This would likely involve intensive cloning, measuring using flow cytometer and/or microscope, modeling using stochastic simulation and (possibly) differential equations.

Possible SURF Activities:
* Construct multiple versions of that simple circuit to systematically explore the compositional context space.
* Characterize the mean expression dynamics (using a plate reader) and expression distribution (using flow cytometry or fluorescence microscopy) of each version of the circuit.
* Quantify differences in mean and distributional expression (if any) between the versions of the circuit.
* Build a simulation for each version of the circuit dynamics using a stochastic simulation or differential equations.
* Develop design strategies to attenuate or insulate against the effects of compositional context (in simulation or experimentally)

===References===
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3440575/ Stefano Cardinale and Adam Arkin (2012) Contextualizing context for synthetic biology -- identifying causes of failure of synthetic biological systems, Journal of Biotechnology 7(7):856-866.]

*[http://ec.asm.org/content/10/1/43.short James Arnone and Michael McAlear (2011), Adjacent Gene Pairing Plays a Role in the Coordinated Expression of Ribosome Biogenesis Genes MPP10 and YJR003C in Saccharomyces cerevisiae, Eukaryotic Cell 10(1):43-53.]

*[http://www.jbioleng.org/content/3/1/4 Jason Kelly et al (2009) Measuring the activity of Biobrick promoters using an in vivo reference standard, Journal of Biological Engineering 3:4.]

*[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.0020074 Yuan-Yuan Li, Hui Yu, Zong-Ming Guo, Ting-Qing Guo, Kang Tu, Yi-Xue Li (2006) Systematic Analysis of Head-to-Head Gene Organization: Evolutionary Conservation and Potential Biological Relevance, PLoS Computational Biology 2(7):e74.]

*[http://www.sciencemag.org/content/307/5717/1965 Juan Pedraza, Alexander van Oudenaarden (2005), Noise Propagation in Gene Networks, Science 307 (5717):1965-1969.]

*[http://www.nature.com/nbt/journal/v22/n7/abs/nbt988.html Jan Korbel, Lars Jensen, Christian von Mering, Peer Bork (2004) Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs, Nature Biotechnology 22:911-917.]

*[http://www.sciencemag.org/content/297/5584/1183.full Michael Elowitz, Alan Levine, Eric Siggia, Peter.Swain (2002) Stochastic Gene Expression in a Single Cell, Science 297: 1183-1186.]

Understanding the Effect of Compositional Context on Biocircuit Performance

2013-01-04T01:53:14Z

Ehyeung: /* References */

'''[[SURF 2013|2013 SURF]] project description'''
* Mentor: Richard Murray
* Co-mentor: Enoch Yeung

Synthetic biocircuits often involve multiple components --- different genes that work together to achieve a desired function. For example, the repressilator employs three distinct genes that are designed to inhibit each other with a cyclic structure to produce oscillation. The toggle switch uses two genes, both repressing each other as they compete to be the dominant active gene. A signal cascade involves a sequence of genes where the arrival of a chemical signal triggers the first gene to activate a second (downstream) gene, which in turn activates a third gene, and so forth. The increasing number of biocircuits fuels hope for the assembly of complex synthetic systems constructed from multiple biocircuits. However, synthetic biologists and engineers are finding that biocircuit context can impact system performance. Biocircuit context can be classified roughly into three categories: compositional context, host context, and environmental context.

The goal of this project is to understand the effect of compositional context on biocircuit performance. Compositional context refers to the effects arising from coupling multiple genes or undesigned interactions between genes located on the same molecule. We will explore how spatial composition, or layout, of different genes can impact performance of one or more biocircuits. To understand how these factors will affect circuit operation, we will take a simple genetic circuit consisting of 2 or more genes and implement it in multiple ways, varying the orientation and relative location of the genes to each other. The dynamic response of the circuit will be measured, including cell-to-cell variability (via flow cytometry or microscopy). The circuit that we test could be a genetic switch, repressilator, incoherent feedforward loop, etc. The project could involve both simulations of circuit dynamics and experimental quantification of circuit dynamics, with comparisons between the two. This would likely involve intensive cloning, measuring using flow cytometer and/or microscope, modeling using stochastic simulation and (possibly) differential equations.

Possible SURF Activities:
* Construct multiple versions of that simple circuit to systematically explore the compositional context space.
* Characterize the mean expression dynamics (using a plate reader) and expression distribution (using flow cytometry or fluorescence microscopy) of each version of the circuit.
* Quantify differences in mean and distributional expression (if any) between the versions of the circuit.
* Build a simulation for each version of the circuit dynamics using a stochastic simulation or differential equations.
* Develop design strategies to attenuate or insulate against the effects of compositional context (in simulation or experimentally)

===References===
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3440575/ Stefano Cardinale and Adam Arkin (2012) Contextualizing context for synthetic biology -- identifying causes of failure of synthetic biological systems, Journal of Biotechnology 7(7):856-866.]

*[http://ec.asm.org/content/10/1/43.short James Arnone and Michael McAlear (2011), Adjacent Gene Pairing Plays a Role in the Coordinated Expression of Ribosome Biogenesis Genes MPP10 and YJR003C in Saccharomyces cerevisiae, Eukaryotic Cell 10(1):43-53.]

*[http://www.jbioleng.org/content/3/1/4 Jason Kelly et al (2009) Measuring the activity of Biobrick promoters using an in vivo reference standard, Journal of Biological Engineering 3:4.]

*[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.0020074 Yuan-Yuan Li, Hui Yu, Zong-Ming Guo, Ting-Qing Guo, Kang Tu, Yi-Xue Li (2006) Systematic Analysis of Head-to-Head Gene Organization: Evolutionary Conservation and Potential Biological Relevance, PLoS Computational Biology 2(7):e74.]

*[http://www.sciencemag.org/content/307/5717/1965 Juan Pedraza, Alexander van Oudenaarden (2005), Noise Propagation in Gene Networks, Science 307 (5717):1965-1969.]

*[http://www.nature.com/nbt/journal/v22/n7/abs/nbt988.html Jan Korbel, Lars Jensen, Christian von Mering, Peer Bork (2004) Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs, Nature Biotechnology 22:911-917.]

*[http://www.sciencemag.org/content/297/5584/1183.full Michael Elowitz, Alan Levine, Eric Siggia, Peter.Swain (2002) Stochastic Gene Expression in a Single Cell, Science 297: 1183-1186.]

===Supplementary Resources===
* [http://openwetware.org/wiki/TABASCO TABASCO Stochastic Simulator]
* [http://www.cds.caltech.edu/~murray/wiki/index.php/BE_262_project,_2010 Past Class Project]

Understanding the Effect of Compositional Context on Biocircuit Performance

2013-01-04T01:49:20Z

Ehyeung: /* References */

'''[[SURF 2013|2013 SURF]] project description'''
* Mentor: Richard Murray
* Co-mentor: Enoch Yeung

Synthetic biocircuits often involve multiple components --- different genes that work together to achieve a desired function. For example, the repressilator employs three distinct genes that are designed to inhibit each other with a cyclic structure to produce oscillation. The toggle switch uses two genes, both repressing each other as they compete to be the dominant active gene. A signal cascade involves a sequence of genes where the arrival of a chemical signal triggers the first gene to activate a second (downstream) gene, which in turn activates a third gene, and so forth. The increasing number of biocircuits fuels hope for the assembly of complex synthetic systems constructed from multiple biocircuits. However, synthetic biologists and engineers are finding that biocircuit context can impact system performance. Biocircuit context can be classified roughly into three categories: compositional context, host context, and environmental context.

The goal of this project is to understand the effect of compositional context on biocircuit performance. Compositional context refers to the effects arising from coupling multiple genes or undesigned interactions between genes located on the same molecule. We will explore how spatial composition, or layout, of different genes can impact performance of one or more biocircuits. To understand how these factors will affect circuit operation, we will take a simple genetic circuit consisting of 2 or more genes and implement it in multiple ways, varying the orientation and relative location of the genes to each other. The dynamic response of the circuit will be measured, including cell-to-cell variability (via flow cytometry or microscopy). The circuit that we test could be a genetic switch, repressilator, incoherent feedforward loop, etc. The project could involve both simulations of circuit dynamics and experimental quantification of circuit dynamics, with comparisons between the two. This would likely involve intensive cloning, measuring using flow cytometer and/or microscope, modeling using stochastic simulation and (possibly) differential equations.

Possible SURF Activities:
* Construct multiple versions of that simple circuit to systematically explore the compositional context space.
* Characterize the mean expression dynamics (using a plate reader) and expression distribution (using flow cytometry or fluorescence microscopy) of each version of the circuit.
* Quantify differences in mean and distributional expression (if any) between the versions of the circuit.
* Build a simulation for each version of the circuit dynamics using a stochastic simulation or differential equations.
* Develop design strategies to attenuate or insulate against the effects of compositional context (in simulation or experimentally)

===References===
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3440575/ Stefano Cardinale and Adam Arkin (2012) Contextualizing context for synthetic biology -- identifying causes of failure of synthetic biological systems, Journal of Biotechnology 7(7):856-866.]

*[http://www.sciencemag.org/content/297/5584/1183.full Michael Elowitz, Alan Levine, Eric Siggia, Peter.Swain (2002) Stochastic Gene Expression in a Single Cell, Science 297: 1183-1186.]

*[http://www.jbioleng.org/content/3/1/4 Jason Kelly et al (2009) Measuring the activity of Biobrick promoters using an in vivo reference standard, Journal of Biological Engineering 3:4.]

*[http://www.nature.com/nbt/journal/v22/n7/abs/nbt988.html Jan Korbel, Lars Jensen, Christian von Mering, Peer Bork (2004) Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs, Nature Biotechnology 22:911-917.]

*[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.0020074 Yuan-Yuan Li, Hui Yu, Zong-Ming Guo, Ting-Qing Guo, Kang Tu, Yi-Xue Li (2006) Systematic Analysis of Head-to-Head Gene Organization: Evolutionary Conservation and Potential Biological Relevance, PLoS Computational Biology 2(7):e74.]

*[http://ec.asm.org/content/10/1/43.short James Arnone and Michael McAlear (2011), Adjacent Gene Pairing Plays a Role in the Coordinated Expression of Ribosome Biogenesis Genes MPP10 and YJR003C in Saccharomyces cerevisiae, Eukaryotic Cell 10(1):43-53.]

*[http://www.sciencemag.org/content/307/5717/1965 Juan Pedraza, Alexander van Oudenaarden (2005), Noise Propagation in Gene Networks, Science 307 (5717):1965-1969.]

===Supplementary Resources===
* [http://openwetware.org/wiki/TABASCO TABASCO Stochastic Simulator]
* [http://www.cds.caltech.edu/~murray/wiki/index.php/BE_262_project,_2010 Past Class Project]

Understanding the Effect of Compositional Context on Biocircuit Performance

2013-01-04T01:49:09Z

Ehyeung: /* References */

'''[[SURF 2013|2013 SURF]] project description'''
* Mentor: Richard Murray
* Co-mentor: Enoch Yeung

Synthetic biocircuits often involve multiple components --- different genes that work together to achieve a desired function. For example, the repressilator employs three distinct genes that are designed to inhibit each other with a cyclic structure to produce oscillation. The toggle switch uses two genes, both repressing each other as they compete to be the dominant active gene. A signal cascade involves a sequence of genes where the arrival of a chemical signal triggers the first gene to activate a second (downstream) gene, which in turn activates a third gene, and so forth. The increasing number of biocircuits fuels hope for the assembly of complex synthetic systems constructed from multiple biocircuits. However, synthetic biologists and engineers are finding that biocircuit context can impact system performance. Biocircuit context can be classified roughly into three categories: compositional context, host context, and environmental context.

The goal of this project is to understand the effect of compositional context on biocircuit performance. Compositional context refers to the effects arising from coupling multiple genes or undesigned interactions between genes located on the same molecule. We will explore how spatial composition, or layout, of different genes can impact performance of one or more biocircuits. To understand how these factors will affect circuit operation, we will take a simple genetic circuit consisting of 2 or more genes and implement it in multiple ways, varying the orientation and relative location of the genes to each other. The dynamic response of the circuit will be measured, including cell-to-cell variability (via flow cytometry or microscopy). The circuit that we test could be a genetic switch, repressilator, incoherent feedforward loop, etc. The project could involve both simulations of circuit dynamics and experimental quantification of circuit dynamics, with comparisons between the two. This would likely involve intensive cloning, measuring using flow cytometer and/or microscope, modeling using stochastic simulation and (possibly) differential equations.

Possible SURF Activities:
* Construct multiple versions of that simple circuit to systematically explore the compositional context space.
* Characterize the mean expression dynamics (using a plate reader) and expression distribution (using flow cytometry or fluorescence microscopy) of each version of the circuit.
* Quantify differences in mean and distributional expression (if any) between the versions of the circuit.
* Build a simulation for each version of the circuit dynamics using a stochastic simulation or differential equations.
* Develop design strategies to attenuate or insulate against the effects of compositional context (in simulation or experimentally)

===References===
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3440575/ Stefano Cardinale and Adam Arkin (2012) Contextualizing context for synthetic biology --identifying causes of failure of synthetic biological systems, Journal of Biotechnology 7(7):856-866.]

*[http://www.sciencemag.org/content/297/5584/1183.full Michael Elowitz, Alan Levine, Eric Siggia, Peter.Swain (2002) Stochastic Gene Expression in a Single Cell, Science 297: 1183-1186.]

*[http://www.jbioleng.org/content/3/1/4 Jason Kelly et al (2009) Measuring the activity of Biobrick promoters using an in vivo reference standard, Journal of Biological Engineering 3:4.]

*[http://www.nature.com/nbt/journal/v22/n7/abs/nbt988.html Jan Korbel, Lars Jensen, Christian von Mering, Peer Bork (2004) Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs, Nature Biotechnology 22:911-917.]

*[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.0020074 Yuan-Yuan Li, Hui Yu, Zong-Ming Guo, Ting-Qing Guo, Kang Tu, Yi-Xue Li (2006) Systematic Analysis of Head-to-Head Gene Organization: Evolutionary Conservation and Potential Biological Relevance, PLoS Computational Biology 2(7):e74.]

*[http://ec.asm.org/content/10/1/43.short James Arnone and Michael McAlear (2011), Adjacent Gene Pairing Plays a Role in the Coordinated Expression of Ribosome Biogenesis Genes MPP10 and YJR003C in Saccharomyces cerevisiae, Eukaryotic Cell 10(1):43-53.]

*[http://www.sciencemag.org/content/307/5717/1965 Juan Pedraza, Alexander van Oudenaarden (2005), Noise Propagation in Gene Networks, Science 307 (5717):1965-1969.]

===Supplementary Resources===
* [http://openwetware.org/wiki/TABASCO TABASCO Stochastic Simulator]
* [http://www.cds.caltech.edu/~murray/wiki/index.php/BE_262_project,_2010 Past Class Project]

Understanding the Effect of Compositional Context on Biocircuit Performance

2013-01-04T01:46:31Z

Ehyeung:

'''[[SURF 2013|2013 SURF]] project description'''
* Mentor: Richard Murray
* Co-mentor: Enoch Yeung

Synthetic biocircuits often involve multiple components --- different genes that work together to achieve a desired function. For example, the repressilator employs three distinct genes that are designed to inhibit each other with a cyclic structure to produce oscillation. The toggle switch uses two genes, both repressing each other as they compete to be the dominant active gene. A signal cascade involves a sequence of genes where the arrival of a chemical signal triggers the first gene to activate a second (downstream) gene, which in turn activates a third gene, and so forth. The increasing number of biocircuits fuels hope for the assembly of complex synthetic systems constructed from multiple biocircuits. However, synthetic biologists and engineers are finding that biocircuit context can impact system performance. Biocircuit context can be classified roughly into three categories: compositional context, host context, and environmental context.

The goal of this project is to understand the effect of compositional context on biocircuit performance. Compositional context refers to the effects arising from coupling multiple genes or undesigned interactions between genes located on the same molecule. We will explore how spatial composition, or layout, of different genes can impact performance of one or more biocircuits. To understand how these factors will affect circuit operation, we will take a simple genetic circuit consisting of 2 or more genes and implement it in multiple ways, varying the orientation and relative location of the genes to each other. The dynamic response of the circuit will be measured, including cell-to-cell variability (via flow cytometry or microscopy). The circuit that we test could be a genetic switch, repressilator, incoherent feedforward loop, etc. The project could involve both simulations of circuit dynamics and experimental quantification of circuit dynamics, with comparisons between the two. This would likely involve intensive cloning, measuring using flow cytometer and/or microscope, modeling using stochastic simulation and (possibly) differential equations.

Possible SURF Activities:
* Construct multiple versions of that simple circuit to systematically explore the compositional context space.
* Characterize the mean expression dynamics (using a plate reader) and expression distribution (using flow cytometry or fluorescence microscopy) of each version of the circuit.
* Quantify differences in mean and distributional expression (if any) between the versions of the circuit.
* Build a simulation for each version of the circuit dynamics using a stochastic simulation or differential equations.
* Develop design strategies to attenuate or insulate against the effects of compositional context (in simulation or experimentally)

===References===
*[http://www.sciencemag.org/content/297/5584/1183.full Michael Elowitz, Alan Levine, Eric Siggia, Peter.Swain (2002) Stochastic Gene Expression in a Single Cell, Science 297: 1183-1186.]

*[http://www.jbioleng.org/content/3/1/4 Jason Kelly et al (2009) Measuring the activity of Biobrick promoters using an in vivo reference standard, Journal of Biological Engineering 3:4.]

*[http://www.nature.com/nbt/journal/v22/n7/abs/nbt988.html Jan Korbel, Lars Jensen, Christian von Mering, Peer Bork (2004) Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs, Nature Biotechnology 22:911-917.]

*[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.0020074 Yuan-Yuan Li, Hui Yu, Zong-Ming Guo, Ting-Qing Guo, Kang Tu, Yi-Xue Li (2006) Systematic Analysis of Head-to-Head Gene Organization: Evolutionary Conservation and Potential Biological Relevance, PLoS Computational Biology 2(7):e74.]

*[http://ec.asm.org/content/10/1/43.short James Arnone and Michael McAlear (2011), Adjacent Gene Pairing Plays a Role in the Coordinated Expression of Ribosome Biogenesis Genes MPP10 and YJR003C in Saccharomyces cerevisiae, Eukaryotic Cell 10(1):43-53.]

*[http://www.sciencemag.org/content/307/5717/1965 Juan Pedraza, Alexander van Oudenaarden (2005), Noise Propagation in Gene Networks, Science 307 (5717):1965-1969.]
===Supplementary Resources===
* [http://openwetware.org/wiki/TABASCO TABASCO Stochastic Simulator]
* [http://www.cds.caltech.edu/~murray/wiki/index.php/BE_262_project,_2010 Past Class Project]

Understanding the Effect of Compositional Context on Biocircuit Performance

2013-01-04T01:46:18Z

Ehyeung: /* References */

'''[[SURF 2013|2013 SURF]] project description'''
* Mentor: Richard Murray
* Co-mentor: Enoch Yeung

Synthetic biocircuits often involve multiple components --- different genes that work together to achieve a desired function. For example, the repressilator employs three distinct genes that are designed to inhibit each other with a cyclic structure to produce oscillation. The toggle switch uses two genes, both repressing each other as they compete to be the dominant active gene. A signal cascade involves a sequence of genes where the arrival of a chemical signal triggers the first gene to activate a second (downstream) gene, which in turn activates a third gene, and so forth. The increasing number of biocircuits fuels hope for the assembly of complex synthetic systems constructed from multiple biocircuits. However, synthetic biologists and engineers are finding that biocircuit context can impact system performance. Biocircuit context can be classified roughly into three categories: compositional context, host context, and environmental context.

The goal of this project is to understand the effect of compositional context on biocircuit performance. Compositional context refers to the effects arising from coupling multiple genes or undesigned interactions between genes located on the same molecule. We will explore how spatial composition, or layout, of different genes can impact performance of one or more biocircuits. To understand how these factors will affect circuit operation, we will take a simple genetic circuit consisting of 2 or more genes and implement it in multiple ways, varying the orientation and relative location of the genes to each other. The dynamic response of the circuit will be measured, including cell-to-cell variability (via flow cytometry or microscopy). The circuit that we test could be a genetic switch, repressilator, incoherent feedforward loop, etc. The project could involve both simulations of circuit dynamics and experimental quantification of circuit dynamics, with comparisons between the two. This would likely involve intensive cloning, measuring using flow cytometer and/or microscope, modeling using stochastic simulation and (possibly) differential equations.

Possible SURF Activities:
* Construct multiple versions of that simple circuit to systematically explore the compositional context space.
* Characterize the mean expression dynamics (using a plate reader) and expression distribution (using flow cytometry or fluorescence microscopy) of each version of the circuit.
* Quantify differences in mean and distributional expression (if any) between the versions of the circuit.
* Build a simulation for each version of the circuit dynamics using a stochastic simulation or differential equations.
* Develop design strategies to attenuate or insulate against the effects of compositional context (in simulation or experimentally)

===References===
*[http://www.sciencemag.org/content/297/5584/1183.full Michael Elowitz, Alan Levine, Eric Siggia, Peter.Swain (2002) Stochastic Gene Expression in a Single Cell, Science 297: 1183-1186.]

*[http://www.jbioleng.org/content/3/1/4 Jason Kelly et al (2009) Measuring the activity of Biobrick promoters using an in vivo reference standard, Journal of Biological Engineering 3:4.]

*[http://www.nature.com/nbt/journal/v22/n7/abs/nbt988.html Jan Korbel, Lars Jensen, Christian von Mering, Peer Bork (2004) Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs, Nature Biotechnology 22:911-917.]

*[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.0020074 Yuan-Yuan Li, Hui Yu, Zong-Ming Guo, Ting-Qing Guo, Kang Tu, Yi-Xue Li (2006) Systematic Analysis of Head-to-Head Gene Organization: Evolutionary Conservation and Potential Biological Relevance, PLoS Computational Biology 2(7):e74.]

*[http://ec.asm.org/content/10/1/43.short James Arnone and Michael McAlear (2011), Adjacent Gene Pairing Plays a Role in the Coordinated Expression of Ribosome Biogenesis Genes MPP10 and YJR003C in Saccharomyces cerevisiae, Eukaryotic Cell 10(1):43-53.]

*[http://www.sciencemag.org/content/307/5717/1965 Juan Pedraza, Alexander van Oudenaarden (2005), Noise Propagation in Gene Networks, Science 307 (5717):1965-1969.]
===Supplementary Resources===
* [http://openwetware.org/wiki/TABASCO TABASCO Stochastic Simulator]
* [http://www.cds.caltech.edu/~murray/wiki/index.php/BE_262_project,_2010 Past Class Project]

Understanding the Effect of Compositional Context on Biocircuit Performance

2013-01-04T01:33:53Z

Ehyeung: /* References */

'''[[SURF 2013|2013 SURF]] project description'''
* Mentor: Richard Murray
* Co-mentor: Enoch Yeung

Synthetic biocircuits often involve multiple components --- different genes that work together to achieve a desired function. For example, the repressilator employs three distinct genes that are designed to inhibit each other with a cyclic structure to produce oscillation. The toggle switch uses two genes, both repressing each other as they compete to be the dominant active gene. A signal cascade involves a sequence of genes where the arrival of a chemical signal triggers the first gene to activate a second (downstream) gene, which in turn activates a third gene, and so forth. The increasing number of biocircuits fuels hope for the assembly of complex synthetic systems constructed from multiple biocircuits. However, synthetic biologists and engineers are finding that biocircuit context can impact system performance. Biocircuit context can be classified roughly into three categories: compositional context, host context, and environmental context.

The goal of this project is to understand the effect of compositional context on biocircuit performance. Compositional context refers to the effects arising from coupling multiple genes or undesigned interactions between genes located on the same molecule. We will explore how spatial composition, or layout, of different genes can impact performance of one or more biocircuits. To understand how these factors will affect circuit operation, we will take a simple genetic circuit consisting of 2 or more genes and implement it in multiple ways, varying the orientation and relative location of the genes to each other. The dynamic response of the circuit will be measured, including cell-to-cell variability (via flow cytometry or microscopy). The circuit that we test could be a genetic switch, repressilator, incoherent feedforward loop, etc. The project could involve both simulations of circuit dynamics and experimental quantification of circuit dynamics, with comparisons between the two. This would likely involve intensive cloning, measuring using flow cytometer and/or microscope, modeling using stochastic simulation and (possibly) differential equations.

Possible SURF Activities:
* Construct multiple versions of that simple circuit to systematically explore the compositional context space.
* Characterize the mean expression dynamics (using a plate reader) and expression distribution (using flow cytometry or fluorescence microscopy) of each version of the circuit.
* Quantify differences in mean and distributional expression (if any) between the versions of the circuit.
* Build a simulation for each version of the circuit dynamics using a stochastic simulation or differential equations.
* Develop design strategies to attenuate or insulate against the effects of compositional context (in simulation or experimentally)

===References===
*[http://www.sciencemag.org/content/297/5584/1183.full Michael Elowitz, Alan Levine, Eric Siggia, Peter.Swain (2002) Stochastic Gene Expression in a Single Cell, Science 297: 1183-1186.]

*[http://www.jbioleng.org/content/3/1/4 Jason Kelly et al (2009) Measuring the activity of Biobrick promoters using an in vivo reference standard, Journal of Biological Engineering 3:4.]

* http://openwetware.org/wiki/TABASCO (highly detailed simular, similar to simulac)
* http://paulsson.med.harvard.edu/Web_pdfs/paulsson2001QRBiophis.pdf
* http://www.nature.com/nbt/journal/v22/n7/abs/nbt988.html (E. Coli analysis of local-bidirectionality layout)
* http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.0020074 (Eukaryote analysis of " ")
* http://ec.asm.org/content/10/1/43.short (for Yeast of " " as well as effect of adding an interspacing sequence/reporter cassette )
* http://www.sciencemag.org/content/307/5717/1965/suppl/DC1 (Noise propagates possibly from adjacency in gene layout)

* http://www.cds.caltech.edu/~murray/wiki/index.php/BE_262_project,_2010

Understanding the Effect of Compositional Context on Biocircuit Performance

2013-01-04T01:33:07Z

Ehyeung: /* References */

'''[[SURF 2013|2013 SURF]] project description'''
* Mentor: Richard Murray
* Co-mentor: Enoch Yeung

Synthetic biocircuits often involve multiple components --- different genes that work together to achieve a desired function. For example, the repressilator employs three distinct genes that are designed to inhibit each other with a cyclic structure to produce oscillation. The toggle switch uses two genes, both repressing each other as they compete to be the dominant active gene. A signal cascade involves a sequence of genes where the arrival of a chemical signal triggers the first gene to activate a second (downstream) gene, which in turn activates a third gene, and so forth. The increasing number of biocircuits fuels hope for the assembly of complex synthetic systems constructed from multiple biocircuits. However, synthetic biologists and engineers are finding that biocircuit context can impact system performance. Biocircuit context can be classified roughly into three categories: compositional context, host context, and environmental context.

The goal of this project is to understand the effect of compositional context on biocircuit performance. Compositional context refers to the effects arising from coupling multiple genes or undesigned interactions between genes located on the same molecule. We will explore how spatial composition, or layout, of different genes can impact performance of one or more biocircuits. To understand how these factors will affect circuit operation, we will take a simple genetic circuit consisting of 2 or more genes and implement it in multiple ways, varying the orientation and relative location of the genes to each other. The dynamic response of the circuit will be measured, including cell-to-cell variability (via flow cytometry or microscopy). The circuit that we test could be a genetic switch, repressilator, incoherent feedforward loop, etc. The project could involve both simulations of circuit dynamics and experimental quantification of circuit dynamics, with comparisons between the two. This would likely involve intensive cloning, measuring using flow cytometer and/or microscope, modeling using stochastic simulation and (possibly) differential equations.

Possible SURF Activities:
* Construct multiple versions of that simple circuit to systematically explore the compositional context space.
* Characterize the mean expression dynamics (using a plate reader) and expression distribution (using flow cytometry or fluorescence microscopy) of each version of the circuit.
* Quantify differences in mean and distributional expression (if any) between the versions of the circuit.
* Build a simulation for each version of the circuit dynamics using a stochastic simulation or differential equations.
* Develop design strategies to attenuate or insulate against the effects of compositional context (in simulation or experimentally)

===References===
* Michael Elowitz, Alan Levine, Eric Siggia, Peter.Swain (2002) Stochastic Gene Expression in a Single Cell, Science 297: 1183-1186.
[http://www.sciencemag.org/content/297/5584/1183.full]
* Jason Kelly et al (2009) Measuring the activity of Biobrick promoters using an in vivo reference standard, Journal of Biological Engineering 3:4.
[http://www.jbioleng.org/content/3/1/4]

* http://openwetware.org/wiki/TABASCO (highly detailed simular, similar to simulac)
* http://paulsson.med.harvard.edu/Web_pdfs/paulsson2001QRBiophis.pdf
* http://www.nature.com/nbt/journal/v22/n7/abs/nbt988.html (E. Coli analysis of local-bidirectionality layout)
* http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.0020074 (Eukaryote analysis of " ")
* http://ec.asm.org/content/10/1/43.short (for Yeast of " " as well as effect of adding an interspacing sequence/reporter cassette )
* http://www.sciencemag.org/content/307/5717/1965/suppl/DC1 (Noise propagates possibly from adjacency in gene layout)

* http://www.cds.caltech.edu/~murray/wiki/index.php/BE_262_project,_2010

Understanding the Effect of Compositional Context on Biocircuit Performance

2013-01-04T01:32:28Z

Ehyeung: /* References */

'''[[SURF 2013|2013 SURF]] project description'''
* Mentor: Richard Murray
* Co-mentor: Enoch Yeung

Synthetic biocircuits often involve multiple components --- different genes that work together to achieve a desired function. For example, the repressilator employs three distinct genes that are designed to inhibit each other with a cyclic structure to produce oscillation. The toggle switch uses two genes, both repressing each other as they compete to be the dominant active gene. A signal cascade involves a sequence of genes where the arrival of a chemical signal triggers the first gene to activate a second (downstream) gene, which in turn activates a third gene, and so forth. The increasing number of biocircuits fuels hope for the assembly of complex synthetic systems constructed from multiple biocircuits. However, synthetic biologists and engineers are finding that biocircuit context can impact system performance. Biocircuit context can be classified roughly into three categories: compositional context, host context, and environmental context.

The goal of this project is to understand the effect of compositional context on biocircuit performance. Compositional context refers to the effects arising from coupling multiple genes or undesigned interactions between genes located on the same molecule. We will explore how spatial composition, or layout, of different genes can impact performance of one or more biocircuits. To understand how these factors will affect circuit operation, we will take a simple genetic circuit consisting of 2 or more genes and implement it in multiple ways, varying the orientation and relative location of the genes to each other. The dynamic response of the circuit will be measured, including cell-to-cell variability (via flow cytometry or microscopy). The circuit that we test could be a genetic switch, repressilator, incoherent feedforward loop, etc. The project could involve both simulations of circuit dynamics and experimental quantification of circuit dynamics, with comparisons between the two. This would likely involve intensive cloning, measuring using flow cytometer and/or microscope, modeling using stochastic simulation and (possibly) differential equations.

Possible SURF Activities:
* Construct multiple versions of that simple circuit to systematically explore the compositional context space.
* Characterize the mean expression dynamics (using a plate reader) and expression distribution (using flow cytometry or fluorescence microscopy) of each version of the circuit.
* Quantify differences in mean and distributional expression (if any) between the versions of the circuit.
* Build a simulation for each version of the circuit dynamics using a stochastic simulation or differential equations.
* Develop design strategies to attenuate or insulate against the effects of compositional context (in simulation or experimentally)

===References===
* Michael Elowitz, Alan Levine, Eric Siggia, Peter.Swain (2002) Stochastic Gene Expression in a Single Cell, Science 297: 1183-1186.

[http://www.sciencemag.org/content/297/5584/1183.full]
* Jason Kelly et al (2009) Measuring the activity of Biobrick promoters using an in vivo reference standard, Journal of Biological Engineering 3:4.

[[http://www.jbioleng.org/content/3/1/4]]

* http://openwetware.org/wiki/TABASCO (highly detailed simular, similar to simulac)
* http://paulsson.med.harvard.edu/Web_pdfs/paulsson2001QRBiophis.pdf
* http://www.nature.com/nbt/journal/v22/n7/abs/nbt988.html (E. Coli analysis of local-bidirectionality layout)
* http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.0020074 (Eukaryote analysis of " ")
* http://ec.asm.org/content/10/1/43.short (for Yeast of " " as well as effect of adding an interspacing sequence/reporter cassette )
* http://www.sciencemag.org/content/307/5717/1965/suppl/DC1 (Noise propagates possibly from adjacency in gene layout)

* http://www.cds.caltech.edu/~murray/wiki/index.php/BE_262_project,_2010

Understanding the Effect of Compositional Context on Biocircuit Performance

2013-01-04T01:32:19Z

Ehyeung: /* References */

'''[[SURF 2013|2013 SURF]] project description'''
* Mentor: Richard Murray
* Co-mentor: Enoch Yeung

Synthetic biocircuits often involve multiple components --- different genes that work together to achieve a desired function. For example, the repressilator employs three distinct genes that are designed to inhibit each other with a cyclic structure to produce oscillation. The toggle switch uses two genes, both repressing each other as they compete to be the dominant active gene. A signal cascade involves a sequence of genes where the arrival of a chemical signal triggers the first gene to activate a second (downstream) gene, which in turn activates a third gene, and so forth. The increasing number of biocircuits fuels hope for the assembly of complex synthetic systems constructed from multiple biocircuits. However, synthetic biologists and engineers are finding that biocircuit context can impact system performance. Biocircuit context can be classified roughly into three categories: compositional context, host context, and environmental context.

The goal of this project is to understand the effect of compositional context on biocircuit performance. Compositional context refers to the effects arising from coupling multiple genes or undesigned interactions between genes located on the same molecule. We will explore how spatial composition, or layout, of different genes can impact performance of one or more biocircuits. To understand how these factors will affect circuit operation, we will take a simple genetic circuit consisting of 2 or more genes and implement it in multiple ways, varying the orientation and relative location of the genes to each other. The dynamic response of the circuit will be measured, including cell-to-cell variability (via flow cytometry or microscopy). The circuit that we test could be a genetic switch, repressilator, incoherent feedforward loop, etc. The project could involve both simulations of circuit dynamics and experimental quantification of circuit dynamics, with comparisons between the two. This would likely involve intensive cloning, measuring using flow cytometer and/or microscope, modeling using stochastic simulation and (possibly) differential equations.

Possible SURF Activities:
* Construct multiple versions of that simple circuit to systematically explore the compositional context space.
* Characterize the mean expression dynamics (using a plate reader) and expression distribution (using flow cytometry or fluorescence microscopy) of each version of the circuit.
* Quantify differences in mean and distributional expression (if any) between the versions of the circuit.
* Build a simulation for each version of the circuit dynamics using a stochastic simulation or differential equations.
* Develop design strategies to attenuate or insulate against the effects of compositional context (in simulation or experimentally)

===References===
* Michael Elowitz, Alan Levine, Eric Siggia, Peter.Swain (2002) Stochastic Gene Expression in a Single Cell, Science 297: 1183-1186.

[ http://www.sciencemag.org/content/297/5584/1183.full ]
* Jason Kelly et al (2009) Measuring the activity of Biobrick promoters using an in vivo reference standard, Journal of Biological Engineering 3:4.

[[http://www.jbioleng.org/content/3/1/4]]

* http://openwetware.org/wiki/TABASCO (highly detailed simular, similar to simulac)
* http://paulsson.med.harvard.edu/Web_pdfs/paulsson2001QRBiophis.pdf
* http://www.nature.com/nbt/journal/v22/n7/abs/nbt988.html (E. Coli analysis of local-bidirectionality layout)
* http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.0020074 (Eukaryote analysis of " ")
* http://ec.asm.org/content/10/1/43.short (for Yeast of " " as well as effect of adding an interspacing sequence/reporter cassette )
* http://www.sciencemag.org/content/307/5717/1965/suppl/DC1 (Noise propagates possibly from adjacency in gene layout)

* http://www.cds.caltech.edu/~murray/wiki/index.php/BE_262_project,_2010

Understanding the Effect of Compositional Context on Biocircuit Performance

2013-01-04T01:31:33Z

Ehyeung: /* References */

'''[[SURF 2013|2013 SURF]] project description'''
* Mentor: Richard Murray
* Co-mentor: Enoch Yeung

Synthetic biocircuits often involve multiple components --- different genes that work together to achieve a desired function. For example, the repressilator employs three distinct genes that are designed to inhibit each other with a cyclic structure to produce oscillation. The toggle switch uses two genes, both repressing each other as they compete to be the dominant active gene. A signal cascade involves a sequence of genes where the arrival of a chemical signal triggers the first gene to activate a second (downstream) gene, which in turn activates a third gene, and so forth. The increasing number of biocircuits fuels hope for the assembly of complex synthetic systems constructed from multiple biocircuits. However, synthetic biologists and engineers are finding that biocircuit context can impact system performance. Biocircuit context can be classified roughly into three categories: compositional context, host context, and environmental context.

The goal of this project is to understand the effect of compositional context on biocircuit performance. Compositional context refers to the effects arising from coupling multiple genes or undesigned interactions between genes located on the same molecule. We will explore how spatial composition, or layout, of different genes can impact performance of one or more biocircuits. To understand how these factors will affect circuit operation, we will take a simple genetic circuit consisting of 2 or more genes and implement it in multiple ways, varying the orientation and relative location of the genes to each other. The dynamic response of the circuit will be measured, including cell-to-cell variability (via flow cytometry or microscopy). The circuit that we test could be a genetic switch, repressilator, incoherent feedforward loop, etc. The project could involve both simulations of circuit dynamics and experimental quantification of circuit dynamics, with comparisons between the two. This would likely involve intensive cloning, measuring using flow cytometer and/or microscope, modeling using stochastic simulation and (possibly) differential equations.

Possible SURF Activities:
* Construct multiple versions of that simple circuit to systematically explore the compositional context space.
* Characterize the mean expression dynamics (using a plate reader) and expression distribution (using flow cytometry or fluorescence microscopy) of each version of the circuit.
* Quantify differences in mean and distributional expression (if any) between the versions of the circuit.
* Build a simulation for each version of the circuit dynamics using a stochastic simulation or differential equations.
* Develop design strategies to attenuate or insulate against the effects of compositional context (in simulation or experimentally)

===References===
* Michael Elowitz, Alan Levine, Eric Siggia, Peter.Swain (2002) Stochastic Gene Expression in a Single Cell, Science 297: 1183-1186.

[[ http://www.sciencemag.org/content/297/5584/1183.full ]]
* Jason Kelly et al (2009) Measuring the activity of Biobrick promoters using an in vivo reference standard, Journal of Biological Engineering 3:4.

[[http://www.jbioleng.org/content/3/1/4]]

* http://openwetware.org/wiki/TABASCO (highly detailed simular, similar to simulac)
* http://paulsson.med.harvard.edu/Web_pdfs/paulsson2001QRBiophis.pdf
* http://www.nature.com/nbt/journal/v22/n7/abs/nbt988.html (E. Coli analysis of local-bidirectionality layout)
* http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.0020074 (Eukaryote analysis of " ")
* http://ec.asm.org/content/10/1/43.short (for Yeast of " " as well as effect of adding an interspacing sequence/reporter cassette )
* http://www.sciencemag.org/content/307/5717/1965/suppl/DC1 (Noise propagates possibly from adjacency in gene layout)

* http://www.cds.caltech.edu/~murray/wiki/index.php/BE_262_project,_2010

Understanding the Effect of Compositional Context on Biocircuit Performance

2013-01-04T01:31:24Z

Ehyeung: /* References */

'''[[SURF 2013|2013 SURF]] project description'''
* Mentor: Richard Murray
* Co-mentor: Enoch Yeung

Synthetic biocircuits often involve multiple components --- different genes that work together to achieve a desired function. For example, the repressilator employs three distinct genes that are designed to inhibit each other with a cyclic structure to produce oscillation. The toggle switch uses two genes, both repressing each other as they compete to be the dominant active gene. A signal cascade involves a sequence of genes where the arrival of a chemical signal triggers the first gene to activate a second (downstream) gene, which in turn activates a third gene, and so forth. The increasing number of biocircuits fuels hope for the assembly of complex synthetic systems constructed from multiple biocircuits. However, synthetic biologists and engineers are finding that biocircuit context can impact system performance. Biocircuit context can be classified roughly into three categories: compositional context, host context, and environmental context.

The goal of this project is to understand the effect of compositional context on biocircuit performance. Compositional context refers to the effects arising from coupling multiple genes or undesigned interactions between genes located on the same molecule. We will explore how spatial composition, or layout, of different genes can impact performance of one or more biocircuits. To understand how these factors will affect circuit operation, we will take a simple genetic circuit consisting of 2 or more genes and implement it in multiple ways, varying the orientation and relative location of the genes to each other. The dynamic response of the circuit will be measured, including cell-to-cell variability (via flow cytometry or microscopy). The circuit that we test could be a genetic switch, repressilator, incoherent feedforward loop, etc. The project could involve both simulations of circuit dynamics and experimental quantification of circuit dynamics, with comparisons between the two. This would likely involve intensive cloning, measuring using flow cytometer and/or microscope, modeling using stochastic simulation and (possibly) differential equations.

Possible SURF Activities:
* Construct multiple versions of that simple circuit to systematically explore the compositional context space.
* Characterize the mean expression dynamics (using a plate reader) and expression distribution (using flow cytometry or fluorescence microscopy) of each version of the circuit.
* Quantify differences in mean and distributional expression (if any) between the versions of the circuit.
* Build a simulation for each version of the circuit dynamics using a stochastic simulation or differential equations.
* Develop design strategies to attenuate or insulate against the effects of compositional context (in simulation or experimentally)

===References===
* Michael Elowitz, Alan Levine, Eric Siggia, Peter.Swain (2002) Stochastic Gene Expression in a Single Cell, Science 297: 1183-1186.

[[ http://www.sciencemag.org/content/297/5584/1183.full ]]
* Jason Kelly et al (2009) Measuring the activity of Biobrick promoters using an in vivo reference standard, Journal of Biological Engineering 3:4.
[[http://www.jbioleng.org/content/3/1/4]]
* http://openwetware.org/wiki/TABASCO (highly detailed simular, similar to simulac)
* http://paulsson.med.harvard.edu/Web_pdfs/paulsson2001QRBiophis.pdf
* http://www.nature.com/nbt/journal/v22/n7/abs/nbt988.html (E. Coli analysis of local-bidirectionality layout)
* http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.0020074 (Eukaryote analysis of " ")
* http://ec.asm.org/content/10/1/43.short (for Yeast of " " as well as effect of adding an interspacing sequence/reporter cassette )
* http://www.sciencemag.org/content/307/5717/1965/suppl/DC1 (Noise propagates possibly from adjacency in gene layout)

* http://www.cds.caltech.edu/~murray/wiki/index.php/BE_262_project,_2010

Understanding the Effect of Compositional Context on Biocircuit Performance

2013-01-04T01:31:08Z

Ehyeung: /* References */

'''[[SURF 2013|2013 SURF]] project description'''
* Mentor: Richard Murray
* Co-mentor: Enoch Yeung

Synthetic biocircuits often involve multiple components --- different genes that work together to achieve a desired function. For example, the repressilator employs three distinct genes that are designed to inhibit each other with a cyclic structure to produce oscillation. The toggle switch uses two genes, both repressing each other as they compete to be the dominant active gene. A signal cascade involves a sequence of genes where the arrival of a chemical signal triggers the first gene to activate a second (downstream) gene, which in turn activates a third gene, and so forth. The increasing number of biocircuits fuels hope for the assembly of complex synthetic systems constructed from multiple biocircuits. However, synthetic biologists and engineers are finding that biocircuit context can impact system performance. Biocircuit context can be classified roughly into three categories: compositional context, host context, and environmental context.

The goal of this project is to understand the effect of compositional context on biocircuit performance. Compositional context refers to the effects arising from coupling multiple genes or undesigned interactions between genes located on the same molecule. We will explore how spatial composition, or layout, of different genes can impact performance of one or more biocircuits. To understand how these factors will affect circuit operation, we will take a simple genetic circuit consisting of 2 or more genes and implement it in multiple ways, varying the orientation and relative location of the genes to each other. The dynamic response of the circuit will be measured, including cell-to-cell variability (via flow cytometry or microscopy). The circuit that we test could be a genetic switch, repressilator, incoherent feedforward loop, etc. The project could involve both simulations of circuit dynamics and experimental quantification of circuit dynamics, with comparisons between the two. This would likely involve intensive cloning, measuring using flow cytometer and/or microscope, modeling using stochastic simulation and (possibly) differential equations.

Possible SURF Activities:
* Construct multiple versions of that simple circuit to systematically explore the compositional context space.
* Characterize the mean expression dynamics (using a plate reader) and expression distribution (using flow cytometry or fluorescence microscopy) of each version of the circuit.
* Quantify differences in mean and distributional expression (if any) between the versions of the circuit.
* Build a simulation for each version of the circuit dynamics using a stochastic simulation or differential equations.
* Develop design strategies to attenuate or insulate against the effects of compositional context (in simulation or experimentally)

===References===
* Michael Elowitz, Alan Levine, Eric Siggia, Peter.Swain (2002) Stochastic Gene Expression in a Single Cell, Science 297: 1183-1186.
[[ http://www.sciencemag.org/content/297/5584/1183.full ]]
* Jason Kelly et al (2009) Measuring the activity of Biobrick promoters using an in vivo reference standard, Journal of Biological Engineering 3:4.
[[http://www.jbioleng.org/content/3/1/4]]
* http://openwetware.org/wiki/TABASCO (highly detailed simular, similar to simulac)
* http://paulsson.med.harvard.edu/Web_pdfs/paulsson2001QRBiophis.pdf
* http://www.nature.com/nbt/journal/v22/n7/abs/nbt988.html (E. Coli analysis of local-bidirectionality layout)
* http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.0020074 (Eukaryote analysis of " ")
* http://ec.asm.org/content/10/1/43.short (for Yeast of " " as well as effect of adding an interspacing sequence/reporter cassette )
* http://www.sciencemag.org/content/307/5717/1965/suppl/DC1 (Noise propagates possibly from adjacency in gene layout)

* http://www.cds.caltech.edu/~murray/wiki/index.php/BE_262_project,_2010

Understanding the Effect of Compositional Context on Biocircuit Performance

2013-01-04T01:30:54Z

Ehyeung:

'''[[SURF 2013|2013 SURF]] project description'''
* Mentor: Richard Murray
* Co-mentor: Enoch Yeung

Synthetic biocircuits often involve multiple components --- different genes that work together to achieve a desired function. For example, the repressilator employs three distinct genes that are designed to inhibit each other with a cyclic structure to produce oscillation. The toggle switch uses two genes, both repressing each other as they compete to be the dominant active gene. A signal cascade involves a sequence of genes where the arrival of a chemical signal triggers the first gene to activate a second (downstream) gene, which in turn activates a third gene, and so forth. The increasing number of biocircuits fuels hope for the assembly of complex synthetic systems constructed from multiple biocircuits. However, synthetic biologists and engineers are finding that biocircuit context can impact system performance. Biocircuit context can be classified roughly into three categories: compositional context, host context, and environmental context.

The goal of this project is to understand the effect of compositional context on biocircuit performance. Compositional context refers to the effects arising from coupling multiple genes or undesigned interactions between genes located on the same molecule. We will explore how spatial composition, or layout, of different genes can impact performance of one or more biocircuits. To understand how these factors will affect circuit operation, we will take a simple genetic circuit consisting of 2 or more genes and implement it in multiple ways, varying the orientation and relative location of the genes to each other. The dynamic response of the circuit will be measured, including cell-to-cell variability (via flow cytometry or microscopy). The circuit that we test could be a genetic switch, repressilator, incoherent feedforward loop, etc. The project could involve both simulations of circuit dynamics and experimental quantification of circuit dynamics, with comparisons between the two. This would likely involve intensive cloning, measuring using flow cytometer and/or microscope, modeling using stochastic simulation and (possibly) differential equations.

Possible SURF Activities:
* Construct multiple versions of that simple circuit to systematically explore the compositional context space.
* Characterize the mean expression dynamics (using a plate reader) and expression distribution (using flow cytometry or fluorescence microscopy) of each version of the circuit.
* Quantify differences in mean and distributional expression (if any) between the versions of the circuit.
* Build a simulation for each version of the circuit dynamics using a stochastic simulation or differential equations.
* Develop design strategies to attenuate or insulate against the effects of compositional context (in simulation or experimentally)

===References===
* Michael Elowitz, Alan Levine, Eric Siggia, Peter.Swain (2002) Stochastic Gene Expression in a Single Cell, Science 297: 1183-1186.
[[http://www.sciencemag.org/content/297/5584/1183.full]]
* Jason Kelly et al (2009) Measuring the activity of Biobrick promoters using an in vivo reference standard, Journal of Biological Engineering 3:4.
[[http://www.jbioleng.org/content/3/1/4]]
* http://openwetware.org/wiki/TABASCO (highly detailed simular, similar to simulac)
* http://paulsson.med.harvard.edu/Web_pdfs/paulsson2001QRBiophis.pdf
* http://www.nature.com/nbt/journal/v22/n7/abs/nbt988.html (E. Coli analysis of local-bidirectionality layout)
* http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.0020074 (Eukaryote analysis of " ")
* http://ec.asm.org/content/10/1/43.short (for Yeast of " " as well as effect of adding an interspacing sequence/reporter cassette )
* http://www.sciencemag.org/content/307/5717/1965/suppl/DC1 (Noise propagates possibly from adjacency in gene layout)

* http://www.cds.caltech.edu/~murray/wiki/index.php/BE_262_project,_2010

Understanding the Effect of Compositional Context on Biocircuit Performance

2013-01-04T01:30:40Z

Ehyeung:

'''[[SURF 2013|2013 SURF]] project description'''
* Mentor: Richard Murray
* Co-mentor: Enoch Yeung

Synthetic biocircuits often involve multiple components --- different genes that work together to achieve a desired function. For example, the repressilator employs three distinct genes that are designed to inhibit each other with a cyclic structure to produce oscillation. The toggle switch uses two genes, both repressing each other as they compete to be the dominant active gene. A signal cascade involves a sequence of genes where the arrival of a chemical signal triggers the first gene to activate a second (downstream) gene, which in turn activates a third gene, and so forth. The increasing number of biocircuits fuels hope for the assembly of complex synthetic systems constructed from multiple biocircuits. However, synthetic biologists and engineers are finding that biocircuit context can impact system performance. Biocircuit context can be classified roughly into three categories: compositional context, host context, and environmental context.

The goal of this project is to understand the effect of compositional context on biocircuit performance. Compositional context refers to the effects arising from coupling multiple genes or undesigned interactions between genes located on the same molecule. We will explore how spatial composition, or layout, of different genes can impact performance of one or more biocircuits. To understand how these factors will affect circuit operation, we will take a simple genetic circuit consisting of 2 or more genes and implement it in multiple ways, varying the orientation and relative location of the genes to each other. The dynamic response of the circuit will be measured, including cell-to-cell variability (via flow cytometry or microscopy). The circuit that we test could be a genetic switch, repressilator, incoherent feedforward loop, etc. The project could involve both simulations of circuit dynamics and experimental quantification of circuit dynamics, with comparisons between the two. This would likely involve intensive cloning, measuring using flow cytometer and/or microscope, modeling using stochastic simulation and (possibly) differential equations.

Possible SURF Activities:
* Construct multiple versions of that simple circuit to systematically explore the compositional context space.
* Characterize the mean expression dynamics (using a plate reader) and expression distribution (using flow cytometry or fluorescence microscopy) of each version of the circuit.
* Quantify differences in mean and distributional expression (if any) between the versions of the circuit.
* Build a simulation for each version of the circuit dynamics using a stochastic simulation or differential equations.
* Develop design strategies to attenuate or insulate against the effects of compositional context (in simulation or experimentally)

===References===
* Michael Elowitz, Alan Levine, Eric Siggia, Peter.Swain (2002) Stochastic Gene Expression in a Single Cell, Science 297: 1183-1186
[[http://www.sciencemag.org/content/297/5584/1183.full]]
* Jason Kelly et al (2009) Measuring the activity of Biobrick promoters using an in vivo reference standard, Journal of Biological Engineering 3:4.
[[http://www.jbioleng.org/content/3/1/4]]
* http://openwetware.org/wiki/TABASCO (highly detailed simular, similar to simulac)
* http://paulsson.med.harvard.edu/Web_pdfs/paulsson2001QRBiophis.pdf
* http://www.nature.com/nbt/journal/v22/n7/abs/nbt988.html (E. Coli analysis of local-bidirectionality layout)
* http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.0020074 (Eukaryote analysis of " ")
* http://ec.asm.org/content/10/1/43.short (for Yeast of " " as well as effect of adding an interspacing sequence/reporter cassette )
* http://www.sciencemag.org/content/307/5717/1965/suppl/DC1 (Noise propagates possibly from adjacency in gene layout)

* http://www.cds.caltech.edu/~murray/wiki/index.php/BE_262_project,_2010

Understanding the Effect of Compositional Context on Biocircuit Performance

2013-01-04T01:30:29Z

Ehyeung:

'''[[SURF 2013|2013 SURF]] project description'''
* Mentor: Richard Murray
* Co-mentor: Enoch Yeung

Synthetic biocircuits often involve multiple components --- different genes that work together to achieve a desired function. For example, the repressilator employs three distinct genes that are designed to inhibit each other with a cyclic structure to produce oscillation. The toggle switch uses two genes, both repressing each other as they compete to be the dominant active gene. A signal cascade involves a sequence of genes where the arrival of a chemical signal triggers the first gene to activate a second (downstream) gene, which in turn activates a third gene, and so forth. The increasing number of biocircuits fuels hope for the assembly of complex synthetic systems constructed from multiple biocircuits. However, synthetic biologists and engineers are finding that biocircuit context can impact system performance. Biocircuit context can be classified roughly into three categories: compositional context, host context, and environmental context.

The goal of this project is to understand the effect of compositional context on biocircuit performance. Compositional context refers to the effects arising from coupling multiple genes or undesigned interactions between genes located on the same molecule. We will explore how spatial composition, or layout, of different genes can impact performance of one or more biocircuits. To understand how these factors will affect circuit operation, we will take a simple genetic circuit consisting of 2 or more genes and implement it in multiple ways, varying the orientation and relative location of the genes to each other. The dynamic response of the circuit will be measured, including cell-to-cell variability (via flow cytometry or microscopy). The circuit that we test could be a genetic switch, repressilator, incoherent feedforward loop, etc. The project could involve both simulations of circuit dynamics and experimental quantification of circuit dynamics, with comparisons between the two. This would likely involve intensive cloning, measuring using flow cytometer and/or microscope, modeling using stochastic simulation and (possibly) differential equations.

Possible SURF Activities:
* Construct multiple versions of that simple circuit to systematically explore the compositional context space.
* Characterize the mean expression dynamics (using a plate reader) and expression distribution (using flow cytometry or fluorescence microscopy) of each version of the circuit.
* Quantify differences in mean and distributional expression (if any) between the versions of the circuit.
* Build a simulation for each version of the circuit dynamics using a stochastic simulation or differential equations.
* Develop design strategies to attenuate or insulate against the effects of compositional context (in simulation or experimentally)

===References===

* Michael Elowitz, Alan Levine, Eric Siggia, Peter.Swain (2002) Stochastic Gene Expression in a Single Cell, Science 297: 1183-1186
[[http://www.sciencemag.org/content/297/5584/1183.full]]
* Jason Kelly et al (2009) Measuring the activity of Biobrick promoters using an in vivo reference standard, Journal of Biological Engineering 3:4.
[[http://www.jbioleng.org/content/3/1/4]]
* http://openwetware.org/wiki/TABASCO (highly detailed simular, similar to simulac)
* http://paulsson.med.harvard.edu/Web_pdfs/paulsson2001QRBiophis.pdf
* http://www.nature.com/nbt/journal/v22/n7/abs/nbt988.html (E. Coli analysis of local-bidirectionality layout)
* http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.0020074 (Eukaryote analysis of " ")
* http://ec.asm.org/content/10/1/43.short (for Yeast of " " as well as effect of adding an interspacing sequence/reporter cassette )
* http://www.sciencemag.org/content/307/5717/1965/suppl/DC1 (Noise propagates possibly from adjacency in gene layout)

* http://www.cds.caltech.edu/~murray/wiki/index.php/BE_262_project,_2010

Understanding the Effect of Compositional Context on Biocircuit Performance

2013-01-04T01:30:03Z

Ehyeung:

'''[[SURF 2013|2013 SURF]] project description'''
* Mentor: Richard Murray
* Co-mentor: Enoch Yeung

Synthetic biocircuits often involve multiple components --- different genes that work together to achieve a desired function. For example, the repressilator employs three distinct genes that are designed to inhibit each other with a cyclic structure to produce oscillation. The toggle switch uses two genes, both repressing each other as they compete to be the dominant active gene. A signal cascade involves a sequence of genes where the arrival of a chemical signal triggers the first gene to activate a second (downstream) gene, which in turn activates a third gene, and so forth. The increasing number of biocircuits fuels hope for the assembly of complex synthetic systems constructed from multiple biocircuits. However, synthetic biologists and engineers are finding that biocircuit context can impact system performance. Biocircuit context can be classified roughly into three categories: compositional context, host context, and environmental context.

The goal of this project is to understand the effect of compositional context on biocircuit performance. Compositional context refers to the effects arising from coupling multiple genes or undesigned interactions between genes located on the same molecule. We will explore how spatial composition, or layout, of different genes can impact performance of one or more biocircuits. To understand how these factors will affect circuit operation, we will take a simple genetic circuit consisting of 2 or more genes and implement it in multiple ways, varying the orientation and relative location of the genes to each other. The dynamic response of the circuit will be measured, including cell-to-cell variability (via flow cytometry or microscopy). The circuit that we test could be a genetic switch, repressilator, incoherent feedforward loop, etc. The project could involve both simulations of circuit dynamics and experimental quantification of circuit dynamics, with comparisons between the two. This would likely involve intensive cloning, measuring using flow cytometer and/or microscope, modeling using stochastic simulation and (possibly) differential equations.

Possible SURF Activities:
* Construct multiple versions of that simple circuit to systematically explore the compositional context space.
* Characterize the mean expression dynamics (using a plate reader) and expression distribution (using flow cytometry or fluorescence microscopy) of each version of the circuit.
* Quantify differences in mean and distributional expression (if any) between the versions of the circuit.
* Build a simulation for each version of the circuit dynamics using a stochastic simulation or differential equations.
* Develop design strategies to attenuate or insulate against the effects of compositional context (in simulation or experimentally)

===References===

# Michael Elowitz, Alan Levine, Eric Siggia, Peter.Swain (2002) Stochastic Gene Expression in a Single Cell, Science 297: 1183-1186
[[http://www.sciencemag.org/content/297/5584/1183.full 1]]
# Jason Kelly et al (2009) Measuring the activity of Biobrick promoters using an in vivo reference standard, Journal of Biological Engineering 3:4.
[[http://www.jbioleng.org/content/3/1/4 2]]
* http://openwetware.org/wiki/TABASCO (highly detailed simular, similar to simulac)
* http://paulsson.med.harvard.edu/Web_pdfs/paulsson2001QRBiophis.pdf
* http://www.nature.com/nbt/journal/v22/n7/abs/nbt988.html (E. Coli analysis of local-bidirectionality layout)
* http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.0020074 (Eukaryote analysis of " ")
* http://ec.asm.org/content/10/1/43.short (for Yeast of " " as well as effect of adding an interspacing sequence/reporter cassette )
* http://www.sciencemag.org/content/307/5717/1965/suppl/DC1 (Noise propagates possibly from adjacency in gene layout)

* http://www.cds.caltech.edu/~murray/wiki/index.php/BE_262_project,_2010

Understanding the Effect of Compositional Context on Biocircuit Performance

2013-01-04T01:19:18Z

Ehyeung:

Synthetic biocircuits often involve multiple components --- different genes that work together to achieve a desired function. For example, the repressilator employs three distinct genes that are designed to inhibit each other with a cyclic structure to produce oscillation. The toggle switch uses two genes, both repressing each other as they compete to be the dominant active gene. A signal cascade involves a sequence of genes where the arrival of a chemical signal triggers the first gene to activate a second (downstream) gene, which in turn activates a third gene, and so forth. The increasing number of biocircuits fuels hope for the assembly of complex synthetic systems constructed from multiple biocircuits. However, synthetic biologists and engineers are finding that biocircuit context can impact system performance. Biocircuit context can be classified roughly into three categories: compositional context, host context, and environmental context.

The goal of this project is to understand the effect of compositional context on biocircuit performance. Compositional context refers to the effects arising from coupling multiple genes or undesigned interactions between genes located on the same molecule. We will explore how spatial composition, or layout, of different genes can impact performance of one or more biocircuits. To understand how these factors will affect circuit operation, we will take a simple genetic circuit consisting of 2 or more genes and implement it in multiple ways, varying the orientation and relative location of the genes to each other. The dynamic response of the circuit will be measured, including cell-to-cell variability (via flow cytometry or microscopy). The circuit that we test could be a genetic switch, repressilator, incoherent feedforward loop, etc. The project could involve both simulations of circuit dynamics and experimental quantification of circuit dynamics, with comparisons between the two. This would likely involve intensive cloning, measuring using flow cytometer and/or microscope, modeling using stochastic simulation and (possibly) differential equations.

Possible SURF Activities:
* Construct multiple versions of that simple circuit to systematically explore the compositional context space.
* Characterize the mean expression dynamics (using a plate reader) and expression distribution (using flow cytometry or fluorescence microscopy) of each version of the circuit.
* Quantify differences in mean and distributional expression (if any) between the versions of the circuit.
* Build a simulation for each version of the circuit dynamics using a stochastic simulation or differential equations.
* Develop design strategies to attenuate or insulate against the effects of compositional context (in simulation or experimentally)

'''References:'''
* http://www.cds.caltech.edu/~murray/wiki/index.php/BE_262_project,_2010
* http://www.sciencemag.org/content/297/5584/1183.full
* http://www.jbioleng.org/content/3/1/4
* http://openwetware.org/wiki/TABASCO (highly detailed simular, similar to simulac)
* http://paulsson.med.harvard.edu/Web_pdfs/paulsson2001QRBiophis.pdf
* http://www.nature.com/nbt/journal/v22/n7/abs/nbt988.html (E. Coli analysis of local-bidirectionality layout)
* http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.0020074 (Eukaryote analysis of " ")
* http://ec.asm.org/content/10/1/43.short (for Yeast of " " as well as effect of adding an interspacing sequence/reporter cassette )
* http://www.sciencemag.org/content/307/5717/1965/suppl/DC1 (Noise propagates possibly from adjacency in gene layout)

Understanding the Effect of Compositional Context on Biocircuit Performance

2013-01-04T01:18:56Z

Ehyeung: Created page with "Synthetic biocircuits often involve multiple components --- different genes that work together to achieve a desired function. For example, the repressilator employs three dis..."