Murray Wiki - User contributions [en]

Jake Beal, 1 Oct 2019

2019-09-30T17:03:33Z

Jparkin: /* Schedule */

Jake Beal will visit Caltech on 1 Oct 2019. If you would like to meet with him, please sign up below.

=== Schedule ===
* 9:00a: RMM group meeting, 111 Keck (if interested)
* 11:00a: James
* 11:45a: seminar setup
* 12:00p: Seminar, 111 Keck (abstract below)
* 1:00p: Lunch with Andrey Shur, Sam Clamons
* 1:45p: Lab tour and calibration discussion (Andrey, Sam, Mark, Miki)
* 2:30p: John Marken
* 3:15p: Elin Larsson
* 4:00p: Open
* 4:45p: Wrap up with Richard

=== Talk abstract ===

Paths to Resilient Biological Information Processing<br>
Jake Beal (Raytheon BBN)<br>

1 October (Tue), 12-1 pm, 111 Keck

Engineered information processing in biological organisms has potential revolutionary implications across many application domains. A major barrier, however, has been the fragility of biological information processing devices to changes in their usage, genetic context, or operating environment. Engineering resilient information processing, however, is not just a biological challenge, but a three-way interplay between device performance, measurement quality, and model accuracy. In this talk, I will discuss how the interplay between these three aspects offer multiple paths for improving the resilience of biological information processing, giving examples of recent progress in reproducible and comparable measurement, the development of high-performance devices and insulators, and precision prediction of genetic circuits.

Dr. Jacob Beal is a Senior Scientist at Raytheon BBN Technologies, where he leads research on synthetic biology and distributed systems engineering. His work in synthetic biology includes development of methods for calibrated flow cytometry, precision analysis and design of genetic regulatory networks, engineering of biological information processing devices, standards for representation and communication of biological designs, and signature-based detection of pathogenic sequences.

John McManus, 5 Mar 2018

2018-03-02T19:25:50Z

Jparkin:

[http://www.jbmcmanus.com John McManus] will be visiting Caltech on 5 Mar 2018. Sign up to meet with him below:

Schedule
* 9 am - meet with Richard for ~30 min
* 9:30 am - TX-TL discussion (Joe M, William P, Zoila J)
* 10:30a-12p - group meeting (including 15 min talk by John)
* 12p-1:30p - lunch with postdocs (Leo G, Michaelle M, Anandh S)
* 1:30p - lab tour (Leo and/or Anandh)
* 2:00p - Andrey
* 2:45p - James
* 3:00p - Azita Emami
* 3:45p - open
* 4:15p - open
* 5 pm - wrap up meeting with Richard for ~30 m

May 2017 meeting schedule

2017-05-08T16:27:58Z

Jparkin: /* 22 May (Mon) */

Richard will be in town several different times in May. Please sign up for a time to meet below. Please note that these are likely the last "sabbatical" meetings until Richard returns to Pasadena in early July. __NOTOC__

{| border=1 width=100%
|- valign=top
| width=33% |
| width=33% |
==== 15 May (Mon) ====
* 9:30 am: Open
* 10:15 am: Open
* 11:00 am: Faculty meeting
* 11:30 am: Open
* 12:15 pm: Lunch
* 1:30 pm: Open
* 2:15 pm: Reed
* 3:00 pm: Swati + Reed
* 3:45 pm: Break
* 4:00 pm: Namita
* 4:45 pm: Open
* 5:30 pm: Open
* 6:15 pm: Done for the day

| width=33% |

==== 16 May (Tue)====
* 9:30 am: Yong
* 10:15 am: Tung
* 11:00 am: Faculty meeting
* 12:00 pm: Lunch
* 1:30 pm: Depart
* 12:00 pm: Lunch
* 1:30 pm: Depart

|- valign=top
| width=33% |

====21 May (Sun) ====
* 1:45 pm: Open
* 2:30 pm: Open
* 3:15 pm: Open
* 4:00 pm: Break
* 4:15 pm: Open
* 5:00 pm: Open
* 5:45 pm: Open
* 6:30 pm: Done for the day

| width=33% |

==== 22 May (Mon) ====
* 10:15 am: Mark
* 11:00 am: Cindy
* 11:45 am: Lunch
* 12:00 pm: DARPA BioCon meeting
* 2:00 pm: Open
* 2:45 pm: Off campus
* 4:15 pm: James
* 5:00 pm: Non-Caltech meetings
* 6:30 pm: Done for the day

| width=33% |

==== 23 May (Tue) ====
* 9:30 am: Faculty discussion
* 10:30 am: Hold (Susan)
* 11:30 am: Lunch
* 12:00 pm: Telecon
* 1:00 pm: Anu thesis defense
* 3:00 pm: Terri (?)
* 3:30 pm: Depart

|- valign=top
| width=33% |

====28 May (Sun) ====
* 1:45 pm: Open
* 2:30 pm: Open
* 3:15 pm: Open
* 4:00 pm: Done for the day
| width=33% |
====29 May (Mon) ====
* 1:45 pm: Open (if needed)
* 2:30 pm: Open (if needed)
* 3:15 pm: Open (if needed)
* 4:00 pm: Done for the day
| width=33% |

==== 30 May (Tue) ====
* 9:30 am: Open
* 10:15 am: Shaobin
* 11:00 am: Stepan seminar
* 12:00 pm: Lunch
* 1:30 pm: Namita
* 2:15 pm: Andrey
* 3:00 pm: Depart
|}

Apr 2017 meeting schedule

2017-04-12T16:49:56Z

Jparkin: /* 20 Apr (Thu) */

Richard will be in town 19-21 Apr. Please sign up for a time to meet below. __NOTOC__

{| border=1
|- valign=top
| width=25% |
==== 19 Apr (Wed) ====
* 9:30 am: Hold (Sofie or Leo)
* 10:30 am: Admin meeting (SP, MC)
* 11:15 am: Shaobin
* 12:00 pm: DARPA BioCon meeting
* 2:00 pm: Candidacy exam
* 3:00 pm: CDS tea
* 3:45 pm: Yong
* 4:30 pm: Admin meeting (LL)
* 5:00 pm: Open (tentative)
* 5:45 pm: Associates event

| width=25% |

==== 20 Apr (Thu) ====
* 9:30 am: Hold (Sofie or Leo)
* 10:30 am: Mark
* 11:15 am: Tony Fragoso
* 12:00 pm: Lunch
* 1:30 pm: EBRC telecon
* 2:30 pm: Anandh
* 3:15 pm: James
* 4:00 pm: Vipul
* 4:45 pm: Break
* 5:00 pm: Tung
* 5:45 pm: Sam
* 6:00 pm: Open (if needed)
* 6:45 pm: Open (if needed)
* 7:30 pm: Done for the day

| width=25% |

==== 21 Apr (Fri) ====
* 9:15 am: Open
* 10:00 am: JPL CIF meeting
* 11:15 am: Karena
* 12:00 pm: Lunch
* 12:45 pm: Open
* 1:30 pm: Namita
* 2:15 pm: Open
* 3:00 pm: Break
* 3:15 pm: Open
* 4:00 pm: Miki
* 4:45 pm: Open
* 5:30 pm: Done for the day

| width=25% |

==== 23 Apr (Sun) ====
* 1:45 pm: Open
* 2:30 pm: Open
* 3:15 pm: Open
* 4:00 pm: Break
* 4:15 pm: Open
* 5:00 pm: Open
* 5:45 pm: Shan
* 6:30 pm: Done for the day
|}

Mar 2017 meeting schedule

2017-02-26T22:38:33Z

Jparkin: /* 6 Mar (Mon) */

Richard will be in town 3-7 Mar. Please sign up for a time to meet below. __NOTOC__

{| border=1
|- valign=top
| width=25% |
==== 3 Mar (Fri) ====
* 10:00 am: DENSO CPM telecon
* 11:00 am: Open
* 11:45 am: Shaobin
* 12:30 pm: Lunch
* 1:00 pm: Hold: DARPA telecon
* 2:00 pm: Open
* 2:45 pm: Open
* 3:30 pm: SBIR telecon (w/ Mark P)
* 4:00 pm: Faculty meeting
* 5:45 pm: Open
* 6:30 pm: Done for the day

| width=25% |

==== 5 Mar (Sun) ====
* 1:45 pm: Open
* 2:30 pm: Open
* 3:15 pm: Open
* 4:00 pm: Break
* 4:15 pm: Open
* 5:00 pm: Open
* 5:45 pm: Sumanth Dathathri
* 6:30 pm: Done for the day

| width=25% |

==== 6 Mar (Mon) ====
* 9:30 am: AFOSR BRI telecon
* 10:30 am: Yong
* 11:15 am: Fragoso
* 12:00 pm: Lunch
* 12:30 pm: Hold: DARPA telecon
* 1:30 pm: Open
* 2:15 pm: Ioannis
* 3:00 pm: Open
* 3:45 pm: Break
* 4:00 pm: James
* 4:45 pm: Open
* 5:30 pm: Open
* 6:15 pm: Done for the day

| width=25% |

==== 7 Mar (Tue) ====
* 9:30 am: Busy
* 10:15 am: Tung
* 11:00 am: Hold: DARPA telecon
* 12:00 pm: Lunch
* 12:45 pm: Hold
* 1:15 pm: Andrew M
* 2:00 pm: Andy Halleran
* 2:45 pm: Depart for airport
|}

SURF discussions, Jan 2017

2017-01-23T23:34:57Z

Jparkin: /* 27 Jan (Fri) */

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

In preparation for our conversation, please do the following:
* SURF students should work with their co-mentors to find a time the meeting/Skype call. (For Skype calls, co-mentors should initiate.)
* Please make sure you have read the material in the description of your project, so that you are prepared to talk about what the project is about and we can narrow in on the key ideas that will be the basis of your proposal
* Please take a look at the [[SURF GOTChA chart]] page, which is the format that we will use for the first iteration of your project proposal.

{| width=100% border=1
|- valign=top
|
==== 25 Jan (Wed) ====
* 8:30 am PST: open
<hr>
* 11:00 am PST: open
<hr>
* 3:00 pm PST: open
* 3:30 pm PST: open
|

==== 26 Jan (Thu) ====
* 1:00 pm PST: open
* 1:30 pm PST: open
<hr>
* 6:30 pm PST: open
* 7:00 pm PST: open
|

==== 27 Jan (Fri) ====
* 9:00 am PST: Joy Doong and James Parkin
* 9:30 am PST: open
* 10:00 am PST: open
* 10:30 am PST: open

|}

The agenda for the phone call is (roughly):

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

Jan 2017 meeting schedule

2017-01-13T21:03:45Z

Jparkin: /* 20 Jan (Fri) */

Richard will be in town 20-24 Jan. Please sign up for a time to meet below. __NOTOC__

{| border=1
|- valign=top
| width=25% |
==== 20 Jan (Fri) ====
* Richard arrives on campus ~9:45 am
* 10:15 am: Mark
* 11:00 am: Yong
* 11:45 am: Anandh
* 12:30 pm: Lunch
* 1:30 pm: Yong and Frances A
* 2:30 pm: Sumanth Dathathri
* 3:15 pm: Reed
* 4:00 pm: Miki
* 4:45 pm: Break
* 5:00 pm: Cindy
* 5:45 pm: James
* 6:30 pm: Done for the day

| width=25% |

==== 22 Jan (Sun) ====
* 1:45 pm: Open
* 2:30 pm: Open
* 3:15 pm: Rory
* 4:00 pm: Break
* 4:15 pm: Open
* 5:00 pm: Open
* 5:45 pm: Open
* 6:30 pm: Done for the day

| width=25% |

==== 23 Jan (Mon) ====
* 8:00 am: Michaelle
* 9:00 am: Hold: Jaymie
* 10:00 am: BioCon meeting
* 12:00 pm: Seminar ([[Michaëlle Mayalu, Jan 2017|Michaelle]])
* 1:00 pm: Hold until needed
* 1:45 pm: Vipul
* 2:30 pm: CDS faculty meeting
* 4:15 pm: Tony Fragoso
* 5:00 pm: Ania
* 5:45 pm: William
* 6:30 pm: Dinner with visitors

| width=25% |

==== 24 Jan (Tue) ====
* 9:45 am: Henrike
* 10:30 am: Karena
* 11:15 am: Tung
* 12:00 pm: Seminar ([[Henrike Niederholtmeyer, Jan 2017|Henrike]])
* 1:15 pm: [[Michaëlle Mayalu, Jan 2017|Michaelle]]
* 2:00 pm: Anu
* 2:45 pm: [[Henrike Niederholtmeyer, Jan 2017|Henrike]]
* 3:30 pm: Depart for airport
|}

SURF 2017: Length and time scales of cell-cell signalling circuits in agar

2017-01-04T00:17:22Z

Jparkin:

'''[[SURF 2017|2017 SURF]] project description'''
* Mentor: Richard Murray
* Co-mentor: James Parkin

One of the focuses of the Murray biolab is biological event detectors, specifically modified bacteria that are designed to alert a researcher that a specific condition in their local environment has occurred. As a part of this focus, we are trying to engineer a bacterial strain that detects the order in which a pair of chemical inducers are applied to opposite ends of an agar plate. The detector bacteria, embedded in the agar, will communicate with their neighbors to determine which chemical appeared first, as no individual cell would detect both chemicals.

The engineered bacteria communicate using protein components borrowed from natural quorum sensing systems. Quorum sensing (QS) systems are the communication paradigm of choice for many synthetic biologists because they are portable and reliable [1, 2, 4, 5]. Augmenting E coli with QS-mediated communication requires only two protein components, a signal synthase and a signal-activated transcription factor. Furthermore, QS signalling chemicals (acyl-homoserine lactones, AHL) freely diffuse through the cell walls of Gram-negative bacteria, no transmembrane transport protein required.

The summer project I am proposing is to investigate the characteristic length and time scales observed from various experimental setups and signalling circuits. Students would use previously-characterized genetic components to compose communication circuits in cells, grow them in various semisolid media preparations, expose them to different patterns of chemical inducers, and analyze the resulting patterns of gene expression in the growing bacteria. From these data, students would quantify the experimentally feasible range of pattern lengths and determine how the behavior of a circuit changes as cells approach stationary phase [1, 3, 5]. These results would provide information to help guide future research into self-patterning or spatiotemporal event detectors.

Students may also investigate how modeling can support this line of inquiry. This may involve anything from recreating experiments in simulators developed by other labs to writing their own numerical simulations from scratch. Similarly, analyzing images or videos of the communicating bacteria as they grow may be approached by identifying features by hand or through developing models that consider both spatially heterogeneous cell growth and reaction-diffusion treatment of cell-cell signaling.

'''Recommended skills:'''

* Fluency with basic molecular biology and bacterial culture techniques
* Experience with scientific programming (MATLAB, R, Python scipy, or similar)
* Students interested in pursuing modeling or simulation should have significant previous work in numerical simulation software, multivariate calculus, and partial differential equations.

'''References: '''
# Liu, C. et al. Sequential Establishment of Stripe Patterns in an Expanding Cell Population. Science 334, 238–241 (2011).
# Dilanji, G. E., Langebrake, J., Leenheer, P. De & Stephen, J. Quorum activation at a distance : spatiotemporal patterns of gene regulation from diffusion of an autoinducer signal. 1–17 (2012).
# Basu, S., Mehreja, R., Thiberge, S., Chen, M.-T. & Weiss, R. Spatiotemporal control of gene expression with pulse-generating networks. Proc. Natl. Acad. Sci. U. S. A. 101, 6355–6360 (2004).
# Basu, S., Gerchman, Y., Collins, C. H., Arnold, F. H. & Weiss, R. A synthetic multicellular system for programmed pattern formation. Nature 434, 1130–1134 (2005).
# Tsimring, L. et al. A synchronized quorum of genetic clocks. Nature 463, 326–330 (2010).

SURF 2017: Length and time scales of cell-cell signalling circuits in agar

2017-01-04T00:15:20Z

Jparkin:

'''[[SURF 2017|2017 SURF]] project description'''
* Mentor: Richard Murray
* Co-mentor: James Parkin

One of the focuses of the Murray biolab is biological event detectors, specifically modified bacteria that are designed to alert a researcher that a specific condition in their local environment has occurred. As a part of this focus, we are trying to engineer a bacterial strain that detects the order in which a pair of chemical inducers are applied to opposite ends of an agar plate. The detector bacteria, embedded in the agar, will communicate with their neighbors to determine which chemical appeared first, as no individual cell would detect both chemicals.

The engineered bacteria communicate using protein components borrowed from natural quorum sensing systems. Quorum sensing (QS) systems are the communication paradigm of choice for many synthetic biologists because they are portable and reliable [1, 2, 4, 5]. Augmenting E coli with QS-mediated communication requires only two protein components, a signal synthase and a signal-activated transcription factor. Furthermore, QS signalling chemicals (acyl-homoserine lactones, AHL) freely diffuse through the cell walls of Gram-negative bacteria, no transmembrane transport protein required.

The summer project I am proposing is to investigate the characteristic length and time scales observed from various experimental setups and signalling circuits. Students would use previously-characterized genetic components to compose communication circuits in cells, grow them in various semisolid media preparations, expose them to different patterns of chemical inducers, and analyze the resulting patterns of gene expression in the growing bacteria. From these data, students would quantify the experimentally feasible range of pattern lengths and determine how the behavior of a circuit changes as cells approach stationary phase [1, 3, 5]. These results would provide information to help guide future research into self-patterning or spatiotemporal event detectors.

Students may also investigate how modeling can support this line of inquiry. This may involve anything from recreating experiments in simulators developed by other labs to writing their own. Similarly, analyzing images or videos of the communicating bacteria as they grow may be approached by identifying features by hand or developing a models considering spatially heterogeneous cell growth and reaction-diffusion treatment of cell-cell signaling.

'''Recommended skills:'''

* Fluency with basic molecular biology and bacterial culture techniques
* Experience with scientific programming (MATLAB, R, Python scipy, or similar)
* Students interested in pursuing modeling or simulation should have significant previous work in numerical simulation software, multivariate calculus, and partial differential equations.

'''Reference : '''
# Liu, C. et al. Sequential Establishment of Stripe Patterns in an Expanding Cell Population. Science 334, 238–241 (2011).
# Dilanji, G. E., Langebrake, J., Leenheer, P. De & Stephen, J. Quorum activation at a distance : spatiotemporal patterns of gene regulation from diffusion of an autoinducer signal. 1–17 (2012).
# Basu, S., Mehreja, R., Thiberge, S., Chen, M.-T. & Weiss, R. Spatiotemporal control of gene expression with pulse-generating networks. Proc. Natl. Acad. Sci. U. S. A. 101, 6355–6360 (2004).
# Basu, S., Gerchman, Y., Collins, C. H., Arnold, F. H. & Weiss, R. A synthetic multicellular system for programmed pattern formation. Nature 434, 1130–1134 (2005).
# Tsimring, L. et al. A synchronized quorum of genetic clocks. Nature 463, 326–330 (2010).

SURF 2017: Length and time scales of cell-cell signalling circuits in agar

2017-01-04T00:12:35Z

Jparkin:

'''[[SURF 2017|2017 SURF]] project description'''
* Mentor: Richard Murray
* Co-mentor: James Parkin

One of the focuses of the Murray biolab is biological event detectors, specifically modified bacteria that are designed to alert a researcher that a specific condition in their local environment has occurred. As a part of this focus, we are trying to engineer a bacterial strain that detects the order in which a pair of chemical inducers are applied to opposite ends of an agar plate. The detector bacteria, embedded in the agar, will communicate with their neighbors to determine which chemical appeared first, as no individual cell would detect both chemicals.

The engineered bacteria communicate using protein components borrowed from natural quorum sensing systems. Quorum sensing (QS) systems are the communication paradigm of choice for many synthetic biologists because they are portable and reliable. Augmenting E coli with QS-mediated communication requires only two protein components, a signal synthase and a signal-activated transcription factor. Furthermore, QS signalling chemicals (acyl-homoserine lactones, AHL) freely diffuse through the cell walls of Gram-negative bacteria, no transmembrane transport protein required.

The summer project I am proposing is to investigate the characteristic length and time scales observed from various experimental setups and signalling circuits. Students would use previously-characterized genetic components to compose communication circuits in cells, grow them in various semisolid media preparations, expose them to different patterns of chemical inducers, and analyze the resulting patterns of gene expression in the growing bacteria. From these data, students would quantify the experimentally feasible range of pattern lengths and determine how the behavior of a circuit changes as cells approach stationary phase. These results would provide information to help guide future research into self-patterning or spatiotemporal event detectors.

Students may also investigate how modeling can support this line of inquiry. This may involve anything from recreating experiments in simulators developed by other labs to writing their own. Similarly, analyzing images or videos of the communicating bacteria as they grow may be approached by identifying features by hand or developing a models considering spatially heterogeneous cell growth and reaction-diffusion treatment of cell-cell signaling.

Recommended skills:

* Fluency with basic molecular biology and bacterial culture techniques
* Experience with scientific programming (MATLAB, R, Python scipy, or similar)
* Students interested in pursuing modeling or simulation should have significant previous work in numerical simulation software, multivariate calculus, and partial differential equations.

References :
# Liu, C. et al. Sequential Establishment of Stripe Patterns in an Expanding Cell Population. Science 334, 238–241 (2011).
# Dilanji, G. E., Langebrake, J., Leenheer, P. De & Stephen, J. Quorum activation at a distance : spatiotemporal patterns of gene regulation from diffusion of an autoinducer signal. 1–17 (2012).
# Basu, S., Mehreja, R., Thiberge, S., Chen, M.-T. & Weiss, R. Spatiotemporal control of gene expression with pulse-generating networks. Proc. Natl. Acad. Sci. U. S. A. 101, 6355–6360 (2004).
# Basu, S., Gerchman, Y., Collins, C. H., Arnold, F. H. & Weiss, R. A synthetic multicellular system for programmed pattern formation. Nature 434, 1130–1134 (2005).
# Tsimring, L. et al. A synchronized quorum of genetic clocks. Nature 463, 326–330 (2010).

SURF 2017: Length and time scales of cell-cell signalling circuits in agar

2017-01-03T21:11:55Z

Jparkin:

'''[[SURF 2017|2017 SURF]] project description'''
* Mentor: Richard Murray
* Co-mentor: James Parkin

One of the focuses of the Murray biolab is biological event detectors, specifically modified bacteria that are designed to alert a researcher that a specific condition in their local environment has occurred. As a part of this focus, we are trying to engineer a bacterial strain that detects the order in which a pair of chemical inducers are applied to opposite ends of an agar plate. The detector bacteria, embedded in the agar, will communicate with their neighbors to determine which chemical appeared first, as no individual cell would detect both chemicals.

The engineered bacteria communicate using protein components borrowed from natural quorum sensing systems. Quorum sensing (QS) systems are the communication paradigm of choice for many synthetic biologists because they are portable and reliable. Augmenting E coli with QS-mediated communication requires only two protein components, a signal synthase and a signal-activated transcription factor. Furthermore, QS signalling chemicals (acyl-homoserine lactones, AHL) freely diffuse through the cell walls of Gram-negative bacteria, no transmembrane transport protein required.

The summer project I am proposing is to investigate the characteristic length and time scales observed from various experimental setups and signalling circuits. Students would use previously-characterized genetic components to compose communication circuits in cells, grow them in various semisolid media preparations, expose them to different patterns of chemical inducers, and analyze the resulting patterns of gene expression in the growing bacteria. From these data, students would quantify the experimentally feasible range of pattern lengths and determine how the behavior of a circuit changes as cells approach stationary phase. These results would provide information to help guide future research into self-patterning or spatiotemporal event detectors.

Students may also investigate how modeling can support this line of inquiry. This may involve anything from recreating experiments in simulators developed by other labs to writing their own. Similarly, analyzing images or videos of the communicating bacteria as they grow may be approached by identifying features by hand or developing a models considering spatially heterogeneous cell growth and reaction-diffusion treatment of cell-cell-signaling.

Recommended skills:

* Fluency with basic molecular biology and bacterial culture techniques
* Experience with scientific programming (MATLAB, R, Python scipy, or similar)
* Students should have significant previous work in numerical simulation, multivariate calculus, and partial differential equations.

# Liu, C. et al. Sequential Establishment of Stripe Patterns in an Expanding Cell Population. Science 334, 238–241 (2011).
# Dilanji, G. E., Langebrake, J., Leenheer, P. De & Stephen, J. Quorum activation at a distance : spatiotemporal patterns of gene regulation from diffusion of an autoinducer signal. 1–17 (2012).
# Basu, S., Mehreja, R., Thiberge, S., Chen, M.-T. & Weiss, R. Spatiotemporal control of gene expression with pulse-generating networks. Proc. Natl. Acad. Sci. U. S. A. 101, 6355–6360 (2004).
# Basu, S., Gerchman, Y., Collins, C. H., Arnold, F. H. & Weiss, R. A synthetic multicellular system for programmed pattern formation. Nature 434, 1130–1134 (2005).
# Tsimring, L. et al. A synchronized quorum of genetic clocks. Nature 463, 326–330 (2010).

SURF 2017: Length and time scales in cell-cell signalling circuits in agar

2017-01-03T10:19:27Z

Jparkin: Jparkin moved page SURF 2017: Length and time scales in cell-cell signalling circuits in agar to SURF 2017: Length and time scales of cell-cell signalling circuits in agar

#REDIRECT [[SURF 2017: Length and time scales of cell-cell signalling circuits in agar]]

SURF 2017: Length and time scales of cell-cell signalling circuits in agar

2017-01-03T10:19:26Z

Jparkin: Jparkin moved page SURF 2017: Length and time scales in cell-cell signalling circuits in agar to SURF 2017: Length and time scales of cell-cell signalling circuits in agar

'''[[SURF 2017|2017 SURF]] project description'''
* Mentor: Richard Murray
* Co-mentor: James Parkin

One of the focuses of the Murray biolab is biological event detectors, specifically modified bacteria that are designed to alert a researcher that a specific condition in their local environment has occurred. I am pursuing a project to engineer a strain that detects the order in which a pair of chemical inducers are applied to opposite ends of an agar plate. The detector bacteria, embedded in the agar, will communicate with their neighbors to determine which chemical appeared first, as no individual cell would detect both chemicals.

The engineered bacteria communicate using protein components borrowed from natural quorum sensing systems. Quorum sensing (QS) systems are the communication paradigm of choice for many synthetic biologists because they are portable and reliable. Augmenting E coli with QS-mediated communication requires only two protein components, a signal synthase and a signal-activated transcription factor. Furthermore, QS signalling chemicals (acyl-homoserine lactones, AHL) freely diffuse through the cell walls of Gram-negative bacteria, no transmembrane transport protein required.

The summer project I am proposing is to investigate the characteristic length and time scales observed from various experimental setups and signalling circuits. Students would use previously-characterized genetic components to compose communication circuits in cells, grow them in various semisolid media preparations, expose them to different patterns of chemical inducers, and analyze the resulting patterns of gene expression in the growing bacteria. From these data, students would quantify the experimentally feasible range of pattern lengths and determine how the behavior of a circuit changes as cells approach stationary phase. These results would provide information to help guide future research into self-patterning or spatiotemporal event detectors.

Students may also investigate how modeling can support this line of inquiry. On the student's discretion, this may involve anything from recreating experiments in simulators developed by other labs to writing their own. Similarly, analyzing images or videos of the communicating bacteria as they grow may be approached by identifying features by hand or developing a models considering spatially heterogeneous cell growth and reaction-diffusion treatment of cell-cell-signaling.

[1] Liu, C. et al. Sequential Establishment of Stripe Patterns in an Expanding Cell Population. Science 334, 238–241 (2011).

[2] Dilanji, G. E., Langebrake, J., Leenheer, P. De & Stephen, J. Quorum activation at a distance : spatiotemporal patterns of gene regulation from diffusion of an autoinducer signal. 1–17 (2012).

[3] Basu, S., Mehreja, R., Thiberge, S., Chen, M.-T. & Weiss, R. Spatiotemporal control of gene expression with pulse-generating networks. Proc. Natl. Acad. Sci. U. S. A. 101, 6355–6360 (2004).

[4] Basu, S., Gerchman, Y., Collins, C. H., Arnold, F. H. & Weiss, R. A synthetic multicellular system for programmed pattern formation. Nature 434, 1130–1134 (2005).

[5] Tsimring, L. et al. A synchronized quorum of genetic clocks. Nature 463, 326–330 (2010).

SURF 2017: Length and time scales in of cell-cell signalling circuits in agar

2017-01-03T10:17:15Z

Jparkin: Jparkin moved page SURF 2017: Length and time scales in of cell-cell signalling circuits in agar to SURF 2017: Length and time scales in cell-cell signalling circuits in agar

#REDIRECT [[SURF 2017: Length and time scales in cell-cell signalling circuits in agar]]

SURF 2017: Length and time scales of cell-cell signalling circuits in agar

2017-01-03T10:17:14Z

Jparkin: Jparkin moved page SURF 2017: Length and time scales in of cell-cell signalling circuits in agar to SURF 2017: Length and time scales in cell-cell signalling circuits in agar

'''[[SURF 2017|2017 SURF]] project description'''
* Mentor: Richard Murray
* Co-mentor: James Parkin

One of the focuses of the Murray biolab is biological event detectors, specifically modified bacteria that are designed to alert a researcher that a specific condition in their local environment has occurred. I am pursuing a project to engineer a strain that detects the order in which a pair of chemical inducers are applied to opposite ends of an agar plate. The detector bacteria, embedded in the agar, will communicate with their neighbors to determine which chemical appeared first, as no individual cell would detect both chemicals.

The engineered bacteria communicate using protein components borrowed from natural quorum sensing systems. Quorum sensing (QS) systems are the communication paradigm of choice for many synthetic biologists because they are portable and reliable. Augmenting E coli with QS-mediated communication requires only two protein components, a signal synthase and a signal-activated transcription factor. Furthermore, QS signalling chemicals (acyl-homoserine lactones, AHL) freely diffuse through the cell walls of Gram-negative bacteria, no transmembrane transport protein required.

The summer project I am proposing is to investigate the characteristic length and time scales observed from various experimental setups and signalling circuits. Students would use previously-characterized genetic components to compose communication circuits in cells, grow them in various semisolid media preparations, expose them to different patterns of chemical inducers, and analyze the resulting patterns of gene expression in the growing bacteria. From these data, students would quantify the experimentally feasible range of pattern lengths and determine how the behavior of a circuit changes as cells approach stationary phase. These results would provide information to help guide future research into self-patterning or spatiotemporal event detectors.

Students may also investigate how modeling can support this line of inquiry. On the student's discretion, this may involve anything from recreating experiments in simulators developed by other labs to writing their own. Similarly, analyzing images or videos of the communicating bacteria as they grow may be approached by identifying features by hand or developing a models considering spatially heterogeneous cell growth and reaction-diffusion treatment of cell-cell-signaling.

[1] Liu, C. et al. Sequential Establishment of Stripe Patterns in an Expanding Cell Population. Science 334, 238–241 (2011).

[2] Dilanji, G. E., Langebrake, J., Leenheer, P. De & Stephen, J. Quorum activation at a distance : spatiotemporal patterns of gene regulation from diffusion of an autoinducer signal. 1–17 (2012).

[3] Basu, S., Mehreja, R., Thiberge, S., Chen, M.-T. & Weiss, R. Spatiotemporal control of gene expression with pulse-generating networks. Proc. Natl. Acad. Sci. U. S. A. 101, 6355–6360 (2004).

[4] Basu, S., Gerchman, Y., Collins, C. H., Arnold, F. H. & Weiss, R. A synthetic multicellular system for programmed pattern formation. Nature 434, 1130–1134 (2005).

[5] Tsimring, L. et al. A synchronized quorum of genetic clocks. Nature 463, 326–330 (2010).

SURF 2017

2017-01-03T10:16:28Z

Jparkin: /* List of available projects */

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

=== Applying for a SURF project ===

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

# A list of SURF project descriptions is given in the table below. Due to the number of SURF projects that we support, we are only able to support students who select from among these projects. Please make sure to read the project descriptions, required skills (if any) and skim a few of the listed references before contacting me about doing a SURF project.
# Students interested in writing proposals for SURF projects should contact me via e-mail by 11 Jan (Wed) and provide the following information:
#* A list of up to three SURF projects from the list below that you are interested in working on
#* A one page resume listing relevant experience and coursework
#* If you are not a Caltech student, I will also need the following additional information:
#** An unofficial copy of your academic transcript
#** Names of two faculty members at your current institution that I can contact for a reference
# Starting on 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 2015 (Amgen applications are due a week earlier)..
# If you are selected for a SURF, please be aware of the following information
#* All SURF projects in my group will start on 16 Jun (Tue). If you can't start on that date, please make sure that you indicate this when you contact me
#* All SURF projects are for a minimum of 10 weeks, although I usually recommend that you try to stay for 12 weeks if possible (at no additional pay). It's hard to complete a project in just 10 weeks and spending a few extra weeks can greatly improve the project.
#* All SURF students in my group will be expected to devote full-time effort to their SURF project, so you cannot have a second job in addition to your SURF.

=== List of available projects ===

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

{| border=1 width=100%
|-
| '''Title''' || '''Grant/Project''' || '''Co-Mentors''' || '''Comments'''
|-
|{{SURF entry|2017|Scalable Robust Synthesis from Temporal Logic Specifications}}
| [[SRC TerraSwarm]]
| Sumanth Dathathri
| Multiple projects may be available
|-
| {{SURF|2017|Integrase based circuits for sequential and temporal control of gene expression }}
| [[ARO ICB]]
| Rory Williams
|
|-
| {{SURF|2017|Synthetic modules for control of bacterial growth}}
| [[DARPA BioCon]]
| Reed McCardell
|
|-
| {{SURF|2017|Length and time scales of cell-cell signalling circuits in agar}}
| [[ARO ICB]]
| James Parkin
|
|-
| {{SURF|2017|Genetically-Programmed Artificial Cells and Multi-Cellular Machines}}
| [[GBMF PMTI]], [[NSF MPP]]
| TBD
| Multiple projects may be available
|}

SURF 2017: Length and time scales of cell-cell signalling circuits in agar

2017-01-03T10:16:00Z

Jparkin: Created page with "'''2017 SURF project description''' * Mentor: Richard Murray * Co-mentor: James Parkin One of the focuses of the Murray biolab is biological event detectors, sp..."

'''[[SURF 2017|2017 SURF]] project description'''
* Mentor: Richard Murray
* Co-mentor: James Parkin

One of the focuses of the Murray biolab is biological event detectors, specifically modified bacteria that are designed to alert a researcher that a specific condition in their local environment has occurred. I am pursuing a project to engineer a strain that detects the order in which a pair of chemical inducers are applied to opposite ends of an agar plate. The detector bacteria, embedded in the agar, will communicate with their neighbors to determine which chemical appeared first, as no individual cell would detect both chemicals.

The engineered bacteria communicate using protein components borrowed from natural quorum sensing systems. Quorum sensing (QS) systems are the communication paradigm of choice for many synthetic biologists because they are portable and reliable. Augmenting E coli with QS-mediated communication requires only two protein components, a signal synthase and a signal-activated transcription factor. Furthermore, QS signalling chemicals (acyl-homoserine lactones, AHL) freely diffuse through the cell walls of Gram-negative bacteria, no transmembrane transport protein required.

The summer project I am proposing is to investigate the characteristic length and time scales observed from various experimental setups and signalling circuits. Students would use previously-characterized genetic components to compose communication circuits in cells, grow them in various semisolid media preparations, expose them to different patterns of chemical inducers, and analyze the resulting patterns of gene expression in the growing bacteria. From these data, students would quantify the experimentally feasible range of pattern lengths and determine how the behavior of a circuit changes as cells approach stationary phase. These results would provide information to help guide future research into self-patterning or spatiotemporal event detectors.

Students may also investigate how modeling can support this line of inquiry. On the student's discretion, this may involve anything from recreating experiments in simulators developed by other labs to writing their own. Similarly, analyzing images or videos of the communicating bacteria as they grow may be approached by identifying features by hand or developing a models considering spatially heterogeneous cell growth and reaction-diffusion treatment of cell-cell-signaling.

[1] Liu, C. et al. Sequential Establishment of Stripe Patterns in an Expanding Cell Population. Science 334, 238–241 (2011).

[2] Dilanji, G. E., Langebrake, J., Leenheer, P. De & Stephen, J. Quorum activation at a distance : spatiotemporal patterns of gene regulation from diffusion of an autoinducer signal. 1–17 (2012).

[3] Basu, S., Mehreja, R., Thiberge, S., Chen, M.-T. & Weiss, R. Spatiotemporal control of gene expression with pulse-generating networks. Proc. Natl. Acad. Sci. U. S. A. 101, 6355–6360 (2004).

[4] Basu, S., Gerchman, Y., Collins, C. H., Arnold, F. H. & Weiss, R. A synthetic multicellular system for programmed pattern formation. Nature 434, 1130–1134 (2005).

[5] Tsimring, L. et al. A synchronized quorum of genetic clocks. Nature 463, 326–330 (2010).

SURF 2017

2017-01-03T06:26:39Z

Jparkin: /* List of available projects */

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

=== Applying for a SURF project ===

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

# A list of SURF project descriptions is given in the table below. Due to the number of SURF projects that we support, we are only able to support students who select from among these projects. Please make sure to read the project descriptions, required skills (if any) and skim a few of the listed references before contacting me about doing a SURF project.
# Students interested in writing proposals for SURF projects should contact me via e-mail by 11 Jan (Wed) and provide the following information:
#* A list of up to three SURF projects from the list below that you are interested in working on
#* A one page resume listing relevant experience and coursework
#* If you are not a Caltech student, I will also need the following additional information:
#** An unofficial copy of your academic transcript
#** Names of two faculty members at your current institution that I can contact for a reference
# Starting on 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 2015 (Amgen applications are due a week earlier)..
# If you are selected for a SURF, please be aware of the following information
#* All SURF projects in my group will start on 16 Jun (Tue). If you can't start on that date, please make sure that you indicate this when you contact me
#* All SURF projects are for a minimum of 10 weeks, although I usually recommend that you try to stay for 12 weeks if possible (at no additional pay). It's hard to complete a project in just 10 weeks and spending a few extra weeks can greatly improve the project.
#* All SURF students in my group will be expected to devote full-time effort to their SURF project, so you cannot have a second job in addition to your SURF.

=== List of available projects ===

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

{| border=1 width=100%
|-
| '''Title''' || '''Grant/Project''' || '''Co-Mentors''' || '''Comments'''
|-
|{{SURF entry|2017|Scalable Robust Synthesis from Temporal Logic Specifications}}
| [[SRC TerraSwarm]]
| Sumanth Dathathri
| Multiple projects may be available
|-
| {{SURF|2017|Integrase based circuits for sequential and temporal control of gene expression }}
| [[ARO ICB]]
| Rory Williams
|
|-
| {{SURF|2017|Synthetic modules for control of bacterial growth}}
| [[DARPA BioCon]]
| Reed McCardell
|
|-
| {{SURF|2017|Length and time scales in of cell-cell signalling circuits in agar}}
| [[ARO ICB]]
| James Parkin
|
|}

Nov 2016 meeting schedule

2016-11-07T02:44:16Z

Jparkin: /* 16 Nov (Wed) */

Richard will be in town 13-16 Nov. Please sign up for a time to meet below.
__NOTOC__

{| border=1
|- valign=top
| width=25% |

==== 13 Nov (Sun) ====
<br>
<br>
<hr>
* 2:45 pm: Hold until needed
* 3:30 pm: Hold until needed
* 4:15 pm: Break
* 5:00 pm: Hold until needed
* 5:45 pm: Hold until needed
* 6:30 pm: Done for the day

| width=25% |

==== 14 Nov (Mon) ====
* 10:30 am: Andy Halleran
* 11:15 am: Tung
<hr>
* 1:30 pm: Vipul
* 2:15 pm: Andrey Shur
* 3:00 pm: Shaobin
* 3:45 pm: Break
* 4:00 pm: Miki
* 4:45 pm: Aryeh
* 5:30 pm: Anu
* 6:15 pm: Done for the day
| width=25% |

====15 Nov (Tue) ====
* 10:30 am: Mark
* 11:15 am: Reed
<hr>
* 1:30 pm: Sumanth
* 2:15 pm: Karena Cai
* 3:00 pm: Tony Fragoso
* 3:45 pm: Break
* 4:00 pm: Anandh
* 4:45 pm: Cindy
* 5:30 pm: Richard
* 6:15 pm: Done for the day
| width=25% |

==== 16 Nov (Wed) ====
* 9:30 am: James
* 10:15 am: Ania
* 11:00 am: Telecon
* 12 pm: Ioannis
* 12:45 pm: Break
<hr>
* 1:30 pm: Sam
* 2:15 pm: Rory
* 3:00 pm: CDS tea
* Depart for airport at ~3:45 pm
|}

Sep/Oct 2016 meeting schedule

2016-09-24T22:45:20Z

Jparkin: /* 30 Sep (Fri) */

Richard will be in town 29 Sept - 3 Oct 2016. Please sign up for a time to meet below.
__NOTOC__

{| border=1
|- valign=top
| width=25% |
==== 29 Sep (Thu) ====
* Flying in from SF in the morning
* 1:00 pm: George
* 1:45 pm: Andrey
* 2:30 pm: Tony Fragoso
* 3:15 pm: Break
* 3:30 pm: Richard C.
* 4:15 pm: Sam
* 5:00 pm: Mark
* 5:45 pm: Break
* 6:00 pm: Reed
* 6:45 pm: Rory
* 7:30 pm: Done for the day
| width=25% |

==== 30 Sep (Fri) ====
* Morning: busy with other meetings/phone calls
* 1:30-3:30 pm: Integrase project meeting (Victoria, Andrey, George, Sam, Ania, Cindy, Jining)
* 3:30 pm: Miki
* 4:30 pm: break
* 4:45 pm: Andrew
* 5:30 pm: Anandh
* 6:15 pm: James
* 7:00 pm: Done for the day
| width=25% |

==== 2 Oct (Sun) ====
* 1:45 pm: YONG
* 2:30 pm: Vipul
* 3:15 pm: Karena
* 4:00 pm: Break
* 4:15 pm: Cindy
* 5:00 pm: Sumanth
* 5:45 pm: Open
* 6:30 pm: Open
* 7:15 pm: Done for the day

| width=25% |

==== 3 Oct (Mon) ====
* 10 am - 12 pm: DARPA BioCon meeting
* 12:00 pm: Candidacy exam
* 1:45 pm: Jaymie
* 2:45 pm: Tung
* 3:30 pm: Shaobin
* 4:15 pm: Victoria
* 5:00 pm: Break
* 5:15 pm: Daniel N
* 6:00 pm: William
* 6:45 pm: Ania
* 7:30 pm: Done for the day
|}

Sep/Oct 2016 meeting schedule

2016-09-24T22:45:02Z

Jparkin: /* 2 Oct (Sun) */

Richard will be in town 29 Sept - 3 Oct 2016. Please sign up for a time to meet below.
__NOTOC__

{| border=1
|- valign=top
| width=25% |
==== 29 Sep (Thu) ====
* Flying in from SF in the morning
* 1:00 pm: George
* 1:45 pm: Andrey
* 2:30 pm: Tony Fragoso
* 3:15 pm: Break
* 3:30 pm: Richard C.
* 4:15 pm: Sam
* 5:00 pm: Mark
* 5:45 pm: Break
* 6:00 pm: Reed
* 6:45 pm: Rory
* 7:30 pm: Done for the day
| width=25% |

==== 30 Sep (Fri) ====
* Morning: busy with other meetings/phone calls
* 1:30-3:30 pm: Integrase project meeting (Victoria, Andrey, George, Sam, Ania, Cindy, Jining)
* 3:30 pm: Miki
* 4:30 pm: break
* 4:45 pm: Andrew
* 5:30 pm: Anandh
* 6:15 pm: Open
* 7:00 pm: Done for the day
| width=25% |

==== 2 Oct (Sun) ====
* 1:45 pm: YONG
* 2:30 pm: Vipul
* 3:15 pm: Karena
* 4:00 pm: Break
* 4:15 pm: Cindy
* 5:00 pm: Sumanth
* 5:45 pm: Open
* 6:30 pm: Open
* 7:15 pm: Done for the day

| width=25% |

==== 3 Oct (Mon) ====
* 10 am - 12 pm: DARPA BioCon meeting
* 12:00 pm: Candidacy exam
* 1:45 pm: Jaymie
* 2:45 pm: Tung
* 3:30 pm: Shaobin
* 4:15 pm: Victoria
* 5:00 pm: Break
* 5:15 pm: Daniel N
* 6:00 pm: William
* 6:45 pm: Ania
* 7:30 pm: Done for the day
|}

Sep/Oct 2016 meeting schedule

2016-09-24T22:43:41Z

Jparkin: /* 2 Oct (Sun) */

Richard will be in town 29 Sept - 3 Oct 2016. Please sign up for a time to meet below.
__NOTOC__

{| border=1
|- valign=top
| width=25% |
==== 29 Sep (Thu) ====
* Flying in from SF in the morning
* 1:00 pm: George
* 1:45 pm: Andrey
* 2:30 pm: Tony Fragoso
* 3:15 pm: Break
* 3:30 pm: Richard C.
* 4:15 pm: Sam
* 5:00 pm: Mark
* 5:45 pm: Break
* 6:00 pm: Reed
* 6:45 pm: Rory
* 7:30 pm: Done for the day
| width=25% |

==== 30 Sep (Fri) ====
* Morning: busy with other meetings/phone calls
* 1:30-3:30 pm: Integrase project meeting (Victoria, Andrey, George, Sam, Ania, Cindy, Jining)
* 3:30 pm: Miki
* 4:30 pm: break
* 4:45 pm: Andrew
* 5:30 pm: Anandh
* 6:15 pm: Open
* 7:00 pm: Done for the day
| width=25% |

==== 2 Oct (Sun) ====
* 1:45 pm: YONG
* 2:30 pm: Vipul
* 3:15 pm: Karena
* 4:00 pm: Break
* 4:15 pm: Cindy
* 5:00 pm: Sumanth
* 5:45 pm: James
* 6:30 pm: Open
* 7:15 pm: Done for the day

| width=25% |

==== 3 Oct (Mon) ====
* 10 am - 12 pm: DARPA BioCon meeting
* 12:00 pm: Candidacy exam
* 1:45 pm: Jaymie
* 2:45 pm: Tung
* 3:30 pm: Shaobin
* 4:15 pm: Victoria
* 5:00 pm: Break
* 5:15 pm: Daniel N
* 6:00 pm: William
* 6:45 pm: Ania
* 7:30 pm: Done for the day
|}

Aug 2016 meeting schedule

2016-08-04T17:07:35Z

Jparkin: /* 9 Aug (Tue) */

Richard will be in town 7-10 August 2016. Please sign up for a time to meet below.
__NOTOC__

{| border=1
|- valign=top
| width=25% |
==== 7 Aug (Sun) ====
* 2:15 pm: Cindy
* 3:00 pm: Karena
* 3:45 pm: Yong
* 4:00 pm: Break
* 4:45 pm: Sam
* 5:30 pm: George
* 6:30 pm: Daniel
| width=25% |

==== 8 Aug (Mon) ====
* 9-11 am: TX-TL project meeting (Clare, Mark, Shaobin, Yong, Vipul, Sam, Miki)
<hr>
* 12:45 pm: Anandh
* 1:30 pm: Shaobin
* 2:15 pm: Richard C
* 3:00 pm: Victoria
* 3:45 pm: Break
* 4:00 pm: Andrew
* 4:45 pm: Anu
* 5:30 pm: Andrey
| width=25% |

==== 9 Aug (Tue) ====
* 8:30 am: Reed
* 9:15 am: Mark
* 10:00 am: Jaymie
* 11 am - 2 pm: DARPA Biological Control project meeting (Anandh, Ania, Cindy, James, Reed, Andrey, George, Sam?)
* 1:00 pm: Tung
* 1:45 pm: James
* 2:30 pm: Tony Fragoso
* 3:15 pm: Break
* 3:30 pm: Vipul
* 4:15 pm: Ioannis
* 5:00 pm: no longer available
| width=25% |

==== 10 Aug (Wed) ====
* 9-11 am: Integrase project meeting (Victoria, Andrey, George, Sam, Ania, Cindy)
* 11:00 am: Ania
* 11:45 am: Unavailable
* 12:45 pm: Miki
* 1:45 pm: Alex
* 2:30 pm: Leave for airport
|}

Research meetings, Jan/Feb 2016

2016-01-19T03:46:38Z

Jparkin: /* 2 Feb 2016 (Tue) */

Please sign up for a slot below. __NOTOC__

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

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

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

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

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