Murray Wiki - User contributions [en]

September 2013 Meetings

2013-08-26T23:03:04Z

Jongmin: /* Wed, 4 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|Open}}
{{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|Open}}
{{agenda item|2:00p|Open}}
{{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|Open}}
{{agenda item|5:30|Open}}
{{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

2013-03-03T04:25:34Z

Jongmin: /* 6 Mar (Wed) */

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|Open}}
{{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|Open}}
{{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|Open}}
{{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|Open}}
{{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|Open}}
{{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

2013-01-26T03:30:52Z

Jongmin: /* 30 Jan (Wed) */

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: Jongmin + Juan
* 14:20: Open
* 14:40: Emzo + Aurelija
|

==== 31 Jan (Thu) ====
* 10:30: Livingston and Zheng
* 10:50: Open
* 11:10: Marcella + Mattias
|}

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: Synthetic logic circuits using RNA aptamers

2013-01-03T03:05:45Z

Jongmin: /* References */

Synthetic biology aims to understand design principles of natural circuits and to achieve novel functions using tools of engineering disciplines. The classic achievements are the construction of a synthetic oscillator and a toggle switch in E. coli. In vitro synthetic biology has emerged as a powerful platform for studying and harnessing biochemical processes independent from complex ancillary processes of cellular environment [1].

Aptamers are promising gene components that can be used for the construction of synthetic gene circuits. A recently found 29-nucleotide aptamer for T7 RNAP showed 50% inhibition of transcription activity at nanomolar concentrations [2], indicating its potential as a tight regulator of power cycling in in vitro circuits.

The project will focus on demonstrating logical molecular circuits using aptamers in vitro. Students are expected to work on transcriptional regulatory circuits [3, 4] and plasmid constructs in cell-free systems --- a particular emphasis will be on developing protocols for aptamer-based regulation. The cell-free expression systems such as a reconstituted expression kit [5] would be tested as a platform to operate such circuits.

----

====References====

1. Adam J Hockenberry and Michael C Jewett, (2012) Synthetic in vitro circuits, Current Opinion in Chemical Biology 16:253-259.
[[http://www.sciencedirect.com/science/article/pii/S1367593112000658]]

2. Shoji Ohuchi, Yusuke Mori, and Yoshikazu Nakamura, (2012) Evolution of an inhibitory RNA aptamer against T7 RNA polymerase, FEBS Open Bio 2:203-207.
[[http://www.sciencedirect.com/science/article/pii/S2211546312000290]]

3. Jongmin Kim and Erik Winfree (2011) Synthetic in vitro transcriptional oscillators, Molecular Systems Biology 7:465.
[[http://www.nature.com/msb/journal/v7/n1/full/msb2010119.html]]

4. Elisa Franco et al., (2011) Timing molecular motion and production with a synthetic transcriptional clock, Proceedings of the National Academy of Sciences USA 108:E784-793.
[[http://www.pnas.org/content/108/40/E784.long]]

5. Yoshihiro Shimizu et al., (2001) Cell-free translation reconstituted with purified components, Nature Biotechnology 19:751-755.
[[http://www.nature.com/nbt/journal/v19/n8/full/nbt0801_751.html]]

SURF 2013: Synthetic logic circuits using RNA aptamers

2013-01-03T03:03:36Z

Jongmin:

Synthetic biology aims to understand design principles of natural circuits and to achieve novel functions using tools of engineering disciplines. The classic achievements are the construction of a synthetic oscillator and a toggle switch in E. coli. In vitro synthetic biology has emerged as a powerful platform for studying and harnessing biochemical processes independent from complex ancillary processes of cellular environment [1].

Aptamers are promising gene components that can be used for the construction of synthetic gene circuits. A recently found 29-nucleotide aptamer for T7 RNAP showed 50% inhibition of transcription activity at nanomolar concentrations [2], indicating its potential as a tight regulator of power cycling in in vitro circuits.

The project will focus on demonstrating logical molecular circuits using aptamers in vitro. Students are expected to work on transcriptional regulatory circuits [3, 4] and plasmid constructs in cell-free systems --- a particular emphasis will be on developing protocols for aptamer-based regulation. The cell-free expression systems such as a reconstituted expression kit [5] would be tested as a platform to operate such circuits.

----

====References====

1. Adam J Hockenberry and Michael C Jewett, (2012) Synthetic in vitro circuits, Current Opinion in Chemical Biology 16:253-259.
[[http://www.sciencedirect.com/science/article/pii/S1367593112000658]]

2. Shoji Ohuchi, Yusuke Mori, and Yoshikazu Nakamura, (2012) Evolution of an inhibitory RNA aptamer against T7 RNA polymerase, FEBS Open Bio 2:203-207.

3. Jongmin Kim and Erik Winfree (2011) Synthetic in vitro transcriptional oscillators, Molecular Systems Biology 7:465.

4. Elisa Franco et al., (2011) Timing molecular motion and production with a synthetic transcriptional clock, Proceedings of the National Academy of Sciences 108:E784-793.

5. Yoshihiro Shimizu et al., (2001) Cell-free translation reconstituted with purified components, Nature Biotechnology 19:751-755.

SURF 2013: Synthetic logic circuits using RNA aptamers

2013-01-03T03:03:07Z

Jongmin:

Synthetic biology aims to understand design principles of natural circuits and to achieve novel functions using tools of engineering disciplines. The classic achievements are the construction of a synthetic oscillator and a toggle switch in E. coli. In vitro synthetic biology has emerged as a powerful platform for studying and harnessing biochemical processes independent from complex ancillary processes of cellular environment [1].

Aptamers are promising gene components that can be used for the construction of synthetic gene circuits. A recently found 29-nucleotide aptamer for T7 RNAP showed 50% inhibition of transcription activity at nanomolar concentrations [2], indicating its potential as a tight regulator of power cycling in in vitro circuits.

The project will focus on demonstrating logical molecular circuits using aptamers in vitro. Students are expected to work on transcriptional regulatory circuits [3, 4] and plasmid constructs in cell-free systems --- a particular emphasis will be on developing protocols for aptamer-based regulation. The cell-free expression systems such as a reconstituted expression kit [5] would be tested as a platform to operate such circuits.

----

====References====

<pubmed> 22676890 </pubmed>

1. Adam J Hockenberry and Michael C Jewett, (2012) Synthetic in vitro circuits, Current Opinion in Chemical Biology 16:253-259.

2. Shoji Ohuchi, Yusuke Mori, and Yoshikazu Nakamura, (2012) Evolution of an inhibitory RNA aptamer against T7 RNA polymerase, FEBS Open Bio 2:203-207.

3. Jongmin Kim and Erik Winfree (2011) Synthetic in vitro transcriptional oscillators, Molecular Systems Biology 7:465.

4. Elisa Franco et al., (2011) Timing molecular motion and production with a synthetic transcriptional clock, Proceedings of the National Academy of Sciences 108:E784-793.

5. Yoshihiro Shimizu et al., (2001) Cell-free translation reconstituted with purified components, Nature Biotechnology 19:751-755.

SURF 2013: Synthetic logic circuits using RNA aptamers

2013-01-03T03:01:41Z

Jongmin: /* References */

Synthetic biology aims to understand design principles of natural circuits and to achieve novel functions using tools of engineering disciplines. The classic achievements are the construction of a synthetic oscillator and a toggle switch in E. coli. In vitro synthetic biology has emerged as a powerful platform for studying and harnessing biochemical processes independent from complex ancillary processes of cellular environment [1].

Aptamers are promising gene components that can be used for the construction of synthetic gene circuits. A recently found 29-nucleotide aptamer for T7 RNAP showed 50% inhibition of transcription activity at nanomolar concentrations [2], indicating its potential as a tight regulator of power cycling in in vitro circuits.

The project will focus on demonstrating logical molecular circuits using aptamers in vitro. Students are expected to work on transcriptional regulatory circuits [3, 4] and plasmid constructs in cell-free systems --- a particular emphasis will be on developing protocols for aptamer-based regulation. The cell-free expression systems such as a reconstituted expression kit [5] would be tested as a platform to operate such circuits.

----

====References====

<pubmed> 22676890 </pubmed>

1. Adam J Hockenberry and Michael C Jewett, (2012) Synthetic in vitro circuits, Current Opinion in Chemical Biology 16:253-259.

2. Shoji Ohuchi, Yusuke Mori, and Yoshikazu Nakamura, (2012) Evolution of an inhibitory RNA aptamer against T7 RNA polymerase, FEBS Open Bio 2:203-207.

3. Jongmin Kim and Erik Winfree (2011) Synthetic in vitro transcriptional oscillators, Molecular Systems Biology 7:465.

4. Elisa Franco et al., (2011) Timing molecular motion and production with a synthetic transcriptional clock, Proceedings of the National Academy of Sciences 108:E784-793.

5. Yoshihiro Shimizu et al., (2001) Cell-free translation reconstituted with purified components, Nature Biotechnology 19:751-755.

SURF 2013: Synthetic logic circuits using RNA aptamers

2013-01-03T03:01:23Z

Jongmin:

Synthetic biology aims to understand design principles of natural circuits and to achieve novel functions using tools of engineering disciplines. The classic achievements are the construction of a synthetic oscillator and a toggle switch in E. coli. In vitro synthetic biology has emerged as a powerful platform for studying and harnessing biochemical processes independent from complex ancillary processes of cellular environment [1].

Aptamers are promising gene components that can be used for the construction of synthetic gene circuits. A recently found 29-nucleotide aptamer for T7 RNAP showed 50% inhibition of transcription activity at nanomolar concentrations [2], indicating its potential as a tight regulator of power cycling in in vitro circuits.

The project will focus on demonstrating logical molecular circuits using aptamers in vitro. Students are expected to work on transcriptional regulatory circuits [3, 4] and plasmid constructs in cell-free systems --- a particular emphasis will be on developing protocols for aptamer-based regulation. The cell-free expression systems such as a reconstituted expression kit [5] would be tested as a platform to operate such circuits.

----

====References====

<pubmed> 22676890 </pubmed>
1. Adam J Hockenberry and Michael C Jewett, (2012) Synthetic in vitro circuits, Current Opinion in Chemical Biology 16:253-259.

2. Shoji Ohuchi, Yusuke Mori, and Yoshikazu Nakamura, (2012) Evolution of an inhibitory RNA aptamer against T7 RNA polymerase, FEBS Open Bio 2:203-207.

3. Jongmin Kim and Erik Winfree (2011) Synthetic in vitro transcriptional oscillators, Molecular Systems Biology 7:465.

4. Elisa Franco et al., (2011) Timing molecular motion and production with a synthetic transcriptional clock, Proceedings of the National Academy of Sciences 108:E784-793.

5. Yoshihiro Shimizu et al., (2001) Cell-free translation reconstituted with purified components, Nature Biotechnology 19:751-755.

SURF 2013: Synthetic logic circuits using RNA aptamers

2013-01-03T02:57:11Z

Jongmin:

Synthetic biology aims to understand design principles of natural circuits and to achieve novel functions using tools of engineering disciplines. The classic achievements are the construction of a synthetic oscillator and a toggle switch in E. coli. In vitro synthetic biology has emerged as a powerful platform for studying and harnessing biochemical processes independent from complex ancillary processes of cellular environment [1].

Aptamers are promising gene components that can be used for the construction of synthetic gene circuits. A recently found 29-nucleotide aptamer for T7 RNAP showed 50% inhibition of transcription activity at nanomolar concentrations [2], indicating its potential as a tight regulator of power cycling in in vitro circuits.

The project will focus on demonstrating logical molecular circuits using aptamers in vitro. Students are expected to work on transcriptional regulatory circuits [3, 4] and plasmid constructs in cell-free systems --- a particular emphasis will be on developing protocols for aptamer-based regulation. The cell-free expression systems such as a reconstituted expression kit [5] would be tested as a platform to operate such circuits.

----

====References====

1. Adam J Hockenberry and Michael C Jewett, (2012) Synthetic in vitro circuits, Current Opinion in Chemical Biology 16:253-259.

2. Shoji Ohuchi, Yusuke Mori, and Yoshikazu Nakamura, (2012) Evolution of an inhibitory RNA aptamer against T7 RNA polymerase, FEBS Open Bio 2:203-207.

3. Jongmin Kim and Erik Winfree (2011) Synthetic in vitro transcriptional oscillators, Molecular Systems Biology 7:465.

4. Elisa Franco et al., (2011) Timing molecular motion and production with a synthetic transcriptional clock, Proceedings of the National Academy of Sciences 108:E784-793.

5. Yoshihiro Shimizu et al., (2001) Cell-free translation reconstituted with purified components, Nature Biotechnology 19:751-755.

SURF 2013: Synthetic logic circuits using RNA aptamers

2013-01-03T02:56:36Z

Jongmin:

Synthetic biology aims to understand design principles of natural circuits and to achieve novel functions using tools of engineering disciplines. The classic achievements are the construction of a synthetic oscillator and a toggle switch in E. coli. In vitro synthetic biology has emerged as a powerful platform for studying and harnessing biochemical processes independent from complex ancillary processes of cellular environment [1].

Aptamers are promising gene components that can be used for the construction of synthetic gene circuits. A recently found 29-nucleotide aptamer for T7 RNAP showed 50% inhibition of transcription activity at nanomolar concentrations [2], indicating its potential as a tight regulator of power cycling in in vitro circuits.

The project will focus on demonstrating logical molecular circuits using aptamers in vitro. Students are expected to work on transcriptional regulatory circuits [3, 4] and plasmid constructs in cell-free systems --- a particular emphasis will be on developing protocols for aptamer-based regulation. The cell-free expression systems such as a reconstituted expression kit [5] would be tested as a platform to operate such circuits.

References

1. Adam J Hockenberry and Michael C Jewett, (2012) Synthetic in vitro circuits, Current Opinion in Chemical Biology 16:253-259.

2. Shoji Ohuchi, Yusuke Mori, and Yoshikazu Nakamura, (2012) Evolution of an inhibitory RNA aptamer against T7 RNA polymerase, FEBS Open Bio 2:203-207.

3. Jongmin Kim and Erik Winfree (2011) Synthetic in vitro transcriptional oscillators, Molecular Systems Biology 7:465.

4. Elisa Franco et al., (2011) Timing molecular motion and production with a synthetic transcriptional clock, Proceedings of the National Academy of Sciences 108:E784-793.

5. Yoshihiro Shimizu et al., (2001) Cell-free translation reconstituted with purified components, Nature Biotechnology 19:751-755.

SURF 2013: Synthetic logic circuits using RNA aptamers

2013-01-03T02:56:11Z

Jongmin: Created page with "Synthetic biology aims to understand design principles of natural circuits and to achieve novel functions using tools of engineering disciplines. The classic achievements are ..."

Synthetic biology aims to understand design principles of natural circuits and to achieve novel functions using tools of engineering disciplines. The classic achievements are the construction of a synthetic oscillator and a toggle switch in E. coli. In vitro synthetic biology has emerged as a powerful platform for studying and harnessing biochemical processes independent from complex ancillary processes of cellular environment [1].
Aptamers are promising gene components that can be used for the construction of synthetic gene circuits. A recently found 29-nucleotide aptamer for T7 RNAP showed 50% inhibition of transcription activity at nanomolar concentrations [2], indicating its potential as a tight regulator of power cycling in in vitro circuits.
The project will focus on demonstrating logical molecular circuits using aptamers in vitro. Students are expected to work on transcriptional regulatory circuits [3, 4] and plasmid constructs in cell-free systems --- a particular emphasis will be on developing protocols for aptamer-based regulation. The cell-free expression systems such as a reconstituted expression kit [5] would be tested as a platform to operate such circuits.
References
1. Adam J Hockenberry and Michael C Jewett, (2012) Synthetic in vitro circuits, Current Opinion in Chemical Biology 16:253-259.
2. Shoji Ohuchi, Yusuke Mori, and Yoshikazu Nakamura, (2012) Evolution of an inhibitory RNA aptamer against T7 RNA polymerase, FEBS Open Bio 2:203-207.
3. Jongmin Kim and Erik Winfree (2011) Synthetic in vitro transcriptional oscillators, Molecular Systems Biology 7:465.
4. Elisa Franco et al., (2011) Timing molecular motion and production with a synthetic transcriptional clock, Proceedings of the National Academy of Sciences 108:E784-793.
5. Yoshihiro Shimizu et al., (2001) Cell-free translation reconstituted with purified components, Nature Biotechnology 19:751-755.

SURF 2013

2013-01-03T02:55:25Z

Jongmin: /* 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'''
|-
| [[The costs and benefits of various designs of biochemical 'decision engines']] || || Dan Siegal-Gaskins ||
|-
| [[Robot Motion Planning with Complex Tasks]] || || Eric Wolff ||
|-
| [[SURF 2013: Experiments with dynamic obstacles and correct-by-construction controllers|Experiments with dynamic obstacles and correct-by-construction controllers]] || || [http://scottman.net Scott C. Livingston] ||
|-
| [[Synthetic logic circuits using RNA aptamers]] || || Jongmin Kim ||
|-
|}

Group Schedule, Fall 2012

2012-09-25T06:12:59Z

Jongmin: /* Week 9: 26-30 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, Summer 2012]]
|}

The schedule for group and subgroup meetings is given below. Everyone should sign up for times to talk in the subgroup meetings. Unless otherwise noted, here are the locations of the meetings:
:{| width=100%
|- valign=top
| width=30% |
* Group meetings - 114 Steele Lab
| width=30% |
* Biocircuits subgroup - 111 Keck
| width=30% |
* NCS subgroup - 110 Steele
|}

{| width=100% border=1
|- valign=top
| width=30% |
=== Week 1: 1-5 Oct ===
'''Biocircuits: 4 Oct (Thu), 10 am - 12 pm'''
* Gita Mahmoudabadi (30 min)
* Research update (15 min)
* Zach/vitrovivo project (15 min)
* Lab updates

'''NCS: 4 Oct (Thu), 4-5:30 pm'''
* Research update (15 min)
* Research update (15 min)
* Research update (15 min)
* Project updates

<hr>
* Richard out of town Tue-Wed
* No group meeting this week

| width=30% |

=== Week 2: 8-12 Oct ===
'''NCS: 10 Oct (Wed), 4:30-6:00 pm'''
* Marcella (15 min)
* Mumu (15 min)
* Research update (15 min)
* Project updates

'''Biocircuits: 11 Oct (Thu), 10 am - 12 pm'''
* Research presentation (30 min)
* Vanessa (15 min)
* Anu (15 min)
* Lab updates

<hr>
* Richard out of town Mon, Tue am, Fri pm
* Aaron Ames visiting on Thu (seminar @ noon)
* No group meeting this week
| width=30% |

=== Week 3: 15-19 Oct ===
* Richard out of town all week
* Biocircuits lab cleanup: 16 Oct (Tue), 10 am - 12 pm

|- valign=top
| width=30% |
=== Week 4: 22-26 Oct ===
'''Biocircuits: 23 Oct (Tue), 10 am - 12 pm'''
* Enoch (30 min)
* Jongmin (15 min)
* Research update (15 min)
* Lab updates

'''NCS: 23 Oct (Tue), 4-5:30 pm'''
* Eric (15 min)
* Scott Livingston (15 min)
* Research update (15 min)
* Project updates

<hr>
* Ram Vasuvian visiting on Mon (seminar @ 11)
* DARPA Living Foundries west coast meeting on Thu (Richard out)
* No group meeting this week

| width=30% |

=== Week 5: 29 Oct - 2 Nov ===
'''NCS: 31 Oct (Wed), 4:30-6:00 pm'''
* Shuo (15 min)
* Research update (15 min)
* Research update (15 min)
* Project updates

'''Biocircuits: 1 Nov (Thu), 10 am - 12 pm'''
* Marcella (30 min)
* Research update (15 min)
* Research update (15 min)
* Lab updates

<hr>
* Richard out of town on Tue
* iGEM World Jamboree, Fri-Mon
* No group meeting this week
| width=30% |

=== Week 6: 5-9 Nov ===
'''Biocircuits: 6 Nov (Tue), 10 am - 12 pm'''
* Anu (30 min)
* Emzo (15 min)
* Research update (15 min)
* Lab updates

'''NCS: 7 Nov (Wed), 4:30-6:00 pm'''
* Fei (15 min)
* Research update (15 min)
* Research update (15 min)
* Project updates

<hr>
* No group meeting this week

|- valign=top
| width=30% |

=== Week 7: 12-16 Nov ===
'''Biocircuits: 15 Nov (Thu), 10 am - 12 pm'''
* Ophelia (30 min)
* Zach (15 min)
* Enoch (15 min)
* Lab updates

'''NCS: 15 Nov (Thu), 4-5:30 pm'''
* Marcella (15 min)
* Mumu (15 min)
* Stephanie (15 min)
* Project updates

<hr>
* No group meeting this week

| width=30% |

=== Week 8: 19-23 Nov ===
* Richard out of town all week
* Biocircuits lab cleanup: 20 Nov (Tue), 10 am - 12 pm
* Thanksgiving break, Thu-Fri
* No group meeting this week

| width=30% |
=== Week 9: 26-30 Nov ===
'''Biocircuits: 27 Nov (Tue), 10 am - 12 pm'''
* Vanessa (30 min)
* Jongmin (15 min)
* Research update (15 min)
* Lab updates

'''NCS: 28 Nov (Wed), 4:30-6:00 pm'''
* Eric (15 min)
* Scott Livingston (15 min)
* Research update (15 min)
* Project updates

<hr>
* DARPA breadboards telecon, Thu @ 9:30 am
* SoCal Control Workshop, Fri (UC San Diego)
* No group meeting this week

|- valign=top
| width=30% |

=== Week 10: 3-7 Dec ===
'''Biocircuits: 4 Dec (Tue), 10 am - 12 pm'''
* Emzo (30 min)
* Marcella (15 min)
* Research update (15 min)
* Lab updates

'''NCS: 5 Dec (Wed), 4:30-6:00 pm'''
* Shuo (15 min)
* Research update (15 min)
* Research update (15 min)
* Project updates

<hr>
* No group meeting this week

| width=30% |

=== Week 11: 10-14 Dec ===
* CDC week, no group meetings
* Biocircuits lab cleanup: 11 Dec (Tue), 10 am - 12 pm

| width=30% |
=== Week 12: 17-21 Dec ===
* Winter break, no group meetings
* Richard around Mon-Thu
|}

Group Schedule, Fall 2012

2012-09-25T06:12:27Z

Jongmin: /* Week 4: 22-26 Oct */

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 2012]]
|}

The schedule for group and subgroup meetings is given below. Everyone should sign up for times to talk in the subgroup meetings. Unless otherwise noted, here are the locations of the meetings:
:{| width=100%
|- valign=top
| width=30% |
* Group meetings - 114 Steele Lab
| width=30% |
* Biocircuits subgroup - 111 Keck
| width=30% |
* NCS subgroup - 110 Steele
|}

{| width=100% border=1
|- valign=top
| width=30% |
=== Week 1: 1-5 Oct ===
'''Biocircuits: 4 Oct (Thu), 10 am - 12 pm'''
* Gita Mahmoudabadi (30 min)
* Research update (15 min)
* Zach/vitrovivo project (15 min)
* Lab updates

'''NCS: 4 Oct (Thu), 4-5:30 pm'''
* Research update (15 min)
* Research update (15 min)
* Research update (15 min)
* Project updates

<hr>
* Richard out of town Tue-Wed
* No group meeting this week

| width=30% |

=== Week 2: 8-12 Oct ===
'''NCS: 10 Oct (Wed), 4:30-6:00 pm'''
* Marcella (15 min)
* Mumu (15 min)
* Research update (15 min)
* Project updates

'''Biocircuits: 11 Oct (Thu), 10 am - 12 pm'''
* Research presentation (30 min)
* Vanessa (15 min)
* Anu (15 min)
* Lab updates

<hr>
* Richard out of town Mon, Tue am, Fri pm
* Aaron Ames visiting on Thu (seminar @ noon)
* No group meeting this week
| width=30% |

=== Week 3: 15-19 Oct ===
* Richard out of town all week
* Biocircuits lab cleanup: 16 Oct (Tue), 10 am - 12 pm

|- valign=top
| width=30% |
=== Week 4: 22-26 Oct ===
'''Biocircuits: 23 Oct (Tue), 10 am - 12 pm'''
* Enoch (30 min)
* Jongmin (15 min)
* Research update (15 min)
* Lab updates

'''NCS: 23 Oct (Tue), 4-5:30 pm'''
* Eric (15 min)
* Scott Livingston (15 min)
* Research update (15 min)
* Project updates

<hr>
* Ram Vasuvian visiting on Mon (seminar @ 11)
* DARPA Living Foundries west coast meeting on Thu (Richard out)
* No group meeting this week

| width=30% |

=== Week 5: 29 Oct - 2 Nov ===
'''NCS: 31 Oct (Wed), 4:30-6:00 pm'''
* Shuo (15 min)
* Research update (15 min)
* Research update (15 min)
* Project updates

'''Biocircuits: 1 Nov (Thu), 10 am - 12 pm'''
* Marcella (30 min)
* Research update (15 min)
* Research update (15 min)
* Lab updates

<hr>
* Richard out of town on Tue
* iGEM World Jamboree, Fri-Mon
* No group meeting this week
| width=30% |

=== Week 6: 5-9 Nov ===
'''Biocircuits: 6 Nov (Tue), 10 am - 12 pm'''
* Anu (30 min)
* Emzo (15 min)
* Research update (15 min)
* Lab updates

'''NCS: 7 Nov (Wed), 4:30-6:00 pm'''
* Fei (15 min)
* Research update (15 min)
* Research update (15 min)
* Project updates

<hr>
* No group meeting this week

|- valign=top
| width=30% |

=== Week 7: 12-16 Nov ===
'''Biocircuits: 15 Nov (Thu), 10 am - 12 pm'''
* Ophelia (30 min)
* Zach (15 min)
* Enoch (15 min)
* Lab updates

'''NCS: 15 Nov (Thu), 4-5:30 pm'''
* Marcella (15 min)
* Mumu (15 min)
* Stephanie (15 min)
* Project updates

<hr>
* No group meeting this week

| width=30% |

=== Week 8: 19-23 Nov ===
* Richard out of town all week
* Biocircuits lab cleanup: 20 Nov (Tue), 10 am - 12 pm
* Thanksgiving break, Thu-Fri
* No group meeting this week

| width=30% |
=== Week 9: 26-30 Nov ===
'''Biocircuits: 27 Nov (Tue), 10 am - 12 pm'''
* Vanessa (30 min)
* Research update (15 min)
* Research update (15 min)
* Lab updates

'''NCS: 28 Nov (Wed), 4:30-6:00 pm'''
* Eric (15 min)
* Scott Livingston (15 min)
* Research update (15 min)
* Project updates

<hr>
* DARPA breadboards telecon, Thu @ 9:30 am
* SoCal Control Workshop, Fri (UC San Diego)
* No group meeting this week

|- valign=top
| width=30% |

=== Week 10: 3-7 Dec ===
'''Biocircuits: 4 Dec (Tue), 10 am - 12 pm'''
* Emzo (30 min)
* Marcella (15 min)
* Research update (15 min)
* Lab updates

'''NCS: 5 Dec (Wed), 4:30-6:00 pm'''
* Shuo (15 min)
* Research update (15 min)
* Research update (15 min)
* Project updates

<hr>
* No group meeting this week

| width=30% |

=== Week 11: 10-14 Dec ===
* CDC week, no group meetings
* Biocircuits lab cleanup: 11 Dec (Tue), 10 am - 12 pm

| width=30% |
=== Week 12: 17-21 Dec ===
* Winter break, no group meetings
* Richard around Mon-Thu
|}

SURF meetings, July 2012

2012-06-27T21:35:34Z

Jongmin: /* Tue, 3 Jul */

Please sign up for one of the slots below: __NOTOC__

{| width=100% border=1
|- valign=top
| width=20% |
==== Mon, 2 Jul ====
* 9:30 am: open
* 9:50 am: open
* 10:10 am: open
* 10:30 am: open
* 10:50 am: Adam (Andrea)
* 11:10 am: Alex (Scott & Pavithra)

| width=20% |

==== Tue, 3 Jul ====
* 9:20 am: open
* 9:40 am: open
 
* 10:50 am: Shaunak(Jongmin)
* 11:10 am: Patrik(Jongmin)

| width=20% |

==== Wed, 4 Jul ====
* Institute holiday

| width=20% |
==== Thu, 5 Jul ====
* No calls

| width=20% |
==== Fri, 6 Jul ====
* 9:20 am: open
* 9:40 am: open
|}

SURF meetings, July 2012

2012-06-27T19:58:36Z

Jongmin: /* Tue, 3 Jul */

Please sign up for one of the slots below: __NOTOC__

{| width=100% border=1
|- valign=top
| width=20% |
==== Mon, 2 Jul ====
* 9:30 am: open
* 9:50 am: open
* 10:10 am: open
* 10:30 am: open
* 10:50 am: Adam (Andrea)
* 11:10 am: open

| width=20% |

==== Tue, 3 Jul ====
* 9:20 am: open
* 9:40 am: open
 
* 11:50 am: Shaunak(Jongmin)
* 11:10 am: Patrik(Jongmin)

| width=20% |
==== Wed, 4 Jul ====
* Institute holiday

| width=20% |
==== Thu, 5 Jul ====
* No calls

| width=20% |
==== Fri, 6 Jul ====
* 9:20 am: open
* 9:40 am: open
|}

Group Schedule, Summer 2012

2012-06-07T23:31:17Z

Jongmin: /* Week 11: 27-31 August */

This page contains information about various upcoming events that are of interest to the group. __NOTOC__
{| width=60%
|- valign=top
| width=50% |
* [http://www.cds.caltech.edu/~murray/calendar.html Richard's calendar (travel)]
| width=50% |
* [[Group Schedule, Spring 2012]]
|}

The schedule for group and subgroup meetings is given below. Everyone should sign up for times to talk in the subgroup meetings.

{| width=100% border=1
|- valign=top
| width=30% |

=== Week 1: 18-22 June ===

'''Biocircuits: 21 Jun (Thu), 10 am - 12 pm'''
* SURF introductions (40 min)
* Ophelia (20-30 min)
* Shaunak K (10-15 min)
* Lab updates

'''Group meeting: 21 Jun (Thu), 12-1'''
* Richard (research overview)

'''NCS/Robotics: 21 Jun (Thu), 4-6 pm'''
* SURF introductions (20 min)
* Eric (15-20 min)
* Clemens (15-20 min)
* Project updates

<hr>
* Richard out of town Mon-Tue
* SURF students start on Tue
| width=30% |

=== Week 2: 25-29 June ===
* American Control Conference (Montreal)
* Richard out of town all week
| width=30% |

=== Week 3: 2-6 July ===
* Richard out of town all week
* Institute holiday on Wed
|- valign=top
|

=== Week 4: 9-13 July ===
'''Biocircuits: 10 Jul (Tue), 10 am - 12 pm'''
* Meeting may shift to Mon, 10a-12p
* Victoria (25-30 min)
* Anu (10-15 min)
* Jongmin (10-15 min)
* Instrument: Microscope/CellASIC
* Lab updates

'''Group meeting: 13 Jul (Fri), 12-1:15'''
* Tim Sullivan?

'''NCS/Robotics: 13 Jul (Fri), 1:15-3 pm'''
* Stephanie (15-20 min)
* Research update (15-20 min)
* Research update (15-20 min)
* Project updates

<hr>
* Richard out of town Tue pm - Thu (Living Foundries PI meeting)
|

=== Week 5: 16-20 July ===
'''Biocircuits: 17 Jul (Tue), 10 am - 12 pm'''
* Anu (30-40 min)
* Zach (10-15 min)
* SURF: Vinay V (10-15 min)
* SURF update (10-15 min)
* Instrument: Computing
* Lab updates

'''NCS/Robotics: 18 Jul (Wed), 4-6 pm'''
* Mumu (15-20 min)
* Research update (15-20 min)
* SURF update (10-15 min)
* SURF update (10-15 min)
* Project updates

'''Group meeting: 19 Jul (Thu), 12-1:15'''
* Chin-Lin Guo (BE)
<hr>
* Shaunak K SURF presentation
|

=== Week 6: 23-27 July ===
'''Biocircuits: 24 Jul (Tue), 10 am - 12 pm'''
* Emzo (30-40 min)
* Enoch (10-15 min)
* SURF update (10-15 min)
* SURF update (10-15 min)
* Instrument: FACSCalibur/Quanta
* Lab updates

'''Group meeting: 25 Jul (Wed), 12-1:15'''
* Open

'''NCS/Robotics: 25 Jul (Wed), 4-6 pm'''
* Pavithra (15-20 min)
* Clemens (10-15 min)
* SURF update (10-15 min)
* SURF update (10-15 min)
* Project updates
<hr>
* Richard out of town Thu-Fri
|- valign=top
|

=== Week 7: 30 July - 3 August ===
'''Biocircuits: 31 Jul (Tue), 12-1:30 pm'''
* Lunch meeting; may shift to Thu
* Research presentation (30-40 min)
* SURF update (10-15 min)
* SURF update (10-15 min)
* Lab updates

'''NCS/Robotics: 1 Aug (Wed), 12-1:30 pm'''
* Lunch meeting; may shift to Thu
* Eric (15-20 min)
* Research update (15-20 min)
* Project updates

<hr>
* KISS workshop; Richard unavailable
|

=== Week 8: 6-10 August ===
'''Biocircuits: 7 Aug (Tue), 10 am - 12 pm'''
* Research presentation (30-40 min)
* Victoria (10-15 min)
* Marcella (10-15 min)
* Instrument: Victor X3/BioTek H1MF
* Lab updates

'''Group meeting: 8 Aug (Wed), 12-1:15'''
* Open

'''NCS/Robotics: 8 Aug (Wed), 4-6 pm'''
* Research update (15-20 min)
* Research update (15-20 min)
* Research update (15-20 min)
* Project updates

|

=== Week 9: 13-17 August ===
* Richard out all week
|- valign=top
|

=== Week 10: 20-24 August ===
'''Biocircuits: 22 Aug (Wed), 10 am - 12 pm'''
* Research presentation [non-MPP] (30-40 min)
* Research presentation [non-MPP] (10-15 min)
* Research update [non-MPP] (10-15 min)
* Instrument: freezers/cold room
* Lab updates

'''NCS/Robotics: 22 Aug (Wed), 4-6 pm'''
* Research update (15-20 min)
* Research update (15-20 min)
* Research update (15-20 min)
* Project updates

'''Group meeting: 23 Aug (Thu), 12-1:15'''
* Lea Goentoro (Bi)
<hr>
* MPP retreat, Sun-Tue
|

=== Week 11: 27-31 August ===
'''Biocircuits: 28 Aug (Tue), 10 am - 12 pm'''
* Jongmin (30-40 min)
* Research update (10-15 min)
* Research update (10-15 min)
* Instruments: Nanodrop/electroporator
* Lab updates

'''NCS/Robotics: 29 Aug (Wed), 4-6 pm'''
* Mumu (15-20 min)
* Research update (15-20 min)
* Research update (15-20 min)
* Project updates

'''Group meeting: 30 Aug (Thu), 12-1:15'''
* Open
<hr>
* Richard out of town on Fri
|

=== Week 12: 3-7 September ===
'''Biocircuits: 4 Sep (Tue), 10 am - 12 pm'''
* Marcella (30-40 min)
* Research update (10-15 min)
* Research update (10-15 min)
* Instrument: gel rigs/gel imager
* Lab updates

'''NCS/Robotics: 5 Sep (Wed), 4-6 pm'''
* Research update (15-20 min)
* Research update (15-20 min)
* Research update (15-20 min)
* Project updates

'''Group meeting: 6 Sep (Thu), 12-1:15'''
* Open
<hr>
* Institute holiday on Mon
|- valign=top
|

=== Week 13: 10-14 September ===
'''Biocircuits: 11 Sep (Tue), 10 am - 12 pm'''
* Zach (30-40 min)
* Research update (10-15 min)
* Research update (10-15 min)
* Instrument: PCR machines/centrifuges
* Lab updates

'''NCS/Robotics: 12 Sep (Wed), 4-6 pm'''
* Research update (15-20 min)
* Research update (15-20 min)
* Research update (15-20 min)
* Project updates

'''Group meeting: 13 Sep (Thu), 12-1:15'''
* Open
<hr>
* Richard out on Fri
|

=== Week 14: 17-21 September ===
* Richard out all week
|
=== Week 15: 24-28 September ===
'''Biocircuits: 25 Sep (Tue), 10 am - 12 pm'''
* Enoch (30-40 min)
* Emzo (10-15 min)
* Research update (10-15 min)
* Lab updates

'''NCS/Robotics: 26 Sep (Wed), 4-6 pm'''
* Stephanie (15-20 min)
* Research update (15-20 min)
* Research update (15-20 min)
* Project updates

'''Group meeting: 26 Sep (Thu), 12-1:15'''
* Open
<hr>
* Richard out on Mon
|}

Group Schedule, Summer 2012

2012-06-07T23:30:51Z

Jongmin: /* Week 4: 9-13 July */

This page contains information about various upcoming events that are of interest to the group. __NOTOC__
{| width=60%
|- valign=top
| width=50% |
* [http://www.cds.caltech.edu/~murray/calendar.html Richard's calendar (travel)]
| width=50% |
* [[Group Schedule, Spring 2012]]
|}

The schedule for group and subgroup meetings is given below. Everyone should sign up for times to talk in the subgroup meetings.

{| width=100% border=1
|- valign=top
| width=30% |

=== Week 1: 18-22 June ===

'''Biocircuits: 21 Jun (Thu), 10 am - 12 pm'''
* SURF introductions (40 min)
* Ophelia (20-30 min)
* Shaunak K (10-15 min)
* Lab updates

'''Group meeting: 21 Jun (Thu), 12-1'''
* Richard (research overview)

'''NCS/Robotics: 21 Jun (Thu), 4-6 pm'''
* SURF introductions (20 min)
* Eric (15-20 min)
* Clemens (15-20 min)
* Project updates

<hr>
* Richard out of town Mon-Tue
* SURF students start on Tue
| width=30% |

=== Week 2: 25-29 June ===
* American Control Conference (Montreal)
* Richard out of town all week
| width=30% |

=== Week 3: 2-6 July ===
* Richard out of town all week
* Institute holiday on Wed
|- valign=top
|

=== Week 4: 9-13 July ===
'''Biocircuits: 10 Jul (Tue), 10 am - 12 pm'''
* Meeting may shift to Mon, 10a-12p
* Victoria (25-30 min)
* Anu (10-15 min)
* Jongmin (10-15 min)
* Instrument: Microscope/CellASIC
* Lab updates

'''Group meeting: 13 Jul (Fri), 12-1:15'''
* Tim Sullivan?

'''NCS/Robotics: 13 Jul (Fri), 1:15-3 pm'''
* Stephanie (15-20 min)
* Research update (15-20 min)
* Research update (15-20 min)
* Project updates

<hr>
* Richard out of town Tue pm - Thu (Living Foundries PI meeting)
|

=== Week 5: 16-20 July ===
'''Biocircuits: 17 Jul (Tue), 10 am - 12 pm'''
* Anu (30-40 min)
* Zach (10-15 min)
* SURF: Vinay V (10-15 min)
* SURF update (10-15 min)
* Instrument: Computing
* Lab updates

'''NCS/Robotics: 18 Jul (Wed), 4-6 pm'''
* Mumu (15-20 min)
* Research update (15-20 min)
* SURF update (10-15 min)
* SURF update (10-15 min)
* Project updates

'''Group meeting: 19 Jul (Thu), 12-1:15'''
* Chin-Lin Guo (BE)
<hr>
* Shaunak K SURF presentation
|

=== Week 6: 23-27 July ===
'''Biocircuits: 24 Jul (Tue), 10 am - 12 pm'''
* Emzo (30-40 min)
* Enoch (10-15 min)
* SURF update (10-15 min)
* SURF update (10-15 min)
* Instrument: FACSCalibur/Quanta
* Lab updates

'''Group meeting: 25 Jul (Wed), 12-1:15'''
* Open

'''NCS/Robotics: 25 Jul (Wed), 4-6 pm'''
* Pavithra (15-20 min)
* Clemens (10-15 min)
* SURF update (10-15 min)
* SURF update (10-15 min)
* Project updates
<hr>
* Richard out of town Thu-Fri
|- valign=top
|

=== Week 7: 30 July - 3 August ===
'''Biocircuits: 31 Jul (Tue), 12-1:30 pm'''
* Lunch meeting; may shift to Thu
* Research presentation (30-40 min)
* SURF update (10-15 min)
* SURF update (10-15 min)
* Lab updates

'''NCS/Robotics: 1 Aug (Wed), 12-1:30 pm'''
* Lunch meeting; may shift to Thu
* Eric (15-20 min)
* Research update (15-20 min)
* Project updates

<hr>
* KISS workshop; Richard unavailable
|

=== Week 8: 6-10 August ===
'''Biocircuits: 7 Aug (Tue), 10 am - 12 pm'''
* Research presentation (30-40 min)
* Victoria (10-15 min)
* Marcella (10-15 min)
* Instrument: Victor X3/BioTek H1MF
* Lab updates

'''Group meeting: 8 Aug (Wed), 12-1:15'''
* Open

'''NCS/Robotics: 8 Aug (Wed), 4-6 pm'''
* Research update (15-20 min)
* Research update (15-20 min)
* Research update (15-20 min)
* Project updates

|

=== Week 9: 13-17 August ===
* Richard out all week
|- valign=top
|

=== Week 10: 20-24 August ===
'''Biocircuits: 22 Aug (Wed), 10 am - 12 pm'''
* Research presentation [non-MPP] (30-40 min)
* Research presentation [non-MPP] (10-15 min)
* Research update [non-MPP] (10-15 min)
* Instrument: freezers/cold room
* Lab updates

'''NCS/Robotics: 22 Aug (Wed), 4-6 pm'''
* Research update (15-20 min)
* Research update (15-20 min)
* Research update (15-20 min)
* Project updates

'''Group meeting: 23 Aug (Thu), 12-1:15'''
* Lea Goentoro (Bi)
<hr>
* MPP retreat, Sun-Tue
|

=== Week 11: 27-31 August ===
'''Biocircuits: 28 Aug (Tue), 10 am - 12 pm'''
* Research presentation (30-40 min)
* Research update (10-15 min)
* Research update (10-15 min)
* Instruments: Nanodrop/electroporator
* Lab updates

'''NCS/Robotics: 29 Aug (Wed), 4-6 pm'''
* Mumu (15-20 min)
* Research update (15-20 min)
* Research update (15-20 min)
* Project updates

'''Group meeting: 30 Aug (Thu), 12-1:15'''
* Open
<hr>
* Richard out of town on Fri
|

=== Week 12: 3-7 September ===
'''Biocircuits: 4 Sep (Tue), 10 am - 12 pm'''
* Marcella (30-40 min)
* Research update (10-15 min)
* Research update (10-15 min)
* Instrument: gel rigs/gel imager
* Lab updates

'''NCS/Robotics: 5 Sep (Wed), 4-6 pm'''
* Research update (15-20 min)
* Research update (15-20 min)
* Research update (15-20 min)
* Project updates

'''Group meeting: 6 Sep (Thu), 12-1:15'''
* Open
<hr>
* Institute holiday on Mon
|- valign=top
|

=== Week 13: 10-14 September ===
'''Biocircuits: 11 Sep (Tue), 10 am - 12 pm'''
* Zach (30-40 min)
* Research update (10-15 min)
* Research update (10-15 min)
* Instrument: PCR machines/centrifuges
* Lab updates

'''NCS/Robotics: 12 Sep (Wed), 4-6 pm'''
* Research update (15-20 min)
* Research update (15-20 min)
* Research update (15-20 min)
* Project updates

'''Group meeting: 13 Sep (Thu), 12-1:15'''
* Open
<hr>
* Richard out on Fri
|

=== Week 14: 17-21 September ===
* Richard out all week
|
=== Week 15: 24-28 September ===
'''Biocircuits: 25 Sep (Tue), 10 am - 12 pm'''
* Enoch (30-40 min)
* Emzo (10-15 min)
* Research update (10-15 min)
* Lab updates

'''NCS/Robotics: 26 Sep (Wed), 4-6 pm'''
* Stephanie (15-20 min)
* Research update (15-20 min)
* Research update (15-20 min)
* Project updates

'''Group meeting: 26 Sep (Thu), 12-1:15'''
* Open
<hr>
* Richard out on Mon
|}

Group Schedule, Spring 2012

2012-03-21T16:23:08Z

Jongmin: /* Week 1: 2-6 Apr */

Group Schedule, Spring 2012

2012-03-21T16:22:41Z

Jongmin: /* Week 8: 21-25 May */

Feb/Mar 2012 Meetings

2012-02-20T22:57:12Z

Jongmin: /* Tue, 6 Mar */

I would like to meet with everyone sometime in the last week of Feb/first week of March. Please sign up for a time below (note that the slots are different lengths). __NOTOC__

{| width=100% border=1
|- valign=top
| width=50% |
{| width=100% cellspacing=0 cellpadding=0
|- bgcolor=yellow
|
 '''In Santa Barbara''' (Vanessa, Ophelia, Dan, Emzo)
==== Tue, 28 Feb ====
* 4:00p - Dan (60m)
* 5:00p - Ophelia (60m)

==== Wed, 29 Feb ====
* 10:00a - Vanessa (60m)
* 3:30p - Open (60m)
|}
<hr>

==== Thu, 1 Mar ====
* 3:00p - Biocircuits subgroup (Dan, Zach, Ophelia)
* 5:00p - Stephanie (45m)
* 5:45p - Necmiye (45m)
* 6:30p - Open (60m)
<hr>

==== Fri, 2 Mar ====
* 9:00a - Open (60m)
* 10:00a - Eugene Lavretsky (75m)
* 11:15a - Hold, Eugene (45m)
:
* 12:00p - Group meeting
* 1:15p - NCS subgroup (Mumu, Pavithra)
* 3:00p - Pavithra (45m)
* 3:45p - Andrea (60m)
* 4:45p - Shaunak (45m)
* 5:30p - Pete (60m)
| width=50% |

==== Sun, 4 Mar ====
* 3:30p - Open (60m)
* 4:30p - Open (60m)
* 5:30p - Open (60m)
<hr>

==== Mon, 5 Mar ====
* 9:00a - Open (60m)
* 10:00a - BE 150
* 11:00a - Ufuk (45m)
* 11:45a - Jun (45m)
:
* 1:00p - Scott Livingston (60m)
* 2:00p - Mumu (60m)
* 3:00p - Robotics subgroup (Pete, Andrea)
* 4:30p - Enoch (60m)
* 5:30p - Shuo (60m)
* 6:30p - Marcella (60m)
<hr>

==== Tue, 6 Mar ====
* 9:00a - Jongmin (60m)
* 10:00a -Eric (60m)
* 11:00a - Anu (60m)

* 2:00p - CDS 90 presentations
* 3:00p - Biocircuits subgroup (Enoch, Vanessa, Victoria)
* 5:00p - iGEM
|}

Gabor Orosz, Feb 2012

2012-02-16T17:02:48Z

Jongmin: /* 21 Feb (Tue) */

Gabor Orosz, an Assistant Professor at U. Michigan, will be visiting Caltech on 21-22 Feb (Tue-Wed).

=== Schedule ===

==== 21 Feb (Tue) ====

{{agenda begin}}
{{agenda item|~10:00a|Marcella Gomez, meet in Steele library}}
{{agenda item|11:00p|Seminar: Marta Kwiatkowska}}
{{agenda item|12:00p|Lunchtime seminar: Gabor Orosz}}
{{agenda item|1:00p|Richard and Marcella (109 Steele)}}
{{agenda item|2:00p|Jongmin}}
{{agenda item|3:00p|Biocircuits subgroup}}
{{agenda item|5:00p|Paul Nguyen}}
{{agenda end}}

==== 22 Feb (Wed) ====

{{agenda begin}}
{{agenda item|9:30a|Open}}
{{agenda item|10:15a|Open}}
{{agenda item|11:00p|Seminar: Marta Kwiatkowska}}
{{agenda item|12:00p|Lunch}}
{{agenda item|1:30p|Necmiye}}
{{agenda item|2:15p|Marcella}}
{{agenda item|3:00p|CDS tea, Annenberg Loung}}
{{agenda item|3:45p|Open}}
{{agenda item|4:30p|Jun Liu}}
{{agenda end}}

Group Schedule, Winter 2012

2012-01-21T16:26:05Z

Jongmin: /* Week 8: 20-24 Feb */

This page contains information about various upcoming events that are of interest to the group. __NOTOC__
{| width=60%
|- valign=top
| width=50% |
* [http://www.cds.caltech.edu/~murray/calendar.html Richard's calendar (travel)]
| width=50% |
* [[Group Schedule, Fall 2011]]
|}

The schedule for group and subgroup meetings is given below. Everyone should sign up for times to talk in the subgroup meetings.


{| width=100% border=1
|- valign=top
| width=30% |

=== Week 1: 4-6 Jan ===
'''NCS: 4 Jan (Wed), 4-6 pm'''
* Jun Liu (15-20 min)
* Joseph Meyerowitz (15-20 min)
* Project updates
'''Group meeting: 5 Jan (Thu), 12-1:15'''
* Ophelia
'''Biocircuits: 5 Jan (Thu), 3-5 pm'''
* Vanessa (10-15 min)
* Jongmin (10-15 min)
* Research update (10-15 min)
* Lab organization, round II
<hr>
Academic holiday, 2-3 Jan 
CDS quals, 6 Jan (RMM busy all day)
| width=30% |

=== Week 2: 9-13 Jan ===
'''Robotics: 12 Jan (Thu), 1-3 pm'''
* Shuo (15-20 min)
* Scott Livingston (15-20 min)
* Short research updates (5 min each)
'''Biocircuits: 12 Jan (Thu), 3-5 pm'''
* Marcella (30-40 min)
* Safety briefing @ 4:00 pm (30-40 min)
* Lab updates
'''Group meeting: 13 Jan (Fri), 12-1:15 pm'''
* Domitilla Del Vecchio (MIT)
| width=30% |

=== Week 3: 16-20 Jan ===
'''Biocircuits: 17 Jan (Tue), 3-5 pm'''
* Anu (10-15 min)
* Enoch (10-15 min)
* Shaunak (10-15 min)
* Lab updates
* Note time shift in day (to "regular" day)
'''NCS: 18 Jan (Wed), 4-6 pm'''
* Eric (15-20 min)
* Mumu (15-20 min)
* Project updates
'''Group meeting: 19 Jan (Thu), 12-1:15'''
* Naira Hovakimyan (UIUC)
<hr>
UTRC visit on 17 Jan (Tue)
|- valign=top
|

=== Week 4: 23-27 Jan ===
'''Group meeting: 23 Jan (Mon), 12-1:15'''
* Necmiye
'''Robotics: 24 Jan (Tue), 1-3 pm'''
* Stephanie (15-20 min)
* Pete (15-20 min)
* Short research updates (5 min each)
'''Biocircuits: 24 Jan (Tue), 3-5 pm'''
* Ophelia (30-40 min)
* Emzo (10-15 min)
* Dan (10-15 min)
* Lab updates
|

=== Week 5: 30 Jan - 3 Feb ===
'''Biocircuits: 31 Jan (Tue), 3-5 pm'''
* Elisa (30-40 min)
* Nikki(10-15 min)
* Zach (10-15 min)
* Lab updates
'''NCS: 1 Feb (Wed), 4-6 pm'''
* Marcella (15-20 min)
* Ufuk (15-20 min)
* Project updates
'''Group meeting: 2 Feb (Thu), 12-1:15'''
* Ufuk
|

=== Week 6: 6 Feb - 10 Feb ===
'''Biocircuits: 7 Feb (Tue), 3-5 pm'''
* Vanessa (30-40 min)
* Paul (10-15 min)
* Victoria (10-15 min)
* Lab updates
'''Group meeting: 8 Feb (Wed), 12-1:15'''
* Andrea
'''Robotics: 8 Feb (Wed), 4-6 pm'''
* Scott Livingston (15-20 min)
* Andrea (15-20 min)
* Short research updates (5 min each)

|- valign=top
|

=== Week 7: 13-17 Feb ===
'''NCS: 15 Feb (Wed), 4-6 pm'''
* Necmiye (15-20 min)
* Scott Livingston (15-20 min)
* Project updates
'''Group meeting: 16 Feb (Thu), 12-1:15'''
* Chris Kempes
'''Biocircuits: 16 Feb (Thu), 3-5 pm'''
* Anu (30-40 min)
* Marcella (10-15 min)
* Research update (10-15 min)
* Lab updates
* Note change in day
|

=== Week 8: 20-24 Feb ===
'''Biocircuits: 21 Feb (Tue), 3-5 pm'''
* Emzo (30-40 min)
* Jongmin (10-15 min)
* Research update (10-15 min)
* Lab updates
'''Robotics: 22 Feb (Wed), 4-6 pm'''
* Shuo (15-20 min)
* Eric (15-20 min)
* Short research updates (5 min each)
'''Group meeting: 23 Feb (Thu), 12-1:15'''
* Jongmin
|

=== Week 9: 27 Feb - 2 Mar ===
'''Biocircuits: 28 Feb (Tue), 3-5 pm'''
* Dan (30-40 min)
* Research update (10-15 min)
* Research update (10-15 min)
* Lab updates
* Will probably shift to 2 Mar, 3-5 pm
'''NCS: 29 Feb (Wed), 4-6 pm'''
* Mumu (15-20 min)
* Pavithra (15-20 min)
* Project updates
* Will probably shift to 2 Mar, 1-3 pm
'''Group meeting: 2 Mar (Fri), 12-1:15'''
* Shaunak
|- valign=top
|

=== Week 10: 5-9 Mar ===
'''Biocircuits: 6 Mar (Tue), 3-5 pm'''
* Enoch (30-40 min)
* Vanessa (10-15 min)
* Research update (10-15 min)
* Lab updates
'''Robotics: 7 Mar (Wed), 4-6 pm'''
* Pete (15-20 min)
* Andrea (15-20 min)
* Short research updates (5 min each)
'''Group meeting: 9 Mar (Fri), 12-1:15'''
* Hold: possible job talk
|

=== Week 11: 12-16 Mar ===
Finals week; Richard out of town
|
=== Week 12: 19-23 Mar ===
Spring break; Richard out of town
|}

Group Schedule, Winter 2012

2012-01-21T16:25:51Z

Jongmin: /* Week 5: 30 Jan - 3 Feb */

This page contains information about various upcoming events that are of interest to the group. __NOTOC__
{| width=60%
|- valign=top
| width=50% |
* [http://www.cds.caltech.edu/~murray/calendar.html Richard's calendar (travel)]
| width=50% |
* [[Group Schedule, Fall 2011]]
|}

The schedule for group and subgroup meetings is given below. Everyone should sign up for times to talk in the subgroup meetings.


{| width=100% border=1
|- valign=top
| width=30% |

=== Week 1: 4-6 Jan ===
'''NCS: 4 Jan (Wed), 4-6 pm'''
* Jun Liu (15-20 min)
* Joseph Meyerowitz (15-20 min)
* Project updates
'''Group meeting: 5 Jan (Thu), 12-1:15'''
* Ophelia
'''Biocircuits: 5 Jan (Thu), 3-5 pm'''
* Vanessa (10-15 min)
* Jongmin (10-15 min)
* Research update (10-15 min)
* Lab organization, round II
<hr>
Academic holiday, 2-3 Jan 
CDS quals, 6 Jan (RMM busy all day)
| width=30% |

=== Week 2: 9-13 Jan ===
'''Robotics: 12 Jan (Thu), 1-3 pm'''
* Shuo (15-20 min)
* Scott Livingston (15-20 min)
* Short research updates (5 min each)
'''Biocircuits: 12 Jan (Thu), 3-5 pm'''
* Marcella (30-40 min)
* Safety briefing @ 4:00 pm (30-40 min)
* Lab updates
'''Group meeting: 13 Jan (Fri), 12-1:15 pm'''
* Domitilla Del Vecchio (MIT)
| width=30% |

=== Week 3: 16-20 Jan ===
'''Biocircuits: 17 Jan (Tue), 3-5 pm'''
* Anu (10-15 min)
* Enoch (10-15 min)
* Shaunak (10-15 min)
* Lab updates
* Note time shift in day (to "regular" day)
'''NCS: 18 Jan (Wed), 4-6 pm'''
* Eric (15-20 min)
* Mumu (15-20 min)
* Project updates
'''Group meeting: 19 Jan (Thu), 12-1:15'''
* Naira Hovakimyan (UIUC)
<hr>
UTRC visit on 17 Jan (Tue)
|- valign=top
|

=== Week 4: 23-27 Jan ===
'''Group meeting: 23 Jan (Mon), 12-1:15'''
* Necmiye
'''Robotics: 24 Jan (Tue), 1-3 pm'''
* Stephanie (15-20 min)
* Pete (15-20 min)
* Short research updates (5 min each)
'''Biocircuits: 24 Jan (Tue), 3-5 pm'''
* Ophelia (30-40 min)
* Emzo (10-15 min)
* Dan (10-15 min)
* Lab updates
|

=== Week 5: 30 Jan - 3 Feb ===
'''Biocircuits: 31 Jan (Tue), 3-5 pm'''
* Elisa (30-40 min)
* Nikki(10-15 min)
* Zach (10-15 min)
* Lab updates
'''NCS: 1 Feb (Wed), 4-6 pm'''
* Marcella (15-20 min)
* Ufuk (15-20 min)
* Project updates
'''Group meeting: 2 Feb (Thu), 12-1:15'''
* Ufuk
|

=== Week 6: 6 Feb - 10 Feb ===
'''Biocircuits: 7 Feb (Tue), 3-5 pm'''
* Vanessa (30-40 min)
* Paul (10-15 min)
* Victoria (10-15 min)
* Lab updates
'''Group meeting: 8 Feb (Wed), 12-1:15'''
* Andrea
'''Robotics: 8 Feb (Wed), 4-6 pm'''
* Scott Livingston (15-20 min)
* Andrea (15-20 min)
* Short research updates (5 min each)

|- valign=top
|

=== Week 7: 13-17 Feb ===
'''NCS: 15 Feb (Wed), 4-6 pm'''
* Necmiye (15-20 min)
* Scott Livingston (15-20 min)
* Project updates
'''Group meeting: 16 Feb (Thu), 12-1:15'''
* Chris Kempes
'''Biocircuits: 16 Feb (Thu), 3-5 pm'''
* Anu (30-40 min)
* Marcella (10-15 min)
* Research update (10-15 min)
* Lab updates
* Note change in day
|

=== Week 8: 20-24 Feb ===
'''Biocircuits: 21 Feb (Tue), 3-5 pm'''
* Emzo (30-40 min)
* Jongmin (10-15 min)
* Research update (10-15 min)
* Lab updates
'''Robotics: 22 Feb (Wed), 4-6 pm'''
* Shuo (15-20 min)
* Eric (15-20 min)
* Short research updates (5 min each)
'''Group meeting: 23 Feb (Thu), 12-1:15'''
* Hold: possible job talk
|

=== Week 9: 27 Feb - 2 Mar ===
'''Biocircuits: 28 Feb (Tue), 3-5 pm'''
* Dan (30-40 min)
* Research update (10-15 min)
* Research update (10-15 min)
* Lab updates
* Will probably shift to 2 Mar, 3-5 pm
'''NCS: 29 Feb (Wed), 4-6 pm'''
* Mumu (15-20 min)
* Pavithra (15-20 min)
* Project updates
* Will probably shift to 2 Mar, 1-3 pm
'''Group meeting: 2 Mar (Fri), 12-1:15'''
* Shaunak
|- valign=top
|

=== Week 10: 5-9 Mar ===
'''Biocircuits: 6 Mar (Tue), 3-5 pm'''
* Enoch (30-40 min)
* Vanessa (10-15 min)
* Research update (10-15 min)
* Lab updates
'''Robotics: 7 Mar (Wed), 4-6 pm'''
* Pete (15-20 min)
* Andrea (15-20 min)
* Short research updates (5 min each)
'''Group meeting: 9 Mar (Fri), 12-1:15'''
* Hold: possible job talk
|

=== Week 11: 12-16 Mar ===
Finals week; Richard out of town
|
=== Week 12: 19-23 Mar ===
Spring break; Richard out of town
|}

Group Schedule, Winter 2012

2011-12-19T08:37:34Z

Jongmin: /* Week 2: 9-13 Jan */

This page contains information about various upcoming events that are of interest to the group. __NOTOC__
{| width=60%
|- valign=top
| width=50% |
* [http://www.cds.caltech.edu/~murray/calendar.html Richard's calendar (travel)]
| width=50% |
* [[Group Schedule, Fall 2011]]
|}

The schedule for group and subgroup meetings is given below. Everyone should sign up for times to talk in the subgroup meetings.


==== Directions: ====
* '''Biocircuits (Tue or Thu, 3-5 pm)''': graduate students should give 1 longer presentation per term + 1-2 additional research updates; postdocs, undergrads should give 1-2 research updates.
* '''NCS (Wed, 4-6 pm)''': grad students should speak 2 times per term for 15-20 min (+ discussion), postdocs and undergrads at least once
* '''Robotics (Wed, 4-6 pm)''': grad students and postdocs should speak 2 times per term for 15-20 min (+ discussion), undergrads at least once; will also do ad hoc updates
* '''Group meeting talks (WThF, 12-1:15)''': postdocs and senior grad students (G4+) should feel free to sign up for a group meeting talk (biocircuit grad students: this can be in place of longer subgroup talk)


<center>
'''Please sign up for at least one presentation in the first six weeks of the term.'''
</center>

Note that some of the meetings might need to shift, as noted; only sign up for those slots if you can make both times listed
 

{| width=100% border=1
|- valign=top
| width=30% |

=== Week 1: 4-6 Jan ===
'''NCS: 4 Jan (Wed), 4-6 pm'''
* Jun Liu (15-20 min)
* Joseph Meyerowitz (15-20 min)
* Project updates
'''Group meeting: 5 Jan (Thu), 12-1:15'''
* Ophelia
'''Biocircuits: 5 Jan (Thu), 3-5 pm'''
* Safety briefing (30-40 min)
* Vanessa (10-15 min)
* Jongmin (10-15 min)
* Lab updates
<hr>
Academic holiday, 2-3 Jan 
CDS quals, 6 Jan (RMM busy all day)
| width=30% |

=== Week 2: 9-13 Jan ===
'''Robotics: 11 Jan (Wed), 4-6 pm'''
* Shuo (15-20 min)
* Scott Livingston (15-20 min)
* Short research updates (5 min each)
* Might shift to Fri, 1-3 pm
'''Biocircuits: 12 Jan (Thu), 3-5 pm'''
* Marcella (30-40 min)
* Research update (10-15 min)
* Research update (10-15 min)
* Lab updates
'''Group meeting: 13 Jan (Fri), 12-1:15 pm'''
* Domitilla Del Vecchio (MIT)
| width=30% |

=== Week 3: 16-20 Jan ===
'''Biocircuits: 17 Jan (Tue), 2-4 pm'''
* Research presentation (30-40 min)
* Dan (10-15 min)
* Shaunak (10-15 min)
* Lab updates
* Note time shift in day (to "regular" day)
'''NCS: 18 Jan (Wed), 4-6 pm'''
* Eric (15-20 min)
* Mumu (15-20 min)
* Project updates
'''Group meeting: 19 Jan (Thu), 12-1:15'''
* Naira Hovakimyan (UIUC)
|- valign=top
|

=== Week 4: 23-27 Jan ===
'''Group meeting: 23 Jan (Mon), 12-1:15'''
* Necmiye
'''Robotics: 24 Jan (Tue), 1-3 pm'''
* Stephanie (15-20 min)
* Pete (15-20 min)
* Short research updates (5 min each)
'''Biocircuits: 24 Jan (Tue), 3-5 pm'''
* Ophelia (30-40 min)
* Emzo (10-15 min)
* Enoch (10-15 min)
* Lab updates
|

=== Week 5: 30 Jan - 3 Feb ===
'''Biocircuits: 31 Jan (Tue), 3-5 pm'''
* Research Presentation (30-40 min)
* Nikki(10-15 min)
* Zach (10-15 min)
* Lab updates
'''NCS: 1 Feb (Wed), 4-6 pm'''
* Marcella (15-20 min)
* Ufuk (15-20 min)
* Project updates
'''Group meeting: 2 Feb (Thu), 12-1:15'''
* Jongmin
|

=== Week 6: 6 Feb - 10 Feb ===
'''Biocircuits: 7 Feb (Tue), 3-5 pm'''
* Vanessa (30-40 min)
* Paul (10-15 min)
* Victoria (10-15 min)
* Lab updates
'''Group meeting: 8 Feb (Wed), 12-1:15'''
* Andrea
'''Robotics: 8 Feb (Wed), 4-6 pm'''
* Scott Livingston (15-20 min)
* Andrea (15-20 min)
* Short research updates (5 min each)

|- valign=top
|

=== Week 7: 13-17 Feb ===
'''NCS: 15 Feb (Wed), 4-6 pm'''
* Necmiye (15-20 min)
* Scott Livingston (15-20 min)
* Project updates
'''Group meeting: 16 Feb (Thu), 12-1:15'''
* Chris Kempes
'''Biocircuits: 16 Feb (Thu), 3-5 pm'''
* Research presentation (30-40 min)
* Marcella (10-15 min)
* Research update (10-15 min)
* Lab updates
* Note change in day
|

=== Week 8: 20-24 Feb ===
'''Biocircuits: 21 Feb (Tue), 3-5 pm'''
* Emzo (30-40 min)
* Jongmin (10-15 min)
* Research update (10-15 min)
* Lab updates
'''Robotics: 22 Feb (Wed), 4-6 pm'''
* Shuo (15-20 min)
* Eric (15-20 min)
* Short research updates (5 min each)
* Meeting may shift to 10 Feb (Fri)
'''Group meeting: 23 Feb (Thu), 12-1:15'''
* Hold: possible job talk
|

=== Week 9: 27 Feb - 2 Mar ===
'''Biocircuits: 28 Feb (Tue), 3-5 pm'''
* Dan (30-40 min)
* Research update (10-15 min)
* Research update (10-15 min)
* Lab updates
* Will probably shift to 2 Mar, 3-5 pm
'''NCS: 29 Feb (Wed), 4-6 pm'''
* Mumu (15-20 min)
* Open (15-20 min)
* Project updates
* Will probably shift to 2 Mar, 1-3 pm
'''Group meeting: 2 Mar (Fri), 12-1:15'''
* Shaunak
|- valign=top
|

=== Week 10: 5-9 Mar ===
'''Biocircuits: 6 Mar (Tue), 3-5 pm'''
* Enoch (30-40 min)
* Vanessa (10-15 min)
* Research update (10-15 min)
* Lab updates
'''Robotics: 7 Mar (Wed), 4-6 pm'''
* Pete (15-20 min)
* Andrea (15-20 min)
* Short research updates (5 min each)
'''Group meeting: 9 Mar (Fri), 12-1:15'''
* Hold: possible job talk
|

=== Week 11: 12-16 Mar ===
Finals week; Richard out of town
|
=== Week 12: 19-23 Mar ===
Spring break; Richard out of town
|}

Group Schedule, Winter 2012

2011-12-19T08:37:18Z

Jongmin: /* Week 1: 4-6 Jan */

This page contains information about various upcoming events that are of interest to the group. __NOTOC__
{| width=60%
|- valign=top
| width=50% |
* [http://www.cds.caltech.edu/~murray/calendar.html Richard's calendar (travel)]
| width=50% |
* [[Group Schedule, Fall 2011]]
|}

The schedule for group and subgroup meetings is given below. Everyone should sign up for times to talk in the subgroup meetings.


==== Directions: ====
* '''Biocircuits (Tue or Thu, 3-5 pm)''': graduate students should give 1 longer presentation per term + 1-2 additional research updates; postdocs, undergrads should give 1-2 research updates.
* '''NCS (Wed, 4-6 pm)''': grad students should speak 2 times per term for 15-20 min (+ discussion), postdocs and undergrads at least once
* '''Robotics (Wed, 4-6 pm)''': grad students and postdocs should speak 2 times per term for 15-20 min (+ discussion), undergrads at least once; will also do ad hoc updates
* '''Group meeting talks (WThF, 12-1:15)''': postdocs and senior grad students (G4+) should feel free to sign up for a group meeting talk (biocircuit grad students: this can be in place of longer subgroup talk)


<center>
'''Please sign up for at least one presentation in the first six weeks of the term.'''
</center>

Note that some of the meetings might need to shift, as noted; only sign up for those slots if you can make both times listed
 

{| width=100% border=1
|- valign=top
| width=30% |

=== Week 1: 4-6 Jan ===
'''NCS: 4 Jan (Wed), 4-6 pm'''
* Jun Liu (15-20 min)
* Joseph Meyerowitz (15-20 min)
* Project updates
'''Group meeting: 5 Jan (Thu), 12-1:15'''
* Ophelia
'''Biocircuits: 5 Jan (Thu), 3-5 pm'''
* Safety briefing (30-40 min)
* Vanessa (10-15 min)
* Jongmin (10-15 min)
* Lab updates
<hr>
Academic holiday, 2-3 Jan 
CDS quals, 6 Jan (RMM busy all day)
| width=30% |

=== Week 2: 9-13 Jan ===
'''Robotics: 11 Jan (Wed), 4-6 pm'''
* Shuo (15-20 min)
* Scott Livingston (15-20 min)
* Short research updates (5 min each)
* Might shift to Fri, 1-3 pm
'''Biocircuits: 12 Jan (Thu), 3-5 pm'''
* Marcella (30-40 min)
* Jongmin (10-15 min)
* Research update (10-15 min)
* Lab updates
'''Group meeting: 13 Jan (Fri), 12-1:15 pm'''
* Domitilla Del Vecchio (MIT)
| width=30% |

=== Week 3: 16-20 Jan ===
'''Biocircuits: 17 Jan (Tue), 2-4 pm'''
* Research presentation (30-40 min)
* Dan (10-15 min)
* Shaunak (10-15 min)
* Lab updates
* Note time shift in day (to "regular" day)
'''NCS: 18 Jan (Wed), 4-6 pm'''
* Eric (15-20 min)
* Mumu (15-20 min)
* Project updates
'''Group meeting: 19 Jan (Thu), 12-1:15'''
* Naira Hovakimyan (UIUC)
|- valign=top
|

=== Week 4: 23-27 Jan ===
'''Group meeting: 23 Jan (Mon), 12-1:15'''
* Necmiye
'''Robotics: 24 Jan (Tue), 1-3 pm'''
* Stephanie (15-20 min)
* Pete (15-20 min)
* Short research updates (5 min each)
'''Biocircuits: 24 Jan (Tue), 3-5 pm'''
* Ophelia (30-40 min)
* Emzo (10-15 min)
* Enoch (10-15 min)
* Lab updates
|

=== Week 5: 30 Jan - 3 Feb ===
'''Biocircuits: 31 Jan (Tue), 3-5 pm'''
* Research Presentation (30-40 min)
* Nikki(10-15 min)
* Zach (10-15 min)
* Lab updates
'''NCS: 1 Feb (Wed), 4-6 pm'''
* Marcella (15-20 min)
* Ufuk (15-20 min)
* Project updates
'''Group meeting: 2 Feb (Thu), 12-1:15'''
* Jongmin
|

=== Week 6: 6 Feb - 10 Feb ===
'''Biocircuits: 7 Feb (Tue), 3-5 pm'''
* Vanessa (30-40 min)
* Paul (10-15 min)
* Victoria (10-15 min)
* Lab updates
'''Group meeting: 8 Feb (Wed), 12-1:15'''
* Andrea
'''Robotics: 8 Feb (Wed), 4-6 pm'''
* Scott Livingston (15-20 min)
* Andrea (15-20 min)
* Short research updates (5 min each)

|- valign=top
|

=== Week 7: 13-17 Feb ===
'''NCS: 15 Feb (Wed), 4-6 pm'''
* Necmiye (15-20 min)
* Scott Livingston (15-20 min)
* Project updates
'''Group meeting: 16 Feb (Thu), 12-1:15'''
* Chris Kempes
'''Biocircuits: 16 Feb (Thu), 3-5 pm'''
* Research presentation (30-40 min)
* Marcella (10-15 min)
* Research update (10-15 min)
* Lab updates
* Note change in day
|

=== Week 8: 20-24 Feb ===
'''Biocircuits: 21 Feb (Tue), 3-5 pm'''
* Emzo (30-40 min)
* Jongmin (10-15 min)
* Research update (10-15 min)
* Lab updates
'''Robotics: 22 Feb (Wed), 4-6 pm'''
* Shuo (15-20 min)
* Eric (15-20 min)
* Short research updates (5 min each)
* Meeting may shift to 10 Feb (Fri)
'''Group meeting: 23 Feb (Thu), 12-1:15'''
* Hold: possible job talk
|

=== Week 9: 27 Feb - 2 Mar ===
'''Biocircuits: 28 Feb (Tue), 3-5 pm'''
* Dan (30-40 min)
* Research update (10-15 min)
* Research update (10-15 min)
* Lab updates
* Will probably shift to 2 Mar, 3-5 pm
'''NCS: 29 Feb (Wed), 4-6 pm'''
* Mumu (15-20 min)
* Open (15-20 min)
* Project updates
* Will probably shift to 2 Mar, 1-3 pm
'''Group meeting: 2 Mar (Fri), 12-1:15'''
* Shaunak
|- valign=top
|

=== Week 10: 5-9 Mar ===
'''Biocircuits: 6 Mar (Tue), 3-5 pm'''
* Enoch (30-40 min)
* Vanessa (10-15 min)
* Research update (10-15 min)
* Lab updates
'''Robotics: 7 Mar (Wed), 4-6 pm'''
* Pete (15-20 min)
* Andrea (15-20 min)
* Short research updates (5 min each)
'''Group meeting: 9 Mar (Fri), 12-1:15'''
* Hold: possible job talk
|

=== Week 11: 12-16 Mar ===
Finals week; Richard out of town
|
=== Week 12: 19-23 Mar ===
Spring break; Richard out of town
|}

Group Schedule, Winter 2012

2011-12-12T18:55:12Z

Jongmin: /* Week 8: 20-24 Feb */

This page contains information about various upcoming events that are of interest to the group. __NOTOC__
{| width=60%
|- valign=top
| width=50% |
* [http://www.cds.caltech.edu/~murray/calendar.html Richard's calendar (travel)]
| width=50% |
* [[Group Schedule, Fall 2011]]
|}

The schedule for group and subgroup meetings is given below. Everyone should sign up for times to talk in the subgroup meetings.


==== Directions: ====
* '''Biocircuits (Tue or Thu, 3-5 pm)''': graduate students should give 1 longer presentation per term + 1-2 additional research updates; postdocs, undergrads should give 1-2 research updates.
* '''NCS (Wed, 4-6 pm)''': grad students should speak 2 times per term for 15-20 min (+ discussion), postdocs and undergrads at least once
* '''Robotics (Wed, 4-6 pm)''': grad students and postdocs should speak 2 times per term for 15-20 min (+ discussion), undergrads at least once; will also do ad hoc updates
* '''Group meeting talks (WThF, 12-1:15)''': postdocs and senior grad students (G4+) should feel free to sign up for a group meeting talk (biocircuit grad students: this can be in place of longer subgroup talk)


<center>
'''Please sign up for at least one presentation in the first six weeks of the term.'''
</center>

Note that some of the meetings might need to shift, as noted; only sign up for those slots if you can make both times listed
 

{| width=100% border=1
|- valign=top
| width=30% |

=== Week 1: 4-6 Jan ===
'''NCS: 4 Jan (Wed), 4-6 pm'''
* Jun Liu (15-20 min)
* Joseph Meyerowitz (15-20 min)
* Project updates
'''Group meeting: 5 Jan (Thu), 12-1:15'''
* Ophelia
'''Biocircuits: 5 Jan (Thu), 3-5 pm'''
* Safety briefing (30-40 min)
* Vanessa (10-15 min)
* Research update (10-15 min)
* Lab updates
<hr>
Academic holiday, 2-3 Jan 
CDS quals, 6 Jan (RMM busy all day)
| width=30% |

=== Week 2: 9-13 Jan ===
'''Robotics: 11 Jan (Wed), 4-6 pm'''
* Shuo (15-20 min)
* Scott Livingston (15-20 min)
* Short research updates (5 min each)
* Might shift to Fri, 1-3 pm
'''Biocircuits: 12 Jan (Thu), 3-5 pm'''
* Marcella (30-40 min)
* Jongmin (10-15 min)
* Research update (10-15 min)
* Lab updates
'''Group meeting: 13 Jan (Fri), 12-1:15 pm'''
* Domitilla Del Vecchio (MIT)
| width=30% |

=== Week 3: 16-20 Jan ===
'''Biocircuits: 17 Jan (Tue), 2-4 pm'''
* Research presentation (30-40 min)
* Dan (10-15 min)
* Shaunak (10-15 min)
* Lab updates
* Note time shift in day (to "regular" day)
'''NCS: 18 Jan (Wed), 4-6 pm'''
* Eric (15-20 min)
* Mumu (15-20 min)
* Project updates
'''Group meeting: 19 Jan (Thu), 12-1:15'''
* Naira Hovakimyan (UIUC)
|- valign=top
|

=== Week 4: 23-27 Jan ===
'''Biocircuits: 24 Jan (Tue), 3-5 pm'''
* Ophelia (30-40 min)
* Emzo (10-15 min)
* Enoch (10-15 min)
* Lab updates
'''Group meeting: 25 Jan (Wed), 12-1:15'''
* Necmiye
'''Robotics: 25 Jan (Wed), 4-6 pm'''
* Stephanie (15-20 min)
* Pete (15-20 min)
* Short research updates (5 min each)
* Might shift to Fri, 1-3 pm
|

=== Week 5: 30 Jan - 3 Feb ===
'''Biocircuits: 31 Jan (Tue), 3-5 pm'''
* Research Presentation (30-40 min)
* Nikki(10-15 min)
* Zach (10-15 min)
* Lab updates
'''NCS: 1 Feb (Wed), 4-6 pm'''
* Marcella (15-20 min)
* Ufuk (15-20 min)
* Project updates
'''Group meeting: 2 Feb (Thu), 12-1:15'''
* Jongmin
|

=== Week 6: 6 Feb - 10 Feb ===
'''Biocircuits: 7 Feb (Tue), 3-5 pm'''
* Vanessa (30-40 min)
* Paul (10-15 min)
* Victoria (10-15 min)
* Lab updates
'''Group meeting: 8 Feb (Wed), 12-1:15'''
* Andrea
'''Robotics: 8 Feb (Wed), 4-6 pm'''
* Scott Livingston (15-20 min)
* Open (15-20 min)
* Short research updates (5 min each)

|- valign=top
|

=== Week 7: 13-17 Feb ===
'''NCS: 15 Feb (Wed), 4-6 pm'''
* Necmiye (15-20 min)
* Scott Livingston (15-20 min)
* Project updates
'''Group meeting: 16 Feb (Thu), 12-1:15'''
* Open
'''Biocircuits: 16 Feb (Thu), 3-5 pm'''
* Research presentation (30-40 min)
* Marcella (10-15 min)
* Research update (10-15 min)
* Lab updates
* Note change in day
|

=== Week 8: 20-24 Feb ===
'''Biocircuits: 21 Feb (Tue), 3-5 pm'''
* Emzo (30-40 min)
* Jongmin (10-15 min)
* Research update (10-15 min)
* Lab updates
'''Robotics: 22 Feb (Wed), 4-6 pm'''
* Shuo (15-20 min)
* Eric (15-20 min)
* Short research updates (5 min each)
'''Group meeting: 23 Feb (Thu), 12-1:15'''
* Hold: possible job talk
|

=== Week 9: 27 Feb - 2 Mar ===
'''Biocircuits: 28 Feb (Tue), 3-5 pm'''
* Dan (30-40 min)
* Research update (10-15 min)
* Research update (10-15 min)
* Lab updates
* Will probably shift to 2 Mar, 3-5 pm
'''NCS: 29 Feb (Wed), 4-6 pm'''
* Mumu (15-20 min)
* Open (15-20 min)
* Project updates
* Will probably shift to 2 Mar, 1-3 pm
'''Group meeting: 2 Mar (Fri), 12-1:15'''
* Shaunak
|- valign=top
|

=== Week 10: 5-9 Mar ===
'''Biocircuits: 6 Mar (Tue), 3-5 pm'''
* Enoch (30-40 min)
* Vanessa (10-15 min)
* Research update (10-15 min)
* Lab updates
'''Robotics: 7 Mar (Wed), 4-6 pm'''
* Pete (15-20 min)
* Open (15-20 min)
* Short research updates (5 min each)
'''Group meeting: 9 Mar (Fri), 12-1:15'''
* Hold: possible job talk
|

=== Week 11: 12-16 Mar ===
Finals week; Richard out of town
|
=== Week 12: 19-23 Mar ===
Spring break; Richard out of town
|}

Group Schedule, Winter 2012

2011-12-12T18:54:51Z

Jongmin: /* Week 8: 20-24 Feb */

This page contains information about various upcoming events that are of interest to the group. __NOTOC__
{| width=60%
|- valign=top
| width=50% |
* [http://www.cds.caltech.edu/~murray/calendar.html Richard's calendar (travel)]
| width=50% |
* [[Group Schedule, Fall 2011]]
|}

The schedule for group and subgroup meetings is given below. Everyone should sign up for times to talk in the subgroup meetings.


==== Directions: ====
* '''Biocircuits (Tue or Thu, 3-5 pm)''': graduate students should give 1 longer presentation per term + 1-2 additional research updates; postdocs, undergrads should give 1-2 research updates.
* '''NCS (Wed, 4-6 pm)''': grad students should speak 2 times per term for 15-20 min (+ discussion), postdocs and undergrads at least once
* '''Robotics (Wed, 4-6 pm)''': grad students and postdocs should speak 2 times per term for 15-20 min (+ discussion), undergrads at least once; will also do ad hoc updates
* '''Group meeting talks (WThF, 12-1:15)''': postdocs and senior grad students (G4+) should feel free to sign up for a group meeting talk (biocircuit grad students: this can be in place of longer subgroup talk)


<center>
'''Please sign up for at least one presentation in the first six weeks of the term.'''
</center>

Note that some of the meetings might need to shift, as noted; only sign up for those slots if you can make both times listed
 

{| width=100% border=1
|- valign=top
| width=30% |

=== Week 1: 4-6 Jan ===
'''NCS: 4 Jan (Wed), 4-6 pm'''
* Jun Liu (15-20 min)
* Joseph Meyerowitz (15-20 min)
* Project updates
'''Group meeting: 5 Jan (Thu), 12-1:15'''
* Ophelia
'''Biocircuits: 5 Jan (Thu), 3-5 pm'''
* Safety briefing (30-40 min)
* Vanessa (10-15 min)
* Research update (10-15 min)
* Lab updates
<hr>
Academic holiday, 2-3 Jan 
CDS quals, 6 Jan (RMM busy all day)
| width=30% |

=== Week 2: 9-13 Jan ===
'''Robotics: 11 Jan (Wed), 4-6 pm'''
* Shuo (15-20 min)
* Scott Livingston (15-20 min)
* Short research updates (5 min each)
* Might shift to Fri, 1-3 pm
'''Biocircuits: 12 Jan (Thu), 3-5 pm'''
* Marcella (30-40 min)
* Jongmin (10-15 min)
* Research update (10-15 min)
* Lab updates
'''Group meeting: 13 Jan (Fri), 12-1:15 pm'''
* Domitilla Del Vecchio (MIT)
| width=30% |

=== Week 3: 16-20 Jan ===
'''Biocircuits: 17 Jan (Tue), 2-4 pm'''
* Research presentation (30-40 min)
* Dan (10-15 min)
* Shaunak (10-15 min)
* Lab updates
* Note time shift in day (to "regular" day)
'''NCS: 18 Jan (Wed), 4-6 pm'''
* Eric (15-20 min)
* Mumu (15-20 min)
* Project updates
'''Group meeting: 19 Jan (Thu), 12-1:15'''
* Naira Hovakimyan (UIUC)
|- valign=top
|

=== Week 4: 23-27 Jan ===
'''Biocircuits: 24 Jan (Tue), 3-5 pm'''
* Ophelia (30-40 min)
* Emzo (10-15 min)
* Enoch (10-15 min)
* Lab updates
'''Group meeting: 25 Jan (Wed), 12-1:15'''
* Necmiye
'''Robotics: 25 Jan (Wed), 4-6 pm'''
* Stephanie (15-20 min)
* Pete (15-20 min)
* Short research updates (5 min each)
* Might shift to Fri, 1-3 pm
|

=== Week 5: 30 Jan - 3 Feb ===
'''Biocircuits: 31 Jan (Tue), 3-5 pm'''
* Research Presentation (30-40 min)
* Nikki(10-15 min)
* Zach (10-15 min)
* Lab updates
'''NCS: 1 Feb (Wed), 4-6 pm'''
* Marcella (15-20 min)
* Ufuk (15-20 min)
* Project updates
'''Group meeting: 2 Feb (Thu), 12-1:15'''
* Jongmin
|

=== Week 6: 6 Feb - 10 Feb ===
'''Biocircuits: 7 Feb (Tue), 3-5 pm'''
* Vanessa (30-40 min)
* Paul (10-15 min)
* Victoria (10-15 min)
* Lab updates
'''Group meeting: 8 Feb (Wed), 12-1:15'''
* Andrea
'''Robotics: 8 Feb (Wed), 4-6 pm'''
* Scott Livingston (15-20 min)
* Open (15-20 min)
* Short research updates (5 min each)

|- valign=top
|

=== Week 7: 13-17 Feb ===
'''NCS: 15 Feb (Wed), 4-6 pm'''
* Necmiye (15-20 min)
* Scott Livingston (15-20 min)
* Project updates
'''Group meeting: 16 Feb (Thu), 12-1:15'''
* Open
'''Biocircuits: 16 Feb (Thu), 3-5 pm'''
* Research presentation (30-40 min)
* Marcella (10-15 min)
* Research update (10-15 min)
* Lab updates
* Note change in day
|

=== Week 8: 20-24 Feb ===
'''Biocircuits: 21 Feb (Tue), 3-5 pm'''
* Emzo (30-40 min)
* Jongmin(10-15 min)
* Research update (10-15 min)
* Lab updates
'''Robotics: 22 Feb (Wed), 4-6 pm'''
* Shuo (15-20 min)
* Eric (15-20 min)
* Short research updates (5 min each)
'''Group meeting: 23 Feb (Thu), 12-1:15'''
* Hold: possible job talk
|

=== Week 9: 27 Feb - 2 Mar ===
'''Biocircuits: 28 Feb (Tue), 3-5 pm'''
* Dan (30-40 min)
* Research update (10-15 min)
* Research update (10-15 min)
* Lab updates
* Will probably shift to 2 Mar, 3-5 pm
'''NCS: 29 Feb (Wed), 4-6 pm'''
* Mumu (15-20 min)
* Open (15-20 min)
* Project updates
* Will probably shift to 2 Mar, 1-3 pm
'''Group meeting: 2 Mar (Fri), 12-1:15'''
* Shaunak
|- valign=top
|

=== Week 10: 5-9 Mar ===
'''Biocircuits: 6 Mar (Tue), 3-5 pm'''
* Enoch (30-40 min)
* Vanessa (10-15 min)
* Research update (10-15 min)
* Lab updates
'''Robotics: 7 Mar (Wed), 4-6 pm'''
* Pete (15-20 min)
* Open (15-20 min)
* Short research updates (5 min each)
'''Group meeting: 9 Mar (Fri), 12-1:15'''
* Hold: possible job talk
|

=== Week 11: 12-16 Mar ===
Finals week; Richard out of town
|
=== Week 12: 19-23 Mar ===
Spring break; Richard out of town
|}

Group Schedule, Winter 2012

2011-12-12T18:54:12Z

Jongmin: /* Week 2: 9-13 Jan */

This page contains information about various upcoming events that are of interest to the group. __NOTOC__
{| width=60%
|- valign=top
| width=50% |
* [http://www.cds.caltech.edu/~murray/calendar.html Richard's calendar (travel)]
| width=50% |
* [[Group Schedule, Fall 2011]]
|}

The schedule for group and subgroup meetings is given below. Everyone should sign up for times to talk in the subgroup meetings.


==== Directions: ====
* '''Biocircuits (Tue or Thu, 3-5 pm)''': graduate students should give 1 longer presentation per term + 1-2 additional research updates; postdocs, undergrads should give 1-2 research updates.
* '''NCS (Wed, 4-6 pm)''': grad students should speak 2 times per term for 15-20 min (+ discussion), postdocs and undergrads at least once
* '''Robotics (Wed, 4-6 pm)''': grad students and postdocs should speak 2 times per term for 15-20 min (+ discussion), undergrads at least once; will also do ad hoc updates
* '''Group meeting talks (WThF, 12-1:15)''': postdocs and senior grad students (G4+) should feel free to sign up for a group meeting talk (biocircuit grad students: this can be in place of longer subgroup talk)


<center>
'''Please sign up for at least one presentation in the first six weeks of the term.'''
</center>

Note that some of the meetings might need to shift, as noted; only sign up for those slots if you can make both times listed
 

{| width=100% border=1
|- valign=top
| width=30% |

=== Week 1: 4-6 Jan ===
'''NCS: 4 Jan (Wed), 4-6 pm'''
* Jun Liu (15-20 min)
* Joseph Meyerowitz (15-20 min)
* Project updates
'''Group meeting: 5 Jan (Thu), 12-1:15'''
* Ophelia
'''Biocircuits: 5 Jan (Thu), 3-5 pm'''
* Safety briefing (30-40 min)
* Vanessa (10-15 min)
* Research update (10-15 min)
* Lab updates
<hr>
Academic holiday, 2-3 Jan 
CDS quals, 6 Jan (RMM busy all day)
| width=30% |

=== Week 2: 9-13 Jan ===
'''Robotics: 11 Jan (Wed), 4-6 pm'''
* Shuo (15-20 min)
* Scott Livingston (15-20 min)
* Short research updates (5 min each)
* Might shift to Fri, 1-3 pm
'''Biocircuits: 12 Jan (Thu), 3-5 pm'''
* Marcella (30-40 min)
* Jongmin (10-15 min)
* Research update (10-15 min)
* Lab updates
'''Group meeting: 13 Jan (Fri), 12-1:15 pm'''
* Domitilla Del Vecchio (MIT)
| width=30% |

=== Week 3: 16-20 Jan ===
'''Biocircuits: 17 Jan (Tue), 2-4 pm'''
* Research presentation (30-40 min)
* Dan (10-15 min)
* Shaunak (10-15 min)
* Lab updates
* Note time shift in day (to "regular" day)
'''NCS: 18 Jan (Wed), 4-6 pm'''
* Eric (15-20 min)
* Mumu (15-20 min)
* Project updates
'''Group meeting: 19 Jan (Thu), 12-1:15'''
* Naira Hovakimyan (UIUC)
|- valign=top
|

=== Week 4: 23-27 Jan ===
'''Biocircuits: 24 Jan (Tue), 3-5 pm'''
* Ophelia (30-40 min)
* Emzo (10-15 min)
* Enoch (10-15 min)
* Lab updates
'''Group meeting: 25 Jan (Wed), 12-1:15'''
* Necmiye
'''Robotics: 25 Jan (Wed), 4-6 pm'''
* Stephanie (15-20 min)
* Pete (15-20 min)
* Short research updates (5 min each)
* Might shift to Fri, 1-3 pm
|

=== Week 5: 30 Jan - 3 Feb ===
'''Biocircuits: 31 Jan (Tue), 3-5 pm'''
* Research Presentation (30-40 min)
* Nikki(10-15 min)
* Zach (10-15 min)
* Lab updates
'''NCS: 1 Feb (Wed), 4-6 pm'''
* Marcella (15-20 min)
* Ufuk (15-20 min)
* Project updates
'''Group meeting: 2 Feb (Thu), 12-1:15'''
* Jongmin
|

=== Week 6: 6 Feb - 10 Feb ===
'''Biocircuits: 7 Feb (Tue), 3-5 pm'''
* Vanessa (30-40 min)
* Paul (10-15 min)
* Victoria (10-15 min)
* Lab updates
'''Group meeting: 8 Feb (Wed), 12-1:15'''
* Andrea
'''Robotics: 8 Feb (Wed), 4-6 pm'''
* Scott Livingston (15-20 min)
* Open (15-20 min)
* Short research updates (5 min each)

|- valign=top
|

=== Week 7: 13-17 Feb ===
'''NCS: 15 Feb (Wed), 4-6 pm'''
* Necmiye (15-20 min)
* Scott Livingston (15-20 min)
* Project updates
'''Group meeting: 16 Feb (Thu), 12-1:15'''
* Open
'''Biocircuits: 16 Feb (Thu), 3-5 pm'''
* Research presentation (30-40 min)
* Marcella (10-15 min)
* Research update (10-15 min)
* Lab updates
* Note change in day
|

=== Week 8: 20-24 Feb ===
'''Biocircuits: 21 Feb (Tue), 3-5 pm'''
* Emzo (30-40 min)
* Research update (10-15 min)
* Research update (10-15 min)
* Lab updates
'''Robotics: 22 Feb (Wed), 4-6 pm'''
* Shuo (15-20 min)
* Eric (15-20 min)
* Short research updates (5 min each)
'''Group meeting: 23 Feb (Thu), 12-1:15'''
* Hold: possible job talk
|

=== Week 9: 27 Feb - 2 Mar ===
'''Biocircuits: 28 Feb (Tue), 3-5 pm'''
* Dan (30-40 min)
* Research update (10-15 min)
* Research update (10-15 min)
* Lab updates
* Will probably shift to 2 Mar, 3-5 pm
'''NCS: 29 Feb (Wed), 4-6 pm'''
* Mumu (15-20 min)
* Open (15-20 min)
* Project updates
* Will probably shift to 2 Mar, 1-3 pm
'''Group meeting: 2 Mar (Fri), 12-1:15'''
* Shaunak
|- valign=top
|

=== Week 10: 5-9 Mar ===
'''Biocircuits: 6 Mar (Tue), 3-5 pm'''
* Enoch (30-40 min)
* Vanessa (10-15 min)
* Research update (10-15 min)
* Lab updates
'''Robotics: 7 Mar (Wed), 4-6 pm'''
* Pete (15-20 min)
* Open (15-20 min)
* Short research updates (5 min each)
'''Group meeting: 9 Mar (Fri), 12-1:15'''
* Hold: possible job talk
|

=== Week 11: 12-16 Mar ===
Finals week; Richard out of town
|
=== Week 12: 19-23 Mar ===
Spring break; Richard out of town
|}

Dec 2011 meetings

2011-12-07T07:04:09Z

Jongmin: /* 20 Dec (Tue) */

The list below has times that I am available to meet on 15-21 Dec. __NOTOC__
* 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 see if you can switch).
* To maximize the chance I get to meet with everyone, '''please sign up for times on 19-22 Dec if you are around that week'''

 
<table width=100% border=1>
<tr valign=top><td width=20%>
==== 15 Dec (Thu) ====
{{agenda begin}}
{{agenda begin}}
{{agenda item|10:00a|Enoch}}
{{agenda item|11:00a|Victoria}}
{{agenda item||}}
{{agenda item|4:30p|Shaunak}}
{{agenda item|5:30p|Hamed}}
{{agenda item|6:30p|Chris Kempes}}
{{agenda end}}
</td><td width=20%>

==== 16 Dec (Fri) ====
{{agenda begin}}
{{agenda item|10:00a|Open}}
{{agenda item|11:00a|Open}}
{{agenda item||}}
{{agenda item|2:30p|Shuo}}
{{agenda item|3:30p|Jongmin/Shaunak}}
{{agenda item|4:30p|Dominic}}
{{agenda item|5:30p|Andrea}}
{{agenda end}}
</td><td width=20%>

==== 19 Dec (Mon) ====
{{agenda begin}}
{{agenda item|12:30p|Mumu}}
{{agenda item|1:30p|Lab inspection}}
{{agenda item||}}
{{agenda item|5:00p|Ophelia}}
{{agenda end}}
</td><td width=20%>

==== 20 Dec (Tue) ====
{{agenda begin}}
{{agenda item|10:00a| Scott Livingston}}
{{agenda item|11:00a|Open}}
{{agenda item||}}
{{agenda item|2:00p|Open}}
{{agenda item|3:00p|Open}}
{{agenda item|4:00p|Jongmin}}
{{agenda end}}
</td><td width=20%>

==== 21 Dec (Wed) ====
{{agenda begin}}
{{agenda item|11:30a|Open}}
{{agenda item||}}
{{agenda item|2:00p| Pavithra}}
{{agenda item|4:00p|Open}}
{{agenda item|5:00p|Open}}
{{agenda end}}
</td></tr>
</table>

Group Schedule, Fall 2011

2011-09-30T02:04:18Z

Jongmin: /* Week 7: 7-11 Nov */

Group Schedule, Fall 2011

2011-09-21T01:09:47Z

Jongmin: /* Week 2: 3-7 Oct */

Group Schedule, Summer 2011

2011-07-10T02:59:21Z

Jongmin: /* 11-15 Jul */

__NOTOC__
This page contains information about various upcoming events that are of interest to the group.
{| width=60%
|- valign=top
| width=50% |
* [http://www.cds.caltech.edu/~murray/calendar.html Richard's calendar (travel)]
| width=50% |
* [[Group Schedule, Spring 2011]]
|}

=== Summer Schedule ===

{| border=1 width=100%
|- valign=top
| '''Week'''
| '''Mini-group meetings'''
| '''Group meeting'''
| '''Other'''
|- valign=top
|
===== 13-17 Jun =====
|
None
|
None
|
RMM out all week
|- valign=top
|
===== 20-24 Jun =====
|
* iGEM: Mon @ 9:30
* SURF meetings, cycle 0: (sign on at [[SURF 2011]] page)
* NCS: Tue, 1-2:30 pm
** Speaker 1: Necmiye (discussion)
** Speaker 2: Linlin
|
Tue @ 12: Necmiye
|
RMM out 22-24 Jun
|- valign=top
|

===== 27 Jun - 1 Jul =====
|
* iGEM: Mon, 9:30a-10:30a
* Robotics: Mon, 1-3 pm
** Speaker 1: Sandeep
** Speaker 2: Sawyer
* Biocircuits: Tue, 9a-2p
** Overview presentations (all; 10 min each)
** Lunch will be provided
* SURF meetings, cycle 1: Tue pm
** 4:00 pm: Yuchen and Ufuk
** 4:30 pm: Klavdia and Sawyer
** 5:00 pm: Ishan and Jongmin
** 5:30 pm: Sandeep and Scott
** 6:00 pm: Arjun and Emzo
|
Mon @ 12: Nils Napp
|
* Nils Napp visiting
* Sean Meyn visiting
* RMM out 29 Jun-1 Jul (ACC)
|- valign=top
|

===== 4-8 Jul =====
|
* Biocircuits: Tue, 10-12
** Speaker 1: Marcella
** Speaker 2: Joe
** Speaker 3: Vanessa
* iGEM: Tue, 5:30-6:30p
* NCS: Thu, 1-3 pm
** Speaker 3: Scott Livingston
** Speaker 4: Jun Liu
* SURF meetings, cycle 1: Thu pm
** 3:00 pm: Magnus and Andrea
** 3:30 pm: Paul and Joe
** 4:00 pm: Petter and Necmiye
** 4:30 pm: Stephanie and Necmiye
** 5:00 pm: Keshav and Emzo

|
Tue @ 12: Henrik Sandberg
|
* Institute holiday on Mon
* Eric Colinet visiting on 5 Jul
* Henrik Sandberg visiting 3-9 Jul
|- valign=top
|

===== 11-15 Jul =====
|
* iGEM: Mon, 9:30a-10:30a
* Robotics: Wed, 1p-3p
** Speaker 3: Shuo
** Speaker 4: Andrea
* Biocircuits: Thu, 10a-12p
** Speaker 4: Ophelia
** Speaker 5: Emzo
** iGEM presentation (30 min)
* SURF meetings, cycle 2: Thu, pm
** 3:00 pm: open
** 3:30 pm: open
** 4:00 pm: open
** 4:30 pm: Ishan and Jongmin
|
Thu @ 12: Dan Wilhelm, 107 ANB
|
|- valign=top
|

===== 18-22 Jul =====
|
* SURF meetings, cycle 2: Thu pm
** 2:30p: Petter and Necmiye
** 3:00p: Keshav and Emzo
** 3:30p: Yuchen and Necmiye
** 4:00p: Klavdia and Sawyer
** 4:30p: Stephanie and Necmiye
* iGEM: Thu, 5-6p
* Biocircuits: Fri, 10a-12p
** Speaker 6: Ye Yuan
** Speaker 7: Dionysios
** SURF 1: Paul
* Robotics: Fri, 1p-3p
** Speaker 5: pete
** SURF 1: Magnus
** SURF 2: Stephanie
* NCS: Fri, 3p-5p
** Speaker 5: Mumu
** Speaker 6: Ufuk
** SURF 1: Petter
|
Fri @ 12: Open
|
* RMM out 18-21 Jul am
* Josh Michener visiting 22 Jul
|- valign=top
|

===== 25-29 Jul =====
|
|
|
* RMM out 25-29 Jul
|- valign=top
|

===== 1-5 Aug =====
|
* iGEM: Thu, 5-6 pm
* Biocircuits: Fri, 10a-12p
** Speaker 8: Marcella
** SURF 2: Ishan
** SURF 3: Arjun
* NCS: Fri, 1p-3p
** Speaker 7: Scott Livingston
** Speaker 8: Eric
** SURF 2: Yuchen
* SURF meetings, cycle 3: Fri, pm
** 3:00p: Klavdia and Sawyer
** 3:30p: open
** 4:00p: open
** 4:30p: open
** 5:00p: open
|
Fri @ 12: Marin Kobilarov
|
* RMM out 1-4 Aug
|- valign=top
|

===== 8-12 Aug =====
|
* Robotics: Tue, 1p-3p
** Speaker 6: open
** SURF 3: Klavdia
* SURF meetings, cycle 3: Tue, pm
** 3:00p: open
** 3:30p: Keshav and Emzo
** 4:00p: Ishan and Jongmin
** 4:30p: Stephanie and Necmiye
* Biocircuits: Thu, 10a-12p
** Speaker 9: Jongmin
** Speaker 10: Shaunak
** SURF 4: Keshav
* iGEM: Thu, 5p-6p
|
Thu @ 12: speaker TBD
|
|- valign=top
|

===== 15-19 Aug =====
|
|
|
RMM out 15-19 Aug
|- valign=top
|

===== 22-26 Aug =====
|
* iGEM: Mon, 9a-10a
* Biocircuits: Mon, 10a-12p
** Speaker 11: open
** Speaker 12: Enoch Yeung
** Speaker 13: open
* Robotics: Mon, 1p-3p
** Speaker 7: open
** Speaker 8: open
* NCS: Mon, 3p-5p
** Speaker 9: Linlin
** Speaker 10: Necmiye
|
Tue @ 12: speaker TBD
|
RMM out: 25 Aug (pm) - 1 Sep (pm)
|- valign=top
|

===== 29 Aug - 2 Sep =====
|
* Robotics: Thu, 1-3p
** Speaker 9: Shuo
** Speaker 10: Pete
* NCS: Thu, 3-5p
** Speaker 11: Open
** Speaker 12: Eric
* iGEM: Thu, 5p-6p
* Biocircuits; Fri, 10a-12p
** Speaker 14: Ophelia
** Speaker 15: open
** Speaker 16: open

|
Fri @ 12p (tentative): speaker TBD
|
* RMM out: 25 Aug (pm) - 1 Sep (pm)
|- valign=top
|

===== 5-9 Sep =====
|
|
|
* RMM out, 5-9 Sep
|- valign=top
|
===== 12-16 Sep =====
|
* Biocircuits: Tue, 10a-12p
** Speaker 17: Emzo
** Speaker 18: open
** Speaker 19: open
* NCS: Wed, 1p-3p
** Speaker 13: Mumu
** Speaker 14: Ufuk
|
Tue @ 12p: Doug MacMynowski
|
|- valign=top
|

===== 19-23 Sep =====
|
* Robotics: Mon, 1p-3p
** Speaker 11: Asghar
** Speaker 12: Andrea
* Biocircuits: Tue, 10a-12p
** Speaker 20: open
** Speaker 21: Enoch Yeung
** Speaker 22: open
|
Tue @ 12p: speaker TBD
|
RMM out, 20 Sep (pm) to 23 Sep
|}

Group Schedule, Summer 2011

2011-06-25T08:04:32Z

Jongmin: /* 8-12 Aug */

__NOTOC__
This page contains information about various upcoming events that are of interest to the group.
{| width=60%
|- valign=top
| width=50% |
* [http://www.cds.caltech.edu/~murray/calendar.html Richard's calendar (travel)]
| width=50% |
* [[Group Schedule, Spring 2011]]
|}

=== Summer Schedule ===

{| border=1 width=100%
|- valign=top
| '''Week'''
| '''Mini-group meetings'''
| '''Group meeting'''
| '''Other'''
|- valign=top
|
===== 13-17 Jun =====
|
None
|
None
|
RMM out all week
|- valign=top
|
===== 20-24 Jun =====
|
* iGEM: Mon @ 9:30
* SURF meetings, cycle 0: (sign on at [[SURF 2011]] page)
* NCS: Tue, 1-2:30 pm
** Speaker 1: Necmiye (discussion)
** Speaker 2: Linlin
|
Tue @ 12: Necmiye
|
RMM out 22-24 Jun
|- valign=top
|

===== 27 Jun - 1 Jul =====
|
* iGEM: Mon, 9:30a-10:30a
* Robotics: Mon, 1-3 pm
** Speaker 1: Sandeep
** Speaker 2: Sawyer
* Biocircuits: Tue, 9a-2p
** Overview presentations (all; 10 min each)
** Lunch will be provided
* SURF meetings, cycle 1: Tue pm
** 4:00 pm: Yuchen and Ufuk
** 4:30 pm: Klavdia and Sawyer
** 5:00 pm: Ishan and Jongmin
** 5:30 pm: open
** 6:00 pm: Hold: Arjun
|
Mon @ 12: Nils Napp
|
* Nils Napp visiting
* Sean Meyn visiting
* RMM out 29 Jun-1 Jul (ACC)
|- valign=top
|

===== 4-8 Jul =====
|
* Biocircuits: Tue, 10-12
** Speaker 1: Marcella
** Speaker 2: Joe
** Speaker 3: Vanessa
* iGEM: Tue, 5:30-6:30p
* NCS: Thu, 1-3 pm
** Speaker 3: Scott Livingston
** Speaker 4: Jun Liu
* SURF meetings, cycle 1: Thu pm
** 3:00 pm: open
** 3:30 pm: open
** 4:00 pm: open
** 4:30 pm: Stephanie and Necmiye
** 5:00 pm: open

|
Tue @ 12: Henrik Sandberg
|
* Institute holiday on Mon
* Eric Colinet visiting on 5 Jul
* Henrik Sandberg visiting 3-9 Jul
|- valign=top
|

===== 11-15 Jul =====
|
* iGEM: Mon, 9:30a-10:30a
* Robotics: Wed, 1p-3p
** Speaker 3: Shuo
** Speaker 4: Andrea
* Biocircuits: Thu, 10a-12p
** Speaker 4: Ophelia
** Speaker 5: open
** iGEM presentation (30 min)
* SURF meetings, cycle 2: Thu, pm
** 3:00 pm: open
** 3:30 pm: open
** 4:00 pm: open
** 4:30 pm: open
|
Thu @ 12: Speaker TBD
|
|- valign=top
|

===== 18-22 Jul =====
|
* SURF meetings, cycle 2: Thu pm
** 2:30p: open
** 3:00p: open
** 3:30p: Ishan and Jongmin
** 4:00p: Klavdia and Sawyer
** 4:30p: Stephanie and Necmiye
* iGEM: Thu, 5-6p
* Biocircuits: Fri, 10a-12p
** Speaker 6: Ye Yuan
** Speaker 7: Dionysios
** SURF 1: Paul
* Robotics: Fri, 1p-3p
** Speaker 5: pete
** SURF 1: Magnus
** SURF 2: Stephanie
* NCS: Fri, 3p-5p
** Speaker 5: Mumu
** Speaker 6: Ufuk
** SURF 1: Petter
|
Fri @ 12: Josh Michener
|
* RMM out 18-21 Jul am
* Josh Michener visiting 22 Jul
|- valign=top
|

===== 25-29 Jul =====
|
|
|
* RMM out 25-29 Jul
|- valign=top
|

===== 1-5 Aug =====
|
* iGEM: Thu, 5-6 pm
* Biocircuits: Fri, 10a-12p
** Speaker 8: Marcella
** SURF 2: Ishan
** SURF 3: Arjun
* NCS: Fri, 1p-3p
** Speaker 7: Scott Livingston
** Speaker 8: Eric
** SURF 2: Yuchen
* SURF meetings, cycle 3: Fri, pm
** 3:00p: Klavdia and Sawyer
** 3:30p: open
** 4:00p: open
** 4:30p: open
** 5:00p: open
|
Fri @ 12: speaker TBD
|
* RMM out 1-4 Aug
|- valign=top
|

===== 8-12 Aug =====
|
* Robotics: Tue, 1p-3p
** Speaker 6: open
** SURF 3: Klavdia
* SURF meetings, cycle 3: Tue, pm
** 3:00p: open
** 4:30p: open
** 4:00p: Ishan and Jongmin
** 5:30p: Stephanie and Necmiye
** 6:00p: open
* Biocircuits: Thu, 10a-12p
** Speaker 9: Jongmin
** Speaker 10: Shaunak
** SURF 4: Keshav
* iGEM: Thu, 5p-6p
|
Thu @ 12: speaker TBD
|
|- valign=top
|

===== 15-19 Aug =====
|
|
|
RMM out 15-19 Aug
|- valign=top
|

===== 22-26 Aug =====
|
* iGEM: Mon, 9a-10a
* Biocircuits: Mon, 10a-12p
** Speaker 11: open
** Speaker 12: Enoch Yeung
** Speaker 13: open
* Robotics: Mon, 1p-3p
** Speaker 7: open
** Speaker 8: open
* NCS: Mon, 3p-5p
** Speaker 9: Linlin
** Speaker 10: Necmiye
|
Tue @ 12: speaker TBD
|
RMM out: 25 Aug (pm) - 1 Sep (pm)
|- valign=top
|

===== 29 Aug - 2 Sep =====
|
* Robotics: Thu, 1-3p
** Speaker 9: Shuo
** Speaker 10: Pete
* NCS: Thu, 3-5p
** Speaker 11: Asghar
** Speaker 12: Eric
* iGEM: Thu, 5p-6p
* Biocircuits; Fri, 10a-12p
** Speaker 14: Ophelia
** Speaker 15: open
** Speaker 16: open

|
Fri @ 12p (tentative): speaker TBD
|
* RMM out: 25 Aug (pm) - 1 Sep (pm)
|- valign=top
|

===== 5-9 Sep =====
|
|
|
* RMM out, 5-9 Sep
|- valign=top
|
===== 12-16 Sep =====
|
* Biocircuits: Tue, 10a-12p
** Speaker 17: open
** Speaker 18: open
** Speaker 19: open
* NCS: Wed, 1p-3p
** Speaker 13: Mumu
** Speaker 14: Ufuk
|
Tue @ 12p: Doug MacMynowski
|
|- valign=top
|

===== 19-23 Sep =====
|
* Robotics: Mon, 1p-3p
** Speaker 11: Asghar
** Speaker 12: Andrea
* Biocircuits: Tue, 10a-12p
** Speaker 20: open
** Speaker 21: Enoch Yeung
** Speaker 22: open
|
Tue @ 12p: speaker TBD
|
RMM out, 20 Sep (pm) to 23 Sep
|}

Group Schedule, Summer 2011

2011-06-22T09:22:33Z

Jongmin: /* 18-22 Jul */

__NOTOC__
This page contains information about various upcoming events that are of interest to the group.
{| width=60%
|- valign=top
| width=50% |
* [http://www.cds.caltech.edu/~murray/calendar.html Richard's calendar (travel)]
| width=50% |
* [[Group Schedule, Spring 2011]]
|}

=== Summer Schedule ===

{| border=1 width=100%
|- valign=top
| '''Week'''
| '''Mini-group meetings'''
| '''Group meeting'''
| '''Other'''
|- valign=top
|
===== 13-17 Jun =====
|
None
|
None
|
RMM out all week
|- valign=top
|
===== 20-24 Jun =====
|
* iGEM: Mon @ 9:30
* SURF meetings, cycle 0: (sign on at [[SURF 2011]] page)
* NCS: Tue, 1-2:30 pm
** Speaker 1: Necmiye (discussion)
** Speaker 2: Linlin
|
Tue @ 12: Necmiye
|
RMM out 22-24 Jun
|- valign=top
|

===== 27 Jun - 1 Jul =====
|
* iGEM: Mon, 9:30a-10:30a
* Robotics: Mon, 1-3 pm
** Speaker 1: Sawyer
** Speaker 2: Sandeep
* Biocircuits: Tue, 9a-2p
** Overview presentations (all; 10 min each)
** Lunch will be provided
* SURF meetings, cycle 1: Tue pm
** 4:00 pm: Klavdia and Sawyer
** 4:30 pm: open
** 5:00 pm: Ishan and Jongmin
** 5:30 pm: open
** 6:00 pm: open
|
Mon @ 12: Nils Napp
|
* Nils Napp visiting
* RMM out 29 Jun-1 Jul (ACC)
|- valign=top
|

===== 4-8 Jul =====
|
* Biocircuits: Tue, 10-12
** Speaker 1: Marcella
** Speaker 2: Joe
** Speaker 3: open
* iGEM: Tue, 5:30-6:30p
* NCS: Thu, 1-3 pm
** Speaker 3: Scott Livingston
** Speaker 4: Jun Liu
* SURF meetings, cycle 1: Thu pm
** 3:00 pm: open
** 3:30 pm: open
** 4:00 pm: open
** 4:30 pm: Stephanie and Necmiye
** 5:00 pm: open

|
Tue @ 12: Henrik Sandberg
|
* Institute holiday on Mon
* Eric Colinet visiting on 5 Jul
* Henrik Sandberg visiting 3-9 Jul
|- valign=top
|

===== 11-15 Jul =====
|
* iGEM: Mon, 9:30a-10:30a
* Robotics: Wed, 1p-3p
** Speaker 3: Shuo
** Speaker 4: Andrea
* Biocircuits: Thu, 10a-12p
** Speaker 4: Ophelia
** Speaker 5: Vanessa
** iGEM presentation (30 min)
* SURF meetings, cycle 2: Thu, pm
** 3:00 pm: open
** 3:30 pm: open
** 4:00 pm: open
** 4:30 pm: open
|
Thu @ 12: Speaker TBD
|
|- valign=top
|

===== 18-22 Jul =====
|
* SURF meetings, cycle 2: Thu pm
** 2:30p: open
** 3:00p: open
** 3:30p: Ishan and Jongmin
** 4:00p: Klavdia and Sawyer
** 4:30p: Stephanie and Necmiye
* iGEM: Thu, 5-6p
* Biocircuits: Fri, 10a-12p
** Speaker 6: Ye Yuan
** Speaker 7: Dionysios
** SURF 1: Paul
* Robotics: Fri, 1p-3p
** Speaker 5: pete
** SURF 1: Magnus
** SURF 2: Stephanie
* NCS: Fri, 3p-5p
** Speaker 5: Mumu
** Speaker 6: Ufuk
** SURF 1: Petter
|
Fri @ 12: Josh Michener
|
* RMM out 18-21 Jul am
* Josh Michener visiting 22 Jul
|- valign=top
|

===== 25-29 Jul =====
|
|
|
* RMM out 25-29 Jul
|- valign=top
|

===== 1-5 Aug =====
|
* iGEM: Thu, 5-6 pm
* Biocircuits: Fri, 10a-12p
** Speaker 8: Marcella
** SURF 2: Ishan
** SURF 3: Arjun
* NCS: Fri, 1p-3p
** Speaker 7: Scott Livingston
** Speaker 8: Eric
** SURF 2: Yuchen
* SURF meetings, cycle 3: Fri, pm
** 3:00p: Klavdia and Sawyer
** 3:30p: open
** 4:00p: open
** 4:30p: open
** 5:00p: open
|
Fri @ 12: speaker TBD
|
* RMM out 1-4 Aug
|- valign=top
|

===== 8-12 Aug =====
|
* Robotics: Tue, 1p-3p
** Speaker 6: open
** SURF 3: Klavdia
* SURF meetings, cycle 3: Tue, pm
** 3:00p: open
** 4:30p: open
** 4:00p: open
** 5:30p: Stephanie and Necmiye
** 6:00p: open
* Biocircuits: Thu, 10a-12p
** Speaker 9: Jongmin
** Speaker 10: Shaunak
** SURF 4: Keshav
* iGEM: Thu, 5p-6p
|
Thu @ 12: speaker TBD
|
|- valign=top
|

===== 15-19 Aug =====
|
|
|
RMM out 15-19 Aug
|- valign=top
|

===== 22-26 Aug =====
|
* iGEM: Mon, 9a-10a
* Biocircuits: Mon, 10a-12p
** Speaker 11: open
** Speaker 12: Enoch Yeung
** Speaker 13: open
* Robotics: Mon, 1p-3p
** Speaker 7: open
** Speaker 8: open
* NCS: Mon, 3p-5p
** Speaker 9: Linlin
** Speaker 10: Necmiye
|
Tue @ 12: speaker TBD
|
RMM out: 25 Aug (pm) - 1 Sep (pm)
|- valign=top
|

===== 29 Aug - 2 Sep =====
|
* Robotics: Thu, 1-3p
** Speaker 9: Shuo
** Speaker 10: Pete
* NCS: Thu, 3-5p
** Speaker 11: Asghar
** Speaker 12: Eric
* iGEM: Thu, 5p-6p
* Biocircuits; Fri, 10a-12p
** Speaker 14: Ophelia
** Speaker 15: open
** Speaker 16: open

|
Fri @ 12p (tentative): speaker TBD
|
* RMM out: 25 Aug (pm) - 1 Sep (pm)
|- valign=top
|

===== 5-9 Sep =====
|
|
|
* RMM out, 5-9 Sep
|- valign=top
|
===== 12-16 Sep =====
|
* Biocircuits: Tue, 10a-12p
** Speaker 17: open
** Speaker 18: open
** Speaker 19: open
* NCS: Wed, 1p-3p
** Speaker 13: Mumu
** Speaker 14: Ufuk
|
Tue @ 12p: speaker TBD
|
|- valign=top
|

===== 19-23 Sep =====
|
* Robotics: Mon, 1p-3p
** Speaker 11: Asghar
** Speaker 12: Andrea
* Biocircuits: Tue, 10a-12p
** Speaker 20: open
** Speaker 21: Enoch Yeung
** Speaker 22: open
|
Tue @ 12p: speaker TBD
|
RMM out, 20 Sep (pm) to 23 Sep
|}

Group Schedule, Summer 2011

2011-06-20T23:13:04Z

Jongmin: /* 27 Jun - 1 Jul */

__NOTOC__
This page contains information about various upcoming events that are of interest to the group.
{| width=60%
|- valign=top
| width=50% |
* [http://www.cds.caltech.edu/~murray/calendar.html Richard's calendar (travel)]
| width=50% |
* [[Group Schedule, Spring 2011]]
|}

=== Summer Schedule ===

{| border=1 width=100%
|- valign=top
| '''Week'''
| '''Mini-group meetings'''
| '''Group meeting'''
| '''Other'''
|- valign=top
|
===== 13-17 Jun =====
|
None
|
None
|
RMM out all week
|- valign=top
|
===== 20-24 Jun =====
|
* iGEM: Mon @ 9:30
* SURF meetings, cycle 0: (sign on at [[SURF 2011]] page)
* NCS: Tue, 1-2:30 pm
** Speaker 1: Necmiye (discussion)
** Speaker 2: Linlin
|
Tue @ 12: Necmiye
|
RMM out 22-24 Jun
|- valign=top
|

===== 27 Jun - 1 Jul =====
|
* iGEM: Mon, 9:30a-10:30a
* Robotics: Mon, 1-3 pm
** Speaker 1: Sawyer
** Speaker 2: Sandeep
* Biocircuits: Tue, 9a-2p
** Overview presentations (all; 10 min each)
** Lunch will be provided
* SURF meetings, cycle 1: Tue pm
** 4:00 pm: open
** 4:30 pm: open
** 5:00 pm: Ishan and Jongmin
** 5:30 pm: open
** 6:00 pm: open
|
Mon @ 12: Nils Napp
|
* Nils Napp visiting
* RMM out 29 Jun-1 Jul (ACC)
|- valign=top
|

===== 4-8 Jul =====
|
* Biocircuits: Tue, 10-12
** Speaker 1: Marcella
** Speaker 2: Joe
** Speaker 3: open
* iGEM: Tue, 5:30-6:30p
* NCS: Thu, 1-3 pm
** Speaker 3: Scott Livingston
** Speaker 4: Jun Liu
* SURF meetings, cycle 1: Thu pm
** 3:00 pm: open
** 3:30 pm: open
** 4:00 pm: Klavdia and Sawyer
** 4:30 pm: Stephanie and Necmiye
** 5:00 pm: open

|
Tue @ 12: Henrik Sandberg
|
* Institute holiday on Mon
* Eric Colinet visiting on 5 Jul
* Henrik Sandberg visiting 3-9 Jul
|- valign=top
|

===== 11-15 Jul =====
|
* iGEM: Mon, 9:30a-10:30a
* Robotics: Wed, 1p-3p
** Speaker 3: Shuo
** Speaker 4: Andrea
* Biocircuits: Thu, 10a-12p
** Speaker 4: Ophelia
** Speaker 5: Vanessa
** iGEM presentation (30 min)
* SURF meetings, cycle 2: Thu, pm
** 3:00 pm: open
** 3:30 pm: open
** 4:00 pm: open
** 4:30 pm: open
|
Thu @ 12: Speaker TBD
|
|- valign=top
|

===== 18-22 Jul =====
|
* SURF meetings, cycle 2: Thu pm
** 2:30p: open
** 3:00p: open
** 3:30p: open
** 4:00p: Klavdia and Sawyer
** 4:30p: Stephanie and Necmiye
* iGEM: Thu, 5-6p
* Biocircuits: Fri, 10a-12p
** Speaker 6: Ye Yuan
** Speaker 7: Dionysios
** SURF 1: Paul
* Robotics: Fri, 1p-3p
** Speaker 5: pete
** SURF 1: Magnus
** SURF 2: Stephanie
* NCS: Fri, 3p-5p
** Speaker 5: Mumu
** Speaker 6: Ufuk
** SURF 1: Petter
|
Fri @ 12: Josh Michener
|
* RMM out 18-21 Jul am
* Josh Michener visiting 22 Jul
|- valign=top
|

===== 25-29 Jul =====
|
|
|
* RMM out 25-29 Jul
|- valign=top
|

===== 1-5 Aug =====
|
* iGEM: Thu, 5-6 pm
* Biocircuits: Fri, 10a-12p
** Speaker 8: Marcella
** SURF 2: Ishan
** SURF 3: Arjun
* NCS: Fri, 1p-3p
** Speaker 7: Scott Livingston
** Speaker 8: Eric
** SURF 2: Yuchen
* SURF meetings, cycle 3: Fri, pm
** 3:00p: Klavdia and Sawyer
** 3:30p: open
** 4:00p: open
** 4:30p: open
** 5:00p: open
|
Fri @ 12: speaker TBD
|
* RMM out 1-4 Aug
|- valign=top
|

===== 8-12 Aug =====
|
* Robotics: Tue, 1p-3p
** Speaker 6: open
** SURF 3: Klavdia
* SURF meetings, cycle 3: Tue, pm
** 3:00p: open
** 4:30p: open
** 4:00p: open
** 5:30p: Stephanie and Necmiye
** 6:00p: open
* Biocircuits: Thu, 10a-12p
** Speaker 9: Jongmin
** Speaker 10: Shaunak
** SURF 4: Keshav
* iGEM: Thu, 5p-6p
|
Thu @ 12: speaker TBD
|
|- valign=top
|

===== 15-19 Aug =====
|
|
|
RMM out 15-19 Aug
|- valign=top
|

===== 22-26 Aug =====
|
* iGEM: Mon, 9a-10a
* Biocircuits: Mon, 10a-12p
** Speaker 11: open
** Speaker 12: Enoch Yeung
** Speaker 13: open
* Robotics: Mon, 1p-3p
** Speaker 7: open
** Speaker 8: open
* NCS: Mon, 3p-5p
** Speaker 9: Linlin
** Speaker 10: Necmiye
|
Tue @ 12: speaker TBD
|
RMM out: 25 Aug (pm) - 1 Sep (pm)
|- valign=top
|

===== 29 Aug - 2 Sep =====
|
* Robotics: Thu, 1-3p
** Speaker 9: Shuo
** Speaker 10: Pete
* NCS: Thu, 3-5p
** Speaker 11: Asghar
** Speaker 12: Eric
* iGEM: Thu, 5p-6p
* Biocircuits; Fri, 10a-12p
** Speaker 14: Ophelia
** Speaker 15: open
** Speaker 16: open

|
Fri @ 12p (tentative): speaker TBD
|
* RMM out: 25 Aug (pm) - 1 Sep (pm)
|- valign=top
|

===== 5-9 Sep =====
|
|
|
* RMM out, 5-9 Sep
|- valign=top
|
===== 12-16 Sep =====
|
* Biocircuits: Tue, 10a-12p
** Speaker 17: open
** Speaker 18: open
** Speaker 19: open
* NCS: Wed, 1p-3p
** Speaker 13: Mumu
** Speaker 14: Ufuk
|
Tue @ 12p: speaker TBD
|
|- valign=top
|

===== 19-23 Sep =====
|
* Robotics: Mon, 1p-3p
** Speaker 11: Asghar
** Speaker 12: Andrea
* Biocircuits: Tue, 10a-12p
** Speaker 20: open
** Speaker 21: Enoch Yeung
** Speaker 22: open
|
Tue @ 12p: speaker TBD
|
RMM out, 20 Sep (pm) to 23 Sep
|}

SURF 2011

2011-06-12T20:21:16Z

Jongmin: /* 20 June 2011 (Mon) */

This page is intended for students working on SURF projects in the Summer of 2011. Mainly for meet to keep track of everything that is going on. __NOTOC__

=== Students ===
{| width=100% border=1
|-
| Student
| Mini-group
| Co-mentor(s)
| Project
| Comments
|-
| Chandrasekhar, Arjun || Biocircuits || (Emzo) || Simulac ||
|-
| Chinchali, Sandeep || Robotics || Scott || LTL grasping ||
|-
| Håkansson, Magnus || Robotics || Andrea || Bootstrapping ||
|-
| Khetarpal, Ishan || Biocircuits || Jongmin || Event detector ||
|-
| Lin, Yuchen || NCS || Necmiye, Scott || TuLiP user interface ||
|-
| Nguyen, Paul || Biocircuits || Joe || sRNA delay circuits ||
|-
| Nilsson, Peter || NCS || Necmiye, Ufuk || TuLiP abstraction algorithms ||
|-
| Sapatnekar, Keshav || Biocircuits || Emzo || Scaffold protein sensor ||
|-
| Tsuei, Stephanie || Robotics || Necmiye || Distributed camera network ||
|-
| Zemlianova, Klavdia || Robotics || (Sawyer) || Multi-modal insect flight control || 20 Jun start
|}

* iGEM: Brown, Julia; Cheng, Puikei; Shelton, Amanda; Thadani, Nicole
* Solar Decathlon: Jones, Sam; Lu, David; Suen, Ka

=== Meetings on 20-21 June ===
I'd like to have a 30 minute meeting with all summer undergraduates on either 20 or 21 June to kick off the summer (I am out of town the week of 13 June, when many of you start). This meeting should be with me and (one of) you co-mentor(s). Please check with the appropriate co-mentor before signing up, to make sure they can also make that time.

{| width=100% border=1
|- valign=top
| width=60% |
==== 20 June 2011 (Mon) ====
{| cellpadding=0 cellspacing=0 width=100%
|- valign=top
| wdith=50% |
{{agenda begin}}
{{agenda item|11:30a|Stephanie and Necmiye}}
{{agenda item|12:00p|Open}}
{{agenda end}}
| width=50% |
{{agenda begin}}
{{agenda item|4:30p|Ishan and Jongmin}}
{{agenda item|5:00p|Keshav and Emzo}}
{{agenda item|5:30p|Paul and Joe}}
{{agenda item|6:00p|Open}}
{{agenda item|6:30p|Open}}
{{agenda end}}
|}
| width=30% |

==== 21 June 2011 (Tue) ====
{{agenda begin}}
{{agenda item|11:00a|Open}}
{{agenda item|11:30a|Open}}
{{agenda end}}
|}

=== Original project descriptions ===

This section contains a list of project areas where I will be supervising projects this year. (OBSOLETE:) Students interested in writing proposals for SURF projects should contact me via e-mail to discuss what areas they are interested in and talk through possible SURF proposal topics. All applications should go through the normal SURF application process, described at www.surf.caltech.edu.

{| border=1 width=100%
|-
| '''Title''' || '''Grant/Project''' || '''Co-Mentors''' || '''Comments'''
|-
| [[SURF 2011: Synthetic biology in a cell-free expression system|Synthetic biology in a cell-free expression system]]
| [[Molecular Programming Project|MPP]]
| Jongmin Kim
|
|-
| [[SURF 2011: Design of Biomolecular Circuits Using Programmable Protein Scaffolds|Design of Biomolecular Circuits Using Programmable Protein Scaffolds]]
| [[Biomolecular Feedback Circuits for Modular, Robust and Rapid Response|ICB]]
| Emzo de los Santos
|
|-
| [[SURF 2011: Effects of Topology on DNA Transcription|Effects of Topology on DNA Transcription]]
| [[Biomolecular Feedback Circuits for Modular, Robust and Rapid Response|ICB]]
| Joseph T. Meyerowitz
|
|-
| [[SURF 2011: Receding Horizon Temporal Logic Planning Toolbox|Receding Horizon Temporal Logic Planning Toolbox]]
| [[Distributed_Sense_and_Control_Systems|MuSyC]]
| Ufuk Topcu
|
|-
| [[SURF 2011: Implementation of Control Protocols for Camera Networks|Implementation of Control Protocols for Camera Networks]]
| [[Distributed_Sense_and_Control_Systems|MuSyC]]
| Necmiye Ozay
|
|}

Group Schedule, Summer 2011

2011-06-12T19:05:15Z

Jongmin: /* 8-12 Aug */

__NOTOC__
{| border=1 width=100%
|- valign=top
| '''Week'''
| '''Mini-group meetings'''
| '''Group meeting'''
| '''Other'''
|- valign=top
|
===== 13-17 Jun =====
|
None
|
None
|
RMM out all week
|- valign=top
|
===== 20-24 Jun =====
|
* iGEM: Mon @ 9:30
* SURF meetings, cycle 0: (sign on at [[SURF 2011]] page)
* NCS: Tue, 1-3 pm
** Speaker 1: Necmiye
** Speaker 2: open
|
Tue @ 12: speaker TBD (external)
|
RMM out 22-24 Jun
|- valign=top
|

===== 27 Jun - 1 Jul =====
|
* Robotics: Mon, 1-3 pm
** Speaker 1: open
** Speaker 2: open
* Biocircuits: Tue, 9a-2p
** Overview presentations (all; 10 min each)
** Lunch will be provided
* SURF meetings, cycle 1: Tue pm
** 4:00 pm: open
** 4:30 pm: open
** 5:00 pm: open
** 5:30 pm: open
** 6:00 pm: open
|
Mon @ 12: Nils Napp
|
* Nils Napp visiting
* RMM out 29 Jun-1 Jul (ACC)
|- valign=top
|

===== 4-8 Jul =====
|
* Biocircuits: Tue, 10-12
** Speaker 1: Marcella
** Speaker 2: open
** Speaker 3: open
* NCS: Thu, 1-3 pm
** Speaker 3: Scott Livingston
** Speaker 4: Marcella
* SURF meetings, cycle 1: Thu pm
** 3:00 pm: open
** 3:30 pm: open
** 4:00 pm: open
** 4:30 pm: open
** 5:00 pm: open

|
Tue @ 12: Henrik Sandberg
|
* Institute holiday on Mon
* Eric Colinet visiting on 5 Jul
* Henrik Sandberg visiting 3-9 Jul
|- valign=top
|

===== 11-15 Jul =====
|
* iGEM: Mon @ 5 pm?
* Biocircuits: Tue, 10a-12p
** Speaker 4: open
** Speaker 5: open
** iGEM presentation (30 min)
* Robotics: Tue, 1p-3p
** Speaker 3: Shuo
** Speaker 4: Sandeep
* SURF meetings, cycle 2: Thu, pm
** 3:00 pm: open
** 3:30 pm: open
** 4:00 pm: open
** 4:30 pm: open
** 5:00 pm: open
|
Mon @ 12: Speaker TBD
|
|- valign=top
|

===== 18-22 Jul =====
|
* SURF meetings, cycle 2: Thu pm
** 2:30p: open
** 3:00p: open
** 3:30p: open
** 4:00p: open
** 4:30p: open
* iGEM: Thu, 5-6p?
* Biocircuits: Fri, 10a-12p
** Speaker 6: Ye Yuan
** Speaker 7: Dionysios
** SURF 1: Paul
* Robotics: Fri, 1p-3p
** Speaker 5: open
** SURF 1: Magnus
** SURF 2: Stephanie
* NCS: Fri, 3p-5p
** Speaker 5: Mumu
** Speaker 6: Ufuk
** SURF 1: Petter
|
Fri @ 12: Josh Michener
|
* RMM out 18-21 Jul am
* Josh Michener visiting 22 Jul
|- valign=top
|

===== 25-29 Jul =====
|
|
|
* RMM out 25-29 Jul
|- valign=top
|

===== 1-5 Aug =====
|
* iGEM: 5-6p?
* Biocircuits: Fri, 10a-12p
** Speaker 8: Marcella
** SURF 2: Ishan
** SURF 3: Arjun
* NCS: Fri, 1p-3p
** Speaker 7: Scott Livingston
** Speaker 8: Marcella
** SURF 2: Yuchen
* SURF meetings, cycle 3: Fri, pm
** 3:00p: open
** 3:30p: open
** 4:00p: open
** 4:30p: open
** 5:00p: open
|
Fri @ 12: speaker TBD
|
* RMM out 1-4 Aug
|- valign=top
|

===== 8-12 Aug =====
|
* Robotics: Tue, 1p-3p
** Speaker 6: open
** SURF 3: Klavdia
* SURF meetings, cycle 3: Tue, pm
** 3:00p: open
** 4:30p: open
** 4:00p: open
** 5:30p: open
** 6:00p: open
* Biocircuits: Thu, 10a-12p
** Speaker 9: Jongmin
** Speaker 10: open
** SURF 4: Keshav
* iGEM: 5p-6p
|
Thu @ 12: speaker TBD
|
|- valign=top
|

===== 15-19 Aug =====
|
|
|
RMM out 15-19 Aug
|- valign=top
|

===== 22-26 Aug =====
|
* Biocircuits: Mon, 10a-12p
** Speaker 11: open
** Speaker 12: open
** Speaker 13: open
* Robotics: Mon, 1p-3p
** Speaker 7: open
** Speaker 8: open
* NCS: Mon, 3p-5p
** Speaker 9: open
** Speaker 10: Necmiye
* iGEM: 5p-6p
|
Tue @ 12: speaker TBD
|
RMM out: 25 Aug (pm) - 1 Sep (pm)
|- valign=top
|

===== 29 Aug - 2 Sep =====
|
* Robotics: Thu, 1-3p
** Speaker 9: Shuo
** Speaker 10: open
* NCS: Thu, 3-5p
** Speaker 11: Asghar
** Speaker 12: open
* iGEM: Thu, 5p-6p
* Biocircuits; Fri, 10a-12p
** Speaker 14: open
** Speaker 15: open
** Speaker 16: open

|
Fri @ 12p (tentative): speaker TBD
|
* RMM out: 25 Aug (pm) - 1 Sep (pm)
|- valign=top
|

===== 5-9 Sep =====
|
|
|
* RMM out, 5-9 Sep
|- valign=top
|
===== 12-16 Sep =====
|
* Biocircuits: Tue, 10a-12p
** Speaker 17: open
** Speaker 18: open
** Speaker 19: open
* NCS: Wed, 1p-3p
** Speaker 13: Mumu
** Speaker 14: Ufuk
|
Tue @ 12p: speaker TBD
|
|- valign=top
|

===== 19-23 Sep =====
|
* Robotics: Mon, 1p-3p
** Speaker 11: Asghar
** Speaker 12: open
* Biocircuits: Tue, 10a-12p
** Speaker 20: open
** Speaker 21: open
** Speaker 22: open
|
Tue @ 12p: speaker TBD
|
RMM out, 20 Sep (pm) to 23 Sep
|}

June 2011 meetings

2011-05-31T19:17:45Z

Jongmin: /* 8 Jun (Wed) */

__NOTOC__
{| border=1 width=100%
|- valign=top
| width=20% |

| width=20% |

| width=20% |
==== 1 Jun (Wed) ====
* 9:15a - Ye
* 10:00a - Matanya
* 11:00a - Marcella
* 1:00p - Anu
* 3:00p - CDS tea
* 4:00p - Fei Y
* 5:00p - (Shuo; lab stuff)
* 5:30p - Dionysios
* 6:30p - Shaunak
| width=20% |
==== 2 Jun (Thu) ====
* 10:00a - Biocircuits
* 12:00p - Group meeting
* 5:30p - Necmiye
| width=20% |
==== 3 Jun (Fri) ====
* UCLA
* BE BBQ
|- valign=top
| width=20% |
==== 6 Jun (Mon) ====
* 10:00a - Vanessa
* 11:00a - Henry J
* 12:30p - Robotics
* 5:30p - Andrea
* 6:30p - Ophelia
| width=20% |

==== 7 Jun (Tue) ====
* 10:00a - NCS
* 12:00p - Group meeting
* 3:30p - Scott Livingston
* 4:30p - Aneesh
* 5:30p - Ufuk
* 6:30p - Open
| width=20% |

==== 8 Jun (Wed) ====
* 9:30a - Eric
* 10:30a - Mumu
* 11:30a - Open
* 1:00p - Jongmin
* 2:00p - Emzo
* 3:00p - CDS tea
* 5:30p - Jun Liu
* 6:30p - Open
* 7:30p - Open
| width=20% |

==== 9 Jun (Thu) ====
* 11:30a - Open
* 1:00p - Open
* 2:00p - Open
* 3:00p - CDS 90
* 4:30p - Enoch Yeung
* 5:30p - Open
* 6:30p - Open
| width=20% |

==== 10 Jun (Fri) ====
* 5:30p - Open
|}

Mini-bootcamp 2011

2011-03-04T11:24:18Z

Jongmin: /* Techniques and equipment: */

This page contains a description of the mini-bootcamp run in Feb 2011. __NOTOC__

=== Group ===
<center>
{| width=90%
|- valign=top
| width=25% |
===== Students =====
* Jorge Goncalves
* Jun Liu
* Yuan Ye
* Enoch Yeung
| width=25% |

===== Part-time students =====
* Elisa Franco
* Richard Murray
| width=25% |
===== Instructors =====
* Emzo de los Santos
* Joe Meyerowitz
* Ophelia Venturelli
* Vanessa Jonsson
* Jongmin Kim
| width=25% |

===== Project advisor =====
* Richard Murray
|}
</center>

=== Bootcamp description ===

{| width=100% border=1
|- valign=top
| rowspan=3 |
The goal of this bootcamp is to measure variability in gene expression that is relevant for synthetically designed circuits. The issue that we are trying to understand is now much variability arises for the expression of a given circuit under degrees of freedom that are typically not controlled in synthetic designs:
* Location and orientation of circuit elements in the plasmid
* Vectors used for expressing the circuit, including copy number and antibiotic resistance
* Growth conditions (temperature, oxygen, media, growth phase)
To understand how these (and other) factors will affect circuit operation, a simple genetic circuit consisting of 2 reporters will be built using different DNA locations and directions, and characterized in a variety of conditions. The dynamic response of the circuit will be measured, including cell-to-cell variability (via flow cytometry and microscopy).

Bootcamp objectives:
* Project 1: Construct a simple genetic circuit that tests the effects of putting different reporters in different configurations in a plasmid. Characterize the differences (if any) in mean expression level of the circuits, possibly in multiple growth conditions, using a plate reader
* Project 2: Characterize differences in expression distributions using flow cytometry (FACS Calibur) and fluorescent microscopy
* Project 3: Perform in vitro testing of the constructs using the PURExpress kit and spectrofluorometer to check for differences in mean expression level
|
[[Image:lambda_switch.png|300px]]
* Circuit layout: directions, ordering
|-
|
[[Image:biobrick_plasmid.png|300px]]
* Copy number
* Origin of replication
* Antibiotic resistance
* [[http:partsregistry.org/Plasmid_backbones|Biobrick plasmids]]
|-
|
* (Cell strain)
* Growth media: LB, M9/glycerol, M9/glucose
* Induction level
* Temperature
|}

=== Schedule ===
{| width=100% border=1
|- valign=top
| width=20% | 14 Feb: 2-4
* Biocircuits mini-group meeting - planning
* Richard
| width=20% | 15 Feb
| width=20% | 16 Feb:
* [[#Session 0: project discussion and lab tour|Session 0: project discussion and lab tour]]
* Richard, Ophelia
* Joe, Elisa
| width=20% | 17 Feb: 2:30-6
* [[Mini-bootcamp_2011/Session 1: lab techniques|Session 1: lab techniques]]
* Emzo, Jongmin
| width=20% | 18 Feb
|- valign=top
| width=20% | 21 Feb: 1-6
* [[#Session 2: cloning|Session 2: cloning]]
* Joe, Emzo
| width=20% | 22 Feb
| width=20% | 23 Feb: 1-6
* [[#Session 3: plate reader|Session 3: plate reader]]
* Ophelia, Richard
| width=20% | 24 Feb
* Project #1
| width=20% | 25 Feb
* Project #1

|- valign=top
| width=20% | 28 Feb
* Project #1
| width=20% | 1 Mar
* Project #1
| width=20% | 2 Mar: TBD
* [[#Session 4: microscopy|Session 4: microscopy]]
* Ophelia, Joe
| width=20% | 3 Mar
*Project #1
| width=20% | 4 Mar
*Project #1
|- valign=top
| width=20% | 7 Mar: TBD
* [[#Session 5: flow cytometry|Session 5: flow cytometry]]
* Joe, Vanessa
| width=20% | 8 Mar: TBD
* [[#Session 6: spectrofluorometer|Session 6: spectrofluorometer]]
* Jongmin, Elisa
| width=20% | 9 Mar
* Project #3
| width=20% | 10 Mar
* Project #3
| width=20% | 11 Mar
* Project #3
|}
 
<hr>
==== Session 0: project discussion and lab tour ====
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
* Overview of project goals
* Tour of 040 Keck
* Lab safety
===== Instructors: =====
* Richard Murray, Ophelia Venturelli
* Joe Meyerowitz, Elisa Franco (lab tour, safety)
<hr>
==== [[Mini-bootcamp_2011/Session 1: lab techniques|Session 1: lab techniques]] ====
This lab session will teach some of the basic techniques that will be used throughout the bootcamp. We assume no background in molecular biology laboratory techniques. By the end of this session, students will be able to transform a plasmid into cells, pick colonies containing the plasmid, grow the cells up to a given optical density, extract the plasmids, and quantify them.
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
* Lab safety
* Laboratory techniques: gloves, pipetting, disposal
* Transforming plasmids into cells, growing, extracting
* Clean up: benches, glassware

===== Instructors: =====
* Emzo
* Jongmin
| width=50% |
===== Techniques and equipment: =====
* Pipetting
* Transformation, selection, growth
* Optical density (OD) measurements (nanodrop?)
* Mini-preps
* Quantification (nanodrop)
* Autoclave
|}
<hr>

==== [[Mini-bootcamp_2011/Session 2: cloning|Session 2: cloning]] ====
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
* Discussion of PCR, primer design, Gibson assembly, gels
* Demonstration of PCR
* Demonstration of Gibson assembly
* Demonstration of electrophoresis, restriction digestion, mapping
* Transform Gibson product

===== Instructors: =====
* Joe
* Emzo
| width=50% |

===== Techniques and equipment: =====
* PCR
* Restriction digests
* Gels
* Gibson assembly
|}
<hr>

==== Session 3: [[plate reader]] ====
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
* Set up dose response with E. coli strains using serial dilution method
* Learn strategies for measuring dynamics in plate reader
:*Growth in shaker (manual time points)
:*Growth in VictorX3 (automated measurements)
* Measure gene expression (GFP) and OD (cell mass) using VictorX3 over a period of time

===== Instructors: =====
* Ophelia
* Richard
| width=50% |

===== Techniques and equipment: =====
* Victor X3 plate reader
|}
<hr>

==== Session 4: [[microscope]] ====
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
* Learn basic principles and design of the Olympus IX-81 light microscope
* Learn how to make agarose pads for imaging E coli
* Basics of Micro-Manager software
* Discuss image analysis

===== Instructors: =====
* Ophelia
* Joe
| width=50% |
===== Techniques and equipment: =====
* Olympus IX-81 microscope
* MATLAB tools for image analysis
|}
<hr>

==== Session 5: flow cytometer ====
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
*
===== Instructors: =====
* Joe
* Vanessa
| width=50% |
===== Techniques and equipment: =====
* FACS Calibur flow cytometer
* MaxQuant (?)
|}
<hr>

==== Session 6: [[Mini-bootcamp_2011/Session_6:_Spectrofluorometer|spectrofluorometer]] ====
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
* Learn basic principles of the Fluorolog 3 spectrofluorometer
* Learn how to run protein gels
* Basics of the PURExpress protein expression kit
* Basics of spectrofluorometer software
===== Instructors: =====
* Jongmin
* Elisa
| width=50% |

===== Techniques and equipment: =====
* PURExpress protein expression kit
* Protein gels
* Fluorolog 3 spectrofluorometer
|}

Mini-bootcamp 2011

2011-03-04T11:23:35Z

Jongmin: /* Session 6: [Mini-bootcamp_2011/Session_6:_Spectrofluorometer|spectrofluorometer] */

Mini-bootcamp 2011

2011-03-04T11:22:40Z

Jongmin: /* Session 6: [https://www.cds.caltech.edu/~murray/wiki/index.php/Mini-bootcamp_2011/Session_6:_Spectrofluorometer|spectrofluorometer] */

This page contains a description of the mini-bootcamp run in Feb 2011. __NOTOC__

=== Group ===
<center>
{| width=90%
|- valign=top
| width=25% |
===== Students =====
* Jorge Goncalves
* Jun Liu
* Yuan Ye
* Enoch Yeung
| width=25% |

===== Part-time students =====
* Elisa Franco
* Richard Murray
| width=25% |
===== Instructors =====
* Emzo de los Santos
* Joe Meyerowitz
* Ophelia Venturelli
* Vanessa Jonsson
* Jongmin Kim
| width=25% |

===== Project advisor =====
* Richard Murray
|}
</center>

=== Bootcamp description ===

{| width=100% border=1
|- valign=top
| rowspan=3 |
The goal of this bootcamp is to measure variability in gene expression that is relevant for synthetically designed circuits. The issue that we are trying to understand is now much variability arises for the expression of a given circuit under degrees of freedom that are typically not controlled in synthetic designs:
* Location and orientation of circuit elements in the plasmid
* Vectors used for expressing the circuit, including copy number and antibiotic resistance
* Growth conditions (temperature, oxygen, media, growth phase)
To understand how these (and other) factors will affect circuit operation, a simple genetic circuit consisting of 2 reporters will be built using different DNA locations and directions, and characterized in a variety of conditions. The dynamic response of the circuit will be measured, including cell-to-cell variability (via flow cytometry and microscopy).

Bootcamp objectives:
* Project 1: Construct a simple genetic circuit that tests the effects of putting different reporters in different configurations in a plasmid. Characterize the differences (if any) in mean expression level of the circuits, possibly in multiple growth conditions, using a plate reader
* Project 2: Characterize differences in expression distributions using flow cytometry (FACS Calibur) and fluorescent microscopy
* Project 3: Perform in vitro testing of the constructs using the PURExpress kit and spectrofluorometer to check for differences in mean expression level
|
[[Image:lambda_switch.png|300px]]
* Circuit layout: directions, ordering
|-
|
[[Image:biobrick_plasmid.png|300px]]
* Copy number
* Origin of replication
* Antibiotic resistance
* [[http:partsregistry.org/Plasmid_backbones|Biobrick plasmids]]
|-
|
* (Cell strain)
* Growth media: LB, M9/glycerol, M9/glucose
* Induction level
* Temperature
|}

=== Schedule ===
{| width=100% border=1
|- valign=top
| width=20% | 14 Feb: 2-4
* Biocircuits mini-group meeting - planning
* Richard
| width=20% | 15 Feb
| width=20% | 16 Feb:
* [[#Session 0: project discussion and lab tour|Session 0: project discussion and lab tour]]
* Richard, Ophelia
* Joe, Elisa
| width=20% | 17 Feb: 2:30-6
* [[Mini-bootcamp_2011/Session 1: lab techniques|Session 1: lab techniques]]
* Emzo, Jongmin
| width=20% | 18 Feb
|- valign=top
| width=20% | 21 Feb: 1-6
* [[#Session 2: cloning|Session 2: cloning]]
* Joe, Emzo
| width=20% | 22 Feb
| width=20% | 23 Feb: 1-6
* [[#Session 3: plate reader|Session 3: plate reader]]
* Ophelia, Richard
| width=20% | 24 Feb
* Project #1
| width=20% | 25 Feb
* Project #1

|- valign=top
| width=20% | 28 Feb
* Project #1
| width=20% | 1 Mar
* Project #1
| width=20% | 2 Mar: TBD
* [[#Session 4: microscopy|Session 4: microscopy]]
* Ophelia, Joe
| width=20% | 3 Mar
*Project #1
| width=20% | 4 Mar
*Project #1
|- valign=top
| width=20% | 7 Mar: TBD
* [[#Session 5: flow cytometry|Session 5: flow cytometry]]
* Joe, Vanessa
| width=20% | 8 Mar: TBD
* [[#Session 6: spectrofluorometer|Session 6: spectrofluorometer]]
* Jongmin, Elisa
| width=20% | 9 Mar
* Project #3
| width=20% | 10 Mar
* Project #3
| width=20% | 11 Mar
* Project #3
|}
 
<hr>
==== Session 0: project discussion and lab tour ====
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
* Overview of project goals
* Tour of 040 Keck
* Lab safety
===== Instructors: =====
* Richard Murray, Ophelia Venturelli
* Joe Meyerowitz, Elisa Franco (lab tour, safety)
<hr>
==== [[Mini-bootcamp_2011/Session 1: lab techniques|Session 1: lab techniques]] ====
This lab session will teach some of the basic techniques that will be used throughout the bootcamp. We assume no background in molecular biology laboratory techniques. By the end of this session, students will be able to transform a plasmid into cells, pick colonies containing the plasmid, grow the cells up to a given optical density, extract the plasmids, and quantify them.
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
* Lab safety
* Laboratory techniques: gloves, pipetting, disposal
* Transforming plasmids into cells, growing, extracting
* Clean up: benches, glassware

===== Instructors: =====
* Emzo
* Jongmin
| width=50% |
===== Techniques and equipment: =====
* Pipetting
* Transformation, selection, growth
* Optical density (OD) measurements (nanodrop?)
* Mini-preps
* Quantification (nanodrop)
* Autoclave
|}
<hr>

==== [[Mini-bootcamp_2011/Session 2: cloning|Session 2: cloning]] ====
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
* Discussion of PCR, primer design, Gibson assembly, gels
* Demonstration of PCR
* Demonstration of Gibson assembly
* Demonstration of electrophoresis, restriction digestion, mapping
* Transform Gibson product

===== Instructors: =====
* Joe
* Emzo
| width=50% |

===== Techniques and equipment: =====
* PCR
* Restriction digests
* Gels
* Gibson assembly
|}
<hr>

==== Session 3: [[plate reader]] ====
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
* Set up dose response with E. coli strains using serial dilution method
* Learn strategies for measuring dynamics in plate reader
:*Growth in shaker (manual time points)
:*Growth in VictorX3 (automated measurements)
* Measure gene expression (GFP) and OD (cell mass) using VictorX3 over a period of time

===== Instructors: =====
* Ophelia
* Richard
| width=50% |

===== Techniques and equipment: =====
* Victor X3 plate reader
|}
<hr>

==== Session 4: [[microscope]] ====
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
* Learn basic principles and design of the Olympus IX-81 light microscope
* Learn how to make agarose pads for imaging E coli
* Basics of Micro-Manager software
* Discuss image analysis

===== Instructors: =====
* Ophelia
* Joe
| width=50% |
===== Techniques and equipment: =====
* Olympus IX-81 microscope
* MATLAB tools for image analysis
|}
<hr>

==== Session 5: flow cytometer ====
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
*
===== Instructors: =====
* Joe
* Vanessa
| width=50% |
===== Techniques and equipment: =====
* FACS Calibur flow cytometer
* MaxQuant (?)
|}
<hr>

==== Session 6: [Mini-bootcamp_2011/Session_6:_Spectrofluorometer|spectrofluorometer] ====
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
* Learn basic principles of the Fluorolog 3 spectrofluorometer
* Learn how to run protein gels
* Basics of the PURExpress protein expression kit
* Basics of spectrofluorometer software
===== Instructors: =====
* Jongmin
* Elisa
| width=50% |

===== Techniques and equipment: =====
* PURExpress protein expression kit
* Protein gels (?)
* Fluorilog 3 spectrofluorometer
|}

Mini-bootcamp 2011

2011-03-04T11:21:26Z

Jongmin: /* Session 6: [https://www.cds.caltech.edu/~murray/wiki/index.php/Mini-bootcamp_2011/Session_6_|spectrofluorometer] */

This page contains a description of the mini-bootcamp run in Feb 2011. __NOTOC__

=== Group ===
<center>
{| width=90%
|- valign=top
| width=25% |
===== Students =====
* Jorge Goncalves
* Jun Liu
* Yuan Ye
* Enoch Yeung
| width=25% |

===== Part-time students =====
* Elisa Franco
* Richard Murray
| width=25% |
===== Instructors =====
* Emzo de los Santos
* Joe Meyerowitz
* Ophelia Venturelli
* Vanessa Jonsson
* Jongmin Kim
| width=25% |

===== Project advisor =====
* Richard Murray
|}
</center>

=== Bootcamp description ===

{| width=100% border=1
|- valign=top
| rowspan=3 |
The goal of this bootcamp is to measure variability in gene expression that is relevant for synthetically designed circuits. The issue that we are trying to understand is now much variability arises for the expression of a given circuit under degrees of freedom that are typically not controlled in synthetic designs:
* Location and orientation of circuit elements in the plasmid
* Vectors used for expressing the circuit, including copy number and antibiotic resistance
* Growth conditions (temperature, oxygen, media, growth phase)
To understand how these (and other) factors will affect circuit operation, a simple genetic circuit consisting of 2 reporters will be built using different DNA locations and directions, and characterized in a variety of conditions. The dynamic response of the circuit will be measured, including cell-to-cell variability (via flow cytometry and microscopy).

Bootcamp objectives:
* Project 1: Construct a simple genetic circuit that tests the effects of putting different reporters in different configurations in a plasmid. Characterize the differences (if any) in mean expression level of the circuits, possibly in multiple growth conditions, using a plate reader
* Project 2: Characterize differences in expression distributions using flow cytometry (FACS Calibur) and fluorescent microscopy
* Project 3: Perform in vitro testing of the constructs using the PURExpress kit and spectrofluorometer to check for differences in mean expression level
|
[[Image:lambda_switch.png|300px]]
* Circuit layout: directions, ordering
|-
|
[[Image:biobrick_plasmid.png|300px]]
* Copy number
* Origin of replication
* Antibiotic resistance
* [[http:partsregistry.org/Plasmid_backbones|Biobrick plasmids]]
|-
|
* (Cell strain)
* Growth media: LB, M9/glycerol, M9/glucose
* Induction level
* Temperature
|}

=== Schedule ===
{| width=100% border=1
|- valign=top
| width=20% | 14 Feb: 2-4
* Biocircuits mini-group meeting - planning
* Richard
| width=20% | 15 Feb
| width=20% | 16 Feb:
* [[#Session 0: project discussion and lab tour|Session 0: project discussion and lab tour]]
* Richard, Ophelia
* Joe, Elisa
| width=20% | 17 Feb: 2:30-6
* [[Mini-bootcamp_2011/Session 1: lab techniques|Session 1: lab techniques]]
* Emzo, Jongmin
| width=20% | 18 Feb
|- valign=top
| width=20% | 21 Feb: 1-6
* [[#Session 2: cloning|Session 2: cloning]]
* Joe, Emzo
| width=20% | 22 Feb
| width=20% | 23 Feb: 1-6
* [[#Session 3: plate reader|Session 3: plate reader]]
* Ophelia, Richard
| width=20% | 24 Feb
* Project #1
| width=20% | 25 Feb
* Project #1

|- valign=top
| width=20% | 28 Feb
* Project #1
| width=20% | 1 Mar
* Project #1
| width=20% | 2 Mar: TBD
* [[#Session 4: microscopy|Session 4: microscopy]]
* Ophelia, Joe
| width=20% | 3 Mar
*Project #1
| width=20% | 4 Mar
*Project #1
|- valign=top
| width=20% | 7 Mar: TBD
* [[#Session 5: flow cytometry|Session 5: flow cytometry]]
* Joe, Vanessa
| width=20% | 8 Mar: TBD
* [[#Session 6: spectrofluorometer|Session 6: spectrofluorometer]]
* Jongmin, Elisa
| width=20% | 9 Mar
* Project #3
| width=20% | 10 Mar
* Project #3
| width=20% | 11 Mar
* Project #3
|}
 
<hr>
==== Session 0: project discussion and lab tour ====
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
* Overview of project goals
* Tour of 040 Keck
* Lab safety
===== Instructors: =====
* Richard Murray, Ophelia Venturelli
* Joe Meyerowitz, Elisa Franco (lab tour, safety)
<hr>
==== [[Mini-bootcamp_2011/Session 1: lab techniques|Session 1: lab techniques]] ====
This lab session will teach some of the basic techniques that will be used throughout the bootcamp. We assume no background in molecular biology laboratory techniques. By the end of this session, students will be able to transform a plasmid into cells, pick colonies containing the plasmid, grow the cells up to a given optical density, extract the plasmids, and quantify them.
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
* Lab safety
* Laboratory techniques: gloves, pipetting, disposal
* Transforming plasmids into cells, growing, extracting
* Clean up: benches, glassware

===== Instructors: =====
* Emzo
* Jongmin
| width=50% |
===== Techniques and equipment: =====
* Pipetting
* Transformation, selection, growth
* Optical density (OD) measurements (nanodrop?)
* Mini-preps
* Quantification (nanodrop)
* Autoclave
|}
<hr>

==== [[Mini-bootcamp_2011/Session 2: cloning|Session 2: cloning]] ====
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
* Discussion of PCR, primer design, Gibson assembly, gels
* Demonstration of PCR
* Demonstration of Gibson assembly
* Demonstration of electrophoresis, restriction digestion, mapping
* Transform Gibson product

===== Instructors: =====
* Joe
* Emzo
| width=50% |

===== Techniques and equipment: =====
* PCR
* Restriction digests
* Gels
* Gibson assembly
|}
<hr>

==== Session 3: [[plate reader]] ====
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
* Set up dose response with E. coli strains using serial dilution method
* Learn strategies for measuring dynamics in plate reader
:*Growth in shaker (manual time points)
:*Growth in VictorX3 (automated measurements)
* Measure gene expression (GFP) and OD (cell mass) using VictorX3 over a period of time

===== Instructors: =====
* Ophelia
* Richard
| width=50% |

===== Techniques and equipment: =====
* Victor X3 plate reader
|}
<hr>

==== Session 4: [[microscope]] ====
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
* Learn basic principles and design of the Olympus IX-81 light microscope
* Learn how to make agarose pads for imaging E coli
* Basics of Micro-Manager software
* Discuss image analysis

===== Instructors: =====
* Ophelia
* Joe
| width=50% |
===== Techniques and equipment: =====
* Olympus IX-81 microscope
* MATLAB tools for image analysis
|}
<hr>

==== Session 5: flow cytometer ====
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
*
===== Instructors: =====
* Joe
* Vanessa
| width=50% |
===== Techniques and equipment: =====
* FACS Calibur flow cytometer
* MaxQuant (?)
|}
<hr>

==== Session 6: [https://www.cds.caltech.edu/~murray/wiki/index.php/Mini-bootcamp_2011/Session_6:_Spectrofluorometer|spectrofluorometer] ====
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
* Learn basic principles of the Fluorolog 3 spectrofluorometer
* Learn how to run protein gels
* Basics of the PURExpress protein expression kit
* Basics of spectrofluorometer software
===== Instructors: =====
* Jongmin
* Elisa
| width=50% |

===== Techniques and equipment: =====
* PURExpress protein expression kit
* Protein gels (?)
* Fluorilog 3 spectrofluorometer
|}

Mini-bootcamp 2011

2011-03-04T11:20:05Z

Jongmin: /* Session 6: [spectrofluorometer] */

This page contains a description of the mini-bootcamp run in Feb 2011. __NOTOC__

=== Group ===
<center>
{| width=90%
|- valign=top
| width=25% |
===== Students =====
* Jorge Goncalves
* Jun Liu
* Yuan Ye
* Enoch Yeung
| width=25% |

===== Part-time students =====
* Elisa Franco
* Richard Murray
| width=25% |
===== Instructors =====
* Emzo de los Santos
* Joe Meyerowitz
* Ophelia Venturelli
* Vanessa Jonsson
* Jongmin Kim
| width=25% |

===== Project advisor =====
* Richard Murray
|}
</center>

=== Bootcamp description ===

{| width=100% border=1
|- valign=top
| rowspan=3 |
The goal of this bootcamp is to measure variability in gene expression that is relevant for synthetically designed circuits. The issue that we are trying to understand is now much variability arises for the expression of a given circuit under degrees of freedom that are typically not controlled in synthetic designs:
* Location and orientation of circuit elements in the plasmid
* Vectors used for expressing the circuit, including copy number and antibiotic resistance
* Growth conditions (temperature, oxygen, media, growth phase)
To understand how these (and other) factors will affect circuit operation, a simple genetic circuit consisting of 2 reporters will be built using different DNA locations and directions, and characterized in a variety of conditions. The dynamic response of the circuit will be measured, including cell-to-cell variability (via flow cytometry and microscopy).

Bootcamp objectives:
* Project 1: Construct a simple genetic circuit that tests the effects of putting different reporters in different configurations in a plasmid. Characterize the differences (if any) in mean expression level of the circuits, possibly in multiple growth conditions, using a plate reader
* Project 2: Characterize differences in expression distributions using flow cytometry (FACS Calibur) and fluorescent microscopy
* Project 3: Perform in vitro testing of the constructs using the PURExpress kit and spectrofluorometer to check for differences in mean expression level
|
[[Image:lambda_switch.png|300px]]
* Circuit layout: directions, ordering
|-
|
[[Image:biobrick_plasmid.png|300px]]
* Copy number
* Origin of replication
* Antibiotic resistance
* [[http:partsregistry.org/Plasmid_backbones|Biobrick plasmids]]
|-
|
* (Cell strain)
* Growth media: LB, M9/glycerol, M9/glucose
* Induction level
* Temperature
|}

=== Schedule ===
{| width=100% border=1
|- valign=top
| width=20% | 14 Feb: 2-4
* Biocircuits mini-group meeting - planning
* Richard
| width=20% | 15 Feb
| width=20% | 16 Feb:
* [[#Session 0: project discussion and lab tour|Session 0: project discussion and lab tour]]
* Richard, Ophelia
* Joe, Elisa
| width=20% | 17 Feb: 2:30-6
* [[Mini-bootcamp_2011/Session 1: lab techniques|Session 1: lab techniques]]
* Emzo, Jongmin
| width=20% | 18 Feb
|- valign=top
| width=20% | 21 Feb: 1-6
* [[#Session 2: cloning|Session 2: cloning]]
* Joe, Emzo
| width=20% | 22 Feb
| width=20% | 23 Feb: 1-6
* [[#Session 3: plate reader|Session 3: plate reader]]
* Ophelia, Richard
| width=20% | 24 Feb
* Project #1
| width=20% | 25 Feb
* Project #1

|- valign=top
| width=20% | 28 Feb
* Project #1
| width=20% | 1 Mar
* Project #1
| width=20% | 2 Mar: TBD
* [[#Session 4: microscopy|Session 4: microscopy]]
* Ophelia, Joe
| width=20% | 3 Mar
*Project #1
| width=20% | 4 Mar
*Project #1
|- valign=top
| width=20% | 7 Mar: TBD
* [[#Session 5: flow cytometry|Session 5: flow cytometry]]
* Joe, Vanessa
| width=20% | 8 Mar: TBD
* [[#Session 6: spectrofluorometer|Session 6: spectrofluorometer]]
* Jongmin, Elisa
| width=20% | 9 Mar
* Project #3
| width=20% | 10 Mar
* Project #3
| width=20% | 11 Mar
* Project #3
|}
 
<hr>
==== Session 0: project discussion and lab tour ====
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
* Overview of project goals
* Tour of 040 Keck
* Lab safety
===== Instructors: =====
* Richard Murray, Ophelia Venturelli
* Joe Meyerowitz, Elisa Franco (lab tour, safety)
<hr>
==== [[Mini-bootcamp_2011/Session 1: lab techniques|Session 1: lab techniques]] ====
This lab session will teach some of the basic techniques that will be used throughout the bootcamp. We assume no background in molecular biology laboratory techniques. By the end of this session, students will be able to transform a plasmid into cells, pick colonies containing the plasmid, grow the cells up to a given optical density, extract the plasmids, and quantify them.
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
* Lab safety
* Laboratory techniques: gloves, pipetting, disposal
* Transforming plasmids into cells, growing, extracting
* Clean up: benches, glassware

===== Instructors: =====
* Emzo
* Jongmin
| width=50% |
===== Techniques and equipment: =====
* Pipetting
* Transformation, selection, growth
* Optical density (OD) measurements (nanodrop?)
* Mini-preps
* Quantification (nanodrop)
* Autoclave
|}
<hr>

==== [[Mini-bootcamp_2011/Session 2: cloning|Session 2: cloning]] ====
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
* Discussion of PCR, primer design, Gibson assembly, gels
* Demonstration of PCR
* Demonstration of Gibson assembly
* Demonstration of electrophoresis, restriction digestion, mapping
* Transform Gibson product

===== Instructors: =====
* Joe
* Emzo
| width=50% |

===== Techniques and equipment: =====
* PCR
* Restriction digests
* Gels
* Gibson assembly
|}
<hr>

==== Session 3: [[plate reader]] ====
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
* Set up dose response with E. coli strains using serial dilution method
* Learn strategies for measuring dynamics in plate reader
:*Growth in shaker (manual time points)
:*Growth in VictorX3 (automated measurements)
* Measure gene expression (GFP) and OD (cell mass) using VictorX3 over a period of time

===== Instructors: =====
* Ophelia
* Richard
| width=50% |

===== Techniques and equipment: =====
* Victor X3 plate reader
|}
<hr>

==== Session 4: [[microscope]] ====
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
* Learn basic principles and design of the Olympus IX-81 light microscope
* Learn how to make agarose pads for imaging E coli
* Basics of Micro-Manager software
* Discuss image analysis

===== Instructors: =====
* Ophelia
* Joe
| width=50% |
===== Techniques and equipment: =====
* Olympus IX-81 microscope
* MATLAB tools for image analysis
|}
<hr>

==== Session 5: flow cytometer ====
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
*
===== Instructors: =====
* Joe
* Vanessa
| width=50% |
===== Techniques and equipment: =====
* FACS Calibur flow cytometer
* MaxQuant (?)
|}
<hr>

==== Session 6: [https://www.cds.caltech.edu/~murray/wiki/index.php/Mini-bootcamp_2011/Session_6_|spectrofluorometer] ====
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
* Learn basic principles of the Fluorolog 3 spectrofluorometer
* Learn how to run protein gels
* Basics of the PURExpress protein expression kit
* Basics of spectrofluorometer software
===== Instructors: =====
* Jongmin
* Elisa
| width=50% |

===== Techniques and equipment: =====
* PURExpress protein expression kit
* Protein gels (?)
* Fluorilog 3 spectrofluorometer
|}

Mini-bootcamp 2011

2011-03-04T11:15:46Z

Jongmin: /* Session 6: spectrofluorometer */

This page contains a description of the mini-bootcamp run in Feb 2011. __NOTOC__

=== Group ===
<center>
{| width=90%
|- valign=top
| width=25% |
===== Students =====
* Jorge Goncalves
* Jun Liu
* Yuan Ye
* Enoch Yeung
| width=25% |

===== Part-time students =====
* Elisa Franco
* Richard Murray
| width=25% |
===== Instructors =====
* Emzo de los Santos
* Joe Meyerowitz
* Ophelia Venturelli
* Vanessa Jonsson
* Jongmin Kim
| width=25% |

===== Project advisor =====
* Richard Murray
|}
</center>

=== Bootcamp description ===

{| width=100% border=1
|- valign=top
| rowspan=3 |
The goal of this bootcamp is to measure variability in gene expression that is relevant for synthetically designed circuits. The issue that we are trying to understand is now much variability arises for the expression of a given circuit under degrees of freedom that are typically not controlled in synthetic designs:
* Location and orientation of circuit elements in the plasmid
* Vectors used for expressing the circuit, including copy number and antibiotic resistance
* Growth conditions (temperature, oxygen, media, growth phase)
To understand how these (and other) factors will affect circuit operation, a simple genetic circuit consisting of 2 reporters will be built using different DNA locations and directions, and characterized in a variety of conditions. The dynamic response of the circuit will be measured, including cell-to-cell variability (via flow cytometry and microscopy).

Bootcamp objectives:
* Project 1: Construct a simple genetic circuit that tests the effects of putting different reporters in different configurations in a plasmid. Characterize the differences (if any) in mean expression level of the circuits, possibly in multiple growth conditions, using a plate reader
* Project 2: Characterize differences in expression distributions using flow cytometry (FACS Calibur) and fluorescent microscopy
* Project 3: Perform in vitro testing of the constructs using the PURExpress kit and spectrofluorometer to check for differences in mean expression level
|
[[Image:lambda_switch.png|300px]]
* Circuit layout: directions, ordering
|-
|
[[Image:biobrick_plasmid.png|300px]]
* Copy number
* Origin of replication
* Antibiotic resistance
* [[http:partsregistry.org/Plasmid_backbones|Biobrick plasmids]]
|-
|
* (Cell strain)
* Growth media: LB, M9/glycerol, M9/glucose
* Induction level
* Temperature
|}

=== Schedule ===
{| width=100% border=1
|- valign=top
| width=20% | 14 Feb: 2-4
* Biocircuits mini-group meeting - planning
* Richard
| width=20% | 15 Feb
| width=20% | 16 Feb:
* [[#Session 0: project discussion and lab tour|Session 0: project discussion and lab tour]]
* Richard, Ophelia
* Joe, Elisa
| width=20% | 17 Feb: 2:30-6
* [[Mini-bootcamp_2011/Session 1: lab techniques|Session 1: lab techniques]]
* Emzo, Jongmin
| width=20% | 18 Feb
|- valign=top
| width=20% | 21 Feb: 1-6
* [[#Session 2: cloning|Session 2: cloning]]
* Joe, Emzo
| width=20% | 22 Feb
| width=20% | 23 Feb: 1-6
* [[#Session 3: plate reader|Session 3: plate reader]]
* Ophelia, Richard
| width=20% | 24 Feb
* Project #1
| width=20% | 25 Feb
* Project #1

|- valign=top
| width=20% | 28 Feb
* Project #1
| width=20% | 1 Mar
* Project #1
| width=20% | 2 Mar: TBD
* [[#Session 4: microscopy|Session 4: microscopy]]
* Ophelia, Joe
| width=20% | 3 Mar
*Project #1
| width=20% | 4 Mar
*Project #1
|- valign=top
| width=20% | 7 Mar: TBD
* [[#Session 5: flow cytometry|Session 5: flow cytometry]]
* Joe, Vanessa
| width=20% | 8 Mar: TBD
* [[#Session 6: spectrofluorometer|Session 6: spectrofluorometer]]
* Jongmin, Elisa
| width=20% | 9 Mar
* Project #3
| width=20% | 10 Mar
* Project #3
| width=20% | 11 Mar
* Project #3
|}
 
<hr>
==== Session 0: project discussion and lab tour ====
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
* Overview of project goals
* Tour of 040 Keck
* Lab safety
===== Instructors: =====
* Richard Murray, Ophelia Venturelli
* Joe Meyerowitz, Elisa Franco (lab tour, safety)
<hr>
==== [[Mini-bootcamp_2011/Session 1: lab techniques|Session 1: lab techniques]] ====
This lab session will teach some of the basic techniques that will be used throughout the bootcamp. We assume no background in molecular biology laboratory techniques. By the end of this session, students will be able to transform a plasmid into cells, pick colonies containing the plasmid, grow the cells up to a given optical density, extract the plasmids, and quantify them.
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
* Lab safety
* Laboratory techniques: gloves, pipetting, disposal
* Transforming plasmids into cells, growing, extracting
* Clean up: benches, glassware

===== Instructors: =====
* Emzo
* Jongmin
| width=50% |
===== Techniques and equipment: =====
* Pipetting
* Transformation, selection, growth
* Optical density (OD) measurements (nanodrop?)
* Mini-preps
* Quantification (nanodrop)
* Autoclave
|}
<hr>

==== [[Mini-bootcamp_2011/Session 2: cloning|Session 2: cloning]] ====
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
* Discussion of PCR, primer design, Gibson assembly, gels
* Demonstration of PCR
* Demonstration of Gibson assembly
* Demonstration of electrophoresis, restriction digestion, mapping
* Transform Gibson product

===== Instructors: =====
* Joe
* Emzo
| width=50% |

===== Techniques and equipment: =====
* PCR
* Restriction digests
* Gels
* Gibson assembly
|}
<hr>

==== Session 3: [[plate reader]] ====
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
* Set up dose response with E. coli strains using serial dilution method
* Learn strategies for measuring dynamics in plate reader
:*Growth in shaker (manual time points)
:*Growth in VictorX3 (automated measurements)
* Measure gene expression (GFP) and OD (cell mass) using VictorX3 over a period of time

===== Instructors: =====
* Ophelia
* Richard
| width=50% |

===== Techniques and equipment: =====
* Victor X3 plate reader
|}
<hr>

==== Session 4: [[microscope]] ====
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
* Learn basic principles and design of the Olympus IX-81 light microscope
* Learn how to make agarose pads for imaging E coli
* Basics of Micro-Manager software
* Discuss image analysis

===== Instructors: =====
* Ophelia
* Joe
| width=50% |
===== Techniques and equipment: =====
* Olympus IX-81 microscope
* MATLAB tools for image analysis
|}
<hr>

==== Session 5: flow cytometer ====
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
*
===== Instructors: =====
* Joe
* Vanessa
| width=50% |
===== Techniques and equipment: =====
* FACS Calibur flow cytometer
* MaxQuant (?)
|}
<hr>

==== Session 6: [spectrofluorometer] ====
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
* Learn basic principles of the Fluorolog 3 spectrofluorometer
* Learn how to run protein gels
* Basics of the PURExpress protein expression kit
* Basics of spectrofluorometer software
===== Instructors: =====
* Jongmin
* Elisa
| width=50% |

===== Techniques and equipment: =====
* PURExpress protein expression kit
* Protein gels (?)
* Fluorilog 3 spectrofluorometer
|}

Mini-bootcamp 2011

2011-03-04T09:08:22Z

Jongmin: /* Session 6: spectrofluorometer */

This page contains a description of the mini-bootcamp run in Feb 2011. __NOTOC__

=== Group ===
<center>
{| width=90%
|- valign=top
| width=25% |
===== Students =====
* Jorge Goncalves
* Jun Liu
* Yuan Ye
* Enoch Yeung
| width=25% |

===== Part-time students =====
* Elisa Franco
* Richard Murray
| width=25% |
===== Instructors =====
* Emzo de los Santos
* Joe Meyerowitz
* Ophelia Venturelli
* Vanessa Jonsson
* Jongmin Kim
| width=25% |

===== Project advisor =====
* Richard Murray
|}
</center>

=== Bootcamp description ===

{| width=100% border=1
|- valign=top
| rowspan=3 |
The goal of this bootcamp is to measure variability in gene expression that is relevant for synthetically designed circuits. The issue that we are trying to understand is now much variability arises for the expression of a given circuit under degrees of freedom that are typically not controlled in synthetic designs:
* Location and orientation of circuit elements in the plasmid
* Vectors used for expressing the circuit, including copy number and antibiotic resistance
* Growth conditions (temperature, oxygen, media, growth phase)
To understand how these (and other) factors will affect circuit operation, a simple genetic circuit consisting of 2 reporters will be built using different DNA locations and directions, and characterized in a variety of conditions. The dynamic response of the circuit will be measured, including cell-to-cell variability (via flow cytometry and microscopy).

Bootcamp objectives:
* Project 1: Construct a simple genetic circuit that tests the effects of putting different reporters in different configurations in a plasmid. Characterize the differences (if any) in mean expression level of the circuits, possibly in multiple growth conditions, using a plate reader
* Project 2: Characterize differences in expression distributions using flow cytometry (FACS Calibur) and fluorescent microscopy
* Project 3: Perform in vitro testing of the constructs using the PURExpress kit and spectrofluorometer to check for differences in mean expression level
|
[[Image:lambda_switch.png|300px]]
* Circuit layout: directions, ordering
|-
|
[[Image:biobrick_plasmid.png|300px]]
* Copy number
* Origin of replication
* Antibiotic resistance
* [[http:partsregistry.org/Plasmid_backbones|Biobrick plasmids]]
|-
|
* (Cell strain)
* Growth media: LB, M9/glycerol, M9/glucose
* Induction level
* Temperature
|}

=== Schedule ===
{| width=100% border=1
|- valign=top
| width=20% | 14 Feb: 2-4
* Biocircuits mini-group meeting - planning
* Richard
| width=20% | 15 Feb
| width=20% | 16 Feb:
* [[#Session 0: project discussion and lab tour|Session 0: project discussion and lab tour]]
* Richard, Ophelia
* Joe, Elisa
| width=20% | 17 Feb: 2:30-6
* [[Mini-bootcamp_2011/Session 1: lab techniques|Session 1: lab techniques]]
* Emzo, Jongmin
| width=20% | 18 Feb
|- valign=top
| width=20% | 21 Feb: 1-6
* [[#Session 2: cloning|Session 2: cloning]]
* Joe, Emzo
| width=20% | 22 Feb
| width=20% | 23 Feb: 1-6
* [[#Session 3: plate reader|Session 3: plate reader]]
* Ophelia, Richard
| width=20% | 24 Feb
* Project #1
| width=20% | 25 Feb
* Project #1

|- valign=top
| width=20% | 28 Feb
* Project #1
| width=20% | 1 Mar
* Project #1
| width=20% | 2 Mar: TBD
* [[#Session 4: microscopy|Session 4: microscopy]]
* Ophelia, Joe
| width=20% | 3 Mar
*Project #1
| width=20% | 4 Mar
*Project #1
|- valign=top
| width=20% | 7 Mar: TBD
* [[#Session 5: flow cytometry|Session 5: flow cytometry]]
* Joe, Vanessa
| width=20% | 8 Mar: TBD
* [[#Session 6: spectrofluorometer|Session 6: spectrofluorometer]]
* Jongmin, Elisa
| width=20% | 9 Mar
* Project #3
| width=20% | 10 Mar
* Project #3
| width=20% | 11 Mar
* Project #3
|}
 
<hr>
==== Session 0: project discussion and lab tour ====
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
* Overview of project goals
* Tour of 040 Keck
* Lab safety
===== Instructors: =====
* Richard Murray, Ophelia Venturelli
* Joe Meyerowitz, Elisa Franco (lab tour, safety)
<hr>
==== [[Mini-bootcamp_2011/Session 1: lab techniques|Session 1: lab techniques]] ====
This lab session will teach some of the basic techniques that will be used throughout the bootcamp. We assume no background in molecular biology laboratory techniques. By the end of this session, students will be able to transform a plasmid into cells, pick colonies containing the plasmid, grow the cells up to a given optical density, extract the plasmids, and quantify them.
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
* Lab safety
* Laboratory techniques: gloves, pipetting, disposal
* Transforming plasmids into cells, growing, extracting
* Clean up: benches, glassware

===== Instructors: =====
* Emzo
* Jongmin
| width=50% |
===== Techniques and equipment: =====
* Pipetting
* Transformation, selection, growth
* Optical density (OD) measurements (nanodrop?)
* Mini-preps
* Quantification (nanodrop)
* Autoclave
|}
<hr>

==== [[Mini-bootcamp_2011/Session 2: cloning|Session 2: cloning]] ====
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
* Discussion of PCR, primer design, Gibson assembly, gels
* Demonstration of PCR
* Demonstration of Gibson assembly
* Demonstration of electrophoresis, restriction digestion, mapping
* Transform Gibson product

===== Instructors: =====
* Joe
* Emzo
| width=50% |

===== Techniques and equipment: =====
* PCR
* Restriction digests
* Gels
* Gibson assembly
|}
<hr>

==== Session 3: [[plate reader]] ====
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
* Set up dose response with E. coli strains using serial dilution method
* Learn strategies for measuring dynamics in plate reader
:*Growth in shaker (manual time points)
:*Growth in VictorX3 (automated measurements)
* Measure gene expression (GFP) and OD (cell mass) using VictorX3 over a period of time

===== Instructors: =====
* Ophelia
* Richard
| width=50% |

===== Techniques and equipment: =====
* Victor X3 plate reader
|}
<hr>

==== Session 4: [[microscope]] ====
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
* Learn basic principles and design of the Olympus IX-81 light microscope
* Learn how to make agarose pads for imaging E coli
* Basics of Micro-Manager software
* Discuss image analysis

===== Instructors: =====
* Ophelia
* Joe
| width=50% |
===== Techniques and equipment: =====
* Olympus IX-81 microscope
* MATLAB tools for image analysis
|}
<hr>

==== Session 5: flow cytometer ====
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
*
===== Instructors: =====
* Joe
* Vanessa
| width=50% |
===== Techniques and equipment: =====
* FACS Calibur flow cytometer
* MaxQuant (?)
|}
<hr>

==== Session 6: spectrofluorometer ====
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
* Learn basic principles of the Fluorolog 3 spectrofluorometer
* Learn how to run protein gels
* Basics of the PURExpress protein expression kit
* Basics of spectrofluorometer software
===== Instructors: =====
* Jongmin
* Elisa
| width=50% |

===== Techniques and equipment: =====
* PURExpress protein expression kit
* Protein gels (?)
* Fluorilog 3 spectrofluorometer
|}

Mini-bootcamp 2011

2011-03-04T09:07:39Z

Jongmin: /* Session 6: spectrofluorometer */

This page contains a description of the mini-bootcamp run in Feb 2011. __NOTOC__

=== Group ===
<center>
{| width=90%
|- valign=top
| width=25% |
===== Students =====
* Jorge Goncalves
* Jun Liu
* Yuan Ye
* Enoch Yeung
| width=25% |

===== Part-time students =====
* Elisa Franco
* Richard Murray
| width=25% |
===== Instructors =====
* Emzo de los Santos
* Joe Meyerowitz
* Ophelia Venturelli
* Vanessa Jonsson
* Jongmin Kim
| width=25% |

===== Project advisor =====
* Richard Murray
|}
</center>

=== Bootcamp description ===

{| width=100% border=1
|- valign=top
| rowspan=3 |
The goal of this bootcamp is to measure variability in gene expression that is relevant for synthetically designed circuits. The issue that we are trying to understand is now much variability arises for the expression of a given circuit under degrees of freedom that are typically not controlled in synthetic designs:
* Location and orientation of circuit elements in the plasmid
* Vectors used for expressing the circuit, including copy number and antibiotic resistance
* Growth conditions (temperature, oxygen, media, growth phase)
To understand how these (and other) factors will affect circuit operation, a simple genetic circuit consisting of 2 reporters will be built using different DNA locations and directions, and characterized in a variety of conditions. The dynamic response of the circuit will be measured, including cell-to-cell variability (via flow cytometry and microscopy).

Bootcamp objectives:
* Project 1: Construct a simple genetic circuit that tests the effects of putting different reporters in different configurations in a plasmid. Characterize the differences (if any) in mean expression level of the circuits, possibly in multiple growth conditions, using a plate reader
* Project 2: Characterize differences in expression distributions using flow cytometry (FACS Calibur) and fluorescent microscopy
* Project 3: Perform in vitro testing of the constructs using the PURExpress kit and spectrofluorometer to check for differences in mean expression level
|
[[Image:lambda_switch.png|300px]]
* Circuit layout: directions, ordering
|-
|
[[Image:biobrick_plasmid.png|300px]]
* Copy number
* Origin of replication
* Antibiotic resistance
* [[http:partsregistry.org/Plasmid_backbones|Biobrick plasmids]]
|-
|
* (Cell strain)
* Growth media: LB, M9/glycerol, M9/glucose
* Induction level
* Temperature
|}

=== Schedule ===
{| width=100% border=1
|- valign=top
| width=20% | 14 Feb: 2-4
* Biocircuits mini-group meeting - planning
* Richard
| width=20% | 15 Feb
| width=20% | 16 Feb:
* [[#Session 0: project discussion and lab tour|Session 0: project discussion and lab tour]]
* Richard, Ophelia
* Joe, Elisa
| width=20% | 17 Feb: 2:30-6
* [[Mini-bootcamp_2011/Session 1: lab techniques|Session 1: lab techniques]]
* Emzo, Jongmin
| width=20% | 18 Feb
|- valign=top
| width=20% | 21 Feb: 1-6
* [[#Session 2: cloning|Session 2: cloning]]
* Joe, Emzo
| width=20% | 22 Feb
| width=20% | 23 Feb: 1-6
* [[#Session 3: plate reader|Session 3: plate reader]]
* Ophelia, Richard
| width=20% | 24 Feb
* Project #1
| width=20% | 25 Feb
* Project #1

|- valign=top
| width=20% | 28 Feb
* Project #1
| width=20% | 1 Mar
* Project #1
| width=20% | 2 Mar: TBD
* [[#Session 4: microscopy|Session 4: microscopy]]
* Ophelia, Joe
| width=20% | 3 Mar
*Project #1
| width=20% | 4 Mar
*Project #1
|- valign=top
| width=20% | 7 Mar: TBD
* [[#Session 5: flow cytometry|Session 5: flow cytometry]]
* Joe, Vanessa
| width=20% | 8 Mar: TBD
* [[#Session 6: spectrofluorometer|Session 6: spectrofluorometer]]
* Jongmin, Elisa
| width=20% | 9 Mar
* Project #3
| width=20% | 10 Mar
* Project #3
| width=20% | 11 Mar
* Project #3
|}
 
<hr>
==== Session 0: project discussion and lab tour ====
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
* Overview of project goals
* Tour of 040 Keck
* Lab safety
===== Instructors: =====
* Richard Murray, Ophelia Venturelli
* Joe Meyerowitz, Elisa Franco (lab tour, safety)
<hr>
==== [[Mini-bootcamp_2011/Session 1: lab techniques|Session 1: lab techniques]] ====
This lab session will teach some of the basic techniques that will be used throughout the bootcamp. We assume no background in molecular biology laboratory techniques. By the end of this session, students will be able to transform a plasmid into cells, pick colonies containing the plasmid, grow the cells up to a given optical density, extract the plasmids, and quantify them.
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
* Lab safety
* Laboratory techniques: gloves, pipetting, disposal
* Transforming plasmids into cells, growing, extracting
* Clean up: benches, glassware

===== Instructors: =====
* Emzo
* Jongmin
| width=50% |
===== Techniques and equipment: =====
* Pipetting
* Transformation, selection, growth
* Optical density (OD) measurements (nanodrop?)
* Mini-preps
* Quantification (nanodrop)
* Autoclave
|}
<hr>

==== [[Mini-bootcamp_2011/Session 2: cloning|Session 2: cloning]] ====
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
* Discussion of PCR, primer design, Gibson assembly, gels
* Demonstration of PCR
* Demonstration of Gibson assembly
* Demonstration of electrophoresis, restriction digestion, mapping
* Transform Gibson product

===== Instructors: =====
* Joe
* Emzo
| width=50% |

===== Techniques and equipment: =====
* PCR
* Restriction digests
* Gels
* Gibson assembly
|}
<hr>

==== Session 3: [[plate reader]] ====
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
* Set up dose response with E. coli strains using serial dilution method
* Learn strategies for measuring dynamics in plate reader
:*Growth in shaker (manual time points)
:*Growth in VictorX3 (automated measurements)
* Measure gene expression (GFP) and OD (cell mass) using VictorX3 over a period of time

===== Instructors: =====
* Ophelia
* Richard
| width=50% |

===== Techniques and equipment: =====
* Victor X3 plate reader
|}
<hr>

==== Session 4: [[microscope]] ====
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
* Learn basic principles and design of the Olympus IX-81 light microscope
* Learn how to make agarose pads for imaging E coli
* Basics of Micro-Manager software
* Discuss image analysis

===== Instructors: =====
* Ophelia
* Joe
| width=50% |
===== Techniques and equipment: =====
* Olympus IX-81 microscope
* MATLAB tools for image analysis
|}
<hr>

==== Session 5: flow cytometer ====
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
*
===== Instructors: =====
* Joe
* Vanessa
| width=50% |
===== Techniques and equipment: =====
* FACS Calibur flow cytometer
* MaxQuant (?)
|}
<hr>

==== Session 6: spectrofluorometer ====
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
* learn basic principles of the Fluorolog 3 spectrofluorometer
* learn how to run protein gels
* basics of the PURExpress protein expression kit
* basics of spectrofluorometer software
===== Instructors: =====
* Jongmin
* Elisa
| width=50% |

===== Techniques and equipment: =====
* PURExpress protein expression kit
* Protein gels (?)
* Fluorilog 3 spectrofluorometer
|}

Mini-bootcamp 2011

2011-03-04T09:04:52Z

Jongmin: /* Session 6: spectrofluorometer */

This page contains a description of the mini-bootcamp run in Feb 2011. __NOTOC__

=== Group ===
<center>
{| width=90%
|- valign=top
| width=25% |
===== Students =====
* Jorge Goncalves
* Jun Liu
* Yuan Ye
* Enoch Yeung
| width=25% |

===== Part-time students =====
* Elisa Franco
* Richard Murray
| width=25% |
===== Instructors =====
* Emzo de los Santos
* Joe Meyerowitz
* Ophelia Venturelli
* Vanessa Jonsson
* Jongmin Kim
| width=25% |

===== Project advisor =====
* Richard Murray
|}
</center>

=== Bootcamp description ===

{| width=100% border=1
|- valign=top
| rowspan=3 |
The goal of this bootcamp is to measure variability in gene expression that is relevant for synthetically designed circuits. The issue that we are trying to understand is now much variability arises for the expression of a given circuit under degrees of freedom that are typically not controlled in synthetic designs:
* Location and orientation of circuit elements in the plasmid
* Vectors used for expressing the circuit, including copy number and antibiotic resistance
* Growth conditions (temperature, oxygen, media, growth phase)
To understand how these (and other) factors will affect circuit operation, a simple genetic circuit consisting of 2 reporters will be built using different DNA locations and directions, and characterized in a variety of conditions. The dynamic response of the circuit will be measured, including cell-to-cell variability (via flow cytometry and microscopy).

Bootcamp objectives:
* Project 1: Construct a simple genetic circuit that tests the effects of putting different reporters in different configurations in a plasmid. Characterize the differences (if any) in mean expression level of the circuits, possibly in multiple growth conditions, using a plate reader
* Project 2: Characterize differences in expression distributions using flow cytometry (FACS Calibur) and fluorescent microscopy
* Project 3: Perform in vitro testing of the constructs using the PURExpress kit and spectrofluorometer to check for differences in mean expression level
|
[[Image:lambda_switch.png|300px]]
* Circuit layout: directions, ordering
|-
|
[[Image:biobrick_plasmid.png|300px]]
* Copy number
* Origin of replication
* Antibiotic resistance
* [[http:partsregistry.org/Plasmid_backbones|Biobrick plasmids]]
|-
|
* (Cell strain)
* Growth media: LB, M9/glycerol, M9/glucose
* Induction level
* Temperature
|}

=== Schedule ===
{| width=100% border=1
|- valign=top
| width=20% | 14 Feb: 2-4
* Biocircuits mini-group meeting - planning
* Richard
| width=20% | 15 Feb
| width=20% | 16 Feb:
* [[#Session 0: project discussion and lab tour|Session 0: project discussion and lab tour]]
* Richard, Ophelia
* Joe, Elisa
| width=20% | 17 Feb: 2:30-6
* [[Mini-bootcamp_2011/Session 1: lab techniques|Session 1: lab techniques]]
* Emzo, Jongmin
| width=20% | 18 Feb
|- valign=top
| width=20% | 21 Feb: 1-6
* [[#Session 2: cloning|Session 2: cloning]]
* Joe, Emzo
| width=20% | 22 Feb
| width=20% | 23 Feb: 1-6
* [[#Session 3: plate reader|Session 3: plate reader]]
* Ophelia, Richard
| width=20% | 24 Feb
* Project #1
| width=20% | 25 Feb
* Project #1

|- valign=top
| width=20% | 28 Feb
* Project #1
| width=20% | 1 Mar
* Project #1
| width=20% | 2 Mar: TBD
* [[#Session 4: microscopy|Session 4: microscopy]]
* Ophelia, Joe
| width=20% | 3 Mar
*Project #1
| width=20% | 4 Mar
*Project #1
|- valign=top
| width=20% | 7 Mar: TBD
* [[#Session 5: flow cytometry|Session 5: flow cytometry]]
* Joe, Vanessa
| width=20% | 8 Mar: TBD
* [[#Session 6: spectrofluorometer|Session 6: spectrofluorometer]]
* Jongmin, Elisa
| width=20% | 9 Mar
* Project #3
| width=20% | 10 Mar
* Project #3
| width=20% | 11 Mar
* Project #3
|}
 
<hr>
==== Session 0: project discussion and lab tour ====
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
* Overview of project goals
* Tour of 040 Keck
* Lab safety
===== Instructors: =====
* Richard Murray, Ophelia Venturelli
* Joe Meyerowitz, Elisa Franco (lab tour, safety)
<hr>
==== [[Mini-bootcamp_2011/Session 1: lab techniques|Session 1: lab techniques]] ====
This lab session will teach some of the basic techniques that will be used throughout the bootcamp. We assume no background in molecular biology laboratory techniques. By the end of this session, students will be able to transform a plasmid into cells, pick colonies containing the plasmid, grow the cells up to a given optical density, extract the plasmids, and quantify them.
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
* Lab safety
* Laboratory techniques: gloves, pipetting, disposal
* Transforming plasmids into cells, growing, extracting
* Clean up: benches, glassware

===== Instructors: =====
* Emzo
* Jongmin
| width=50% |
===== Techniques and equipment: =====
* Pipetting
* Transformation, selection, growth
* Optical density (OD) measurements (nanodrop?)
* Mini-preps
* Quantification (nanodrop)
* Autoclave
|}
<hr>

==== [[Mini-bootcamp_2011/Session 2: cloning|Session 2: cloning]] ====
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
* Discussion of PCR, primer design, Gibson assembly, gels
* Demonstration of PCR
* Demonstration of Gibson assembly
* Demonstration of electrophoresis, restriction digestion, mapping
* Transform Gibson product

===== Instructors: =====
* Joe
* Emzo
| width=50% |

===== Techniques and equipment: =====
* PCR
* Restriction digests
* Gels
* Gibson assembly
|}
<hr>

==== Session 3: [[plate reader]] ====
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
* Set up dose response with E. coli strains using serial dilution method
* Learn strategies for measuring dynamics in plate reader
:*Growth in shaker (manual time points)
:*Growth in VictorX3 (automated measurements)
* Measure gene expression (GFP) and OD (cell mass) using VictorX3 over a period of time

===== Instructors: =====
* Ophelia
* Richard
| width=50% |

===== Techniques and equipment: =====
* Victor X3 plate reader
|}
<hr>

==== Session 4: [[microscope]] ====
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
* Learn basic principles and design of the Olympus IX-81 light microscope
* Learn how to make agarose pads for imaging E coli
* Basics of Micro-Manager software
* Discuss image analysis

===== Instructors: =====
* Ophelia
* Joe
| width=50% |
===== Techniques and equipment: =====
* Olympus IX-81 microscope
* MATLAB tools for image analysis
|}
<hr>

==== Session 5: flow cytometer ====
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
*
===== Instructors: =====
* Joe
* Vanessa
| width=50% |
===== Techniques and equipment: =====
* FACS Calibur flow cytometer
* MaxQuant (?)
|}
<hr>

==== Session 6: spectrofluorometer ====
{| width=100%
|- valign=top
| width=50% |
===== Session goals: =====
*
*
*
*
===== Instructors: =====
* Jongmin
* Elisa
| width=50% |

===== Techniques and equipment: =====
* PURExpress protein expression kit
* Protein gels (?)
* Fluorilog 3 spectrofluorometer
|}

Mini-bootcamp 2011

2011-02-08T21:45:00Z

Jongmin: /* Instructors */

Mini-bootcamp 2011

2011-02-08T21:44:14Z

Jongmin: /* Instructors: */