Murray Wiki - User contributions [en]

Group Schedule, Winter 2020

2020-01-14T19:52:26Z

Xrren: /* Week 10: 9-13 Mar */

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, Fall 2019]]
|}

The schedule for group and subgroup meetings is given below. Contact Richard if you need to change the schedule. Unless otherwise noted, biocircuits meetings are in 111 Keck and NCS meetings are in 110 Steele.

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

| width=25% |
=== Week 1: 6-10 Jan ===
'''Biocircuits: <s>Tue, 10a-12p</s> Thu, 9a-11a'''
* Andrey
* James
'''NCS: Wed, 2p-3p'''
* Chuchu

| width=25% |

=== Week 2: 13-17 Jan===
'''Biocircuits: Tue, 10a-12p'''
* [[http:docs.google.com/presentation/d/1G5EExMEddM0j4MsxgDDn4i1rqZlicP1NFRZwufi_9RU/|Individual updates]]
* Meeting may shift to 9a-11a
'''NCS: Wed, <s>2p-3p</s> 1:30p-2:30p'''
* Francesca
| width=25% |

=== Week 3: 20-24 Jan ===
'''Biocircuits: Tue, 10a-12p'''
* TBD
'''NCS: Wed, 2p-3p'''
* Prithvi


| width=25% |

=== Week 4: 27-31 Jan ===
'''Biocircuits: Tue, 10a-12p'''
* John
* Reed
* Meeting may shift to 3p-5p
'''NCS: Wed, 2p-3p'''
* Sumanth

|- valign=top
| width=25% |

=== Week 5: 3-7 Feb ===
'''Biocircuits: Tue, 10a-12p'''
* [[http:docs.google.com/presentation/d/1mk32NlP3jCZOVcuGsfP7EWW7jrn909-ySrUrmg3bNxQ|Individual updates]]
'''NCS: Wed, 2p-3p'''
* Karena


| width=25% |

=== Week 6: 10-14 Feb ===
'''Biocircuits: Tue, 10a-12p'''
* TBD
* Meeting may shift to 9a-11a
'''NCS: Wed, 2p-3p'''
* Richard C


| width=25% |

=== Week 7: 17-21 Feb ===
'''Biocircuits: Tue, 10a-12p'''
* Leo
* Sam
'''NCS: Wed, 2p-3p'''
* Tung

| width=25% |

=== Week 8: 24-28 Feb ===
'''Biocircuits: Tue, 10a-12p'''
* [[http:docs.google.com/presentation/d/1N4256hP3pr9ja3Qr4DYYDCnD9XOJeyc2cwBHU5Y2RUQ|Individual updates]]
* Meeting may shift to 9a-11a
'''NCS: Wed, 2p-3p'''
* Reza


|- valign=top
| width=25% |

=== Week 9: 2-6 Mar ===
'''Biocircuits: Tue, 10a-12p'''
* Liana
* Sophie
'''NCS: Wed, 2p-3p'''
* UG/visitor

| width=25% |

=== Week 10: 9-13 Mar ===
'''Biocircuits: Tue, 10a-12p'''
* Ayush
* Cindy
* Meeting may be cancelled
'''NCS: Wed, 2p-3p'''
* Yuxiao
* Meeting may be cancelled

| width=25% |

=== Week 11: 16-20 Mar ===
'''Biocircuits: Tue, 10a-12p'''
* [[http:docs.google.com/presentation/d/1Fe9_7Y9qM6UqJLlByVmxeJ7PPTLwMiFUcbowFfT0Bho|Individual updates]]
* Meeting may be cancelled
'''NCS: Wed, 2p-3p'''
* Apurva
* Meeting may be cancelled


| width=25% |

=== Week 12: 23-27 Mar ===
* Spring break

|}

Group Schedule, Winter 2020

2020-01-14T19:52:13Z

Xrren: /* Week 7: 17-21 Feb */

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, Fall 2019]]
|}

The schedule for group and subgroup meetings is given below. Contact Richard if you need to change the schedule. Unless otherwise noted, biocircuits meetings are in 111 Keck and NCS meetings are in 110 Steele.

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

| width=25% |
=== Week 1: 6-10 Jan ===
'''Biocircuits: <s>Tue, 10a-12p</s> Thu, 9a-11a'''
* Andrey
* James
'''NCS: Wed, 2p-3p'''
* Chuchu

| width=25% |

=== Week 2: 13-17 Jan===
'''Biocircuits: Tue, 10a-12p'''
* [[http:docs.google.com/presentation/d/1G5EExMEddM0j4MsxgDDn4i1rqZlicP1NFRZwufi_9RU/|Individual updates]]
* Meeting may shift to 9a-11a
'''NCS: Wed, <s>2p-3p</s> 1:30p-2:30p'''
* Francesca
| width=25% |

=== Week 3: 20-24 Jan ===
'''Biocircuits: Tue, 10a-12p'''
* TBD
'''NCS: Wed, 2p-3p'''
* Prithvi


| width=25% |

=== Week 4: 27-31 Jan ===
'''Biocircuits: Tue, 10a-12p'''
* John
* Reed
* Meeting may shift to 3p-5p
'''NCS: Wed, 2p-3p'''
* Sumanth

|- valign=top
| width=25% |

=== Week 5: 3-7 Feb ===
'''Biocircuits: Tue, 10a-12p'''
* [[http:docs.google.com/presentation/d/1mk32NlP3jCZOVcuGsfP7EWW7jrn909-ySrUrmg3bNxQ|Individual updates]]
'''NCS: Wed, 2p-3p'''
* Karena


| width=25% |

=== Week 6: 10-14 Feb ===
'''Biocircuits: Tue, 10a-12p'''
* TBD
* Meeting may shift to 9a-11a
'''NCS: Wed, 2p-3p'''
* Richard C


| width=25% |

=== Week 7: 17-21 Feb ===
'''Biocircuits: Tue, 10a-12p'''
* Leo
* Sam
'''NCS: Wed, 2p-3p'''
* Tung

| width=25% |

=== Week 8: 24-28 Feb ===
'''Biocircuits: Tue, 10a-12p'''
* [[http:docs.google.com/presentation/d/1N4256hP3pr9ja3Qr4DYYDCnD9XOJeyc2cwBHU5Y2RUQ|Individual updates]]
* Meeting may shift to 9a-11a
'''NCS: Wed, 2p-3p'''
* Reza


|- valign=top
| width=25% |

=== Week 9: 2-6 Mar ===
'''Biocircuits: Tue, 10a-12p'''
* Liana
* Sophie
'''NCS: Wed, 2p-3p'''
* UG/visitor

| width=25% |

=== Week 10: 9-13 Mar ===
'''Biocircuits: Tue, 10a-12p'''
* Ayush
* Sam
* Meeting may be cancelled
'''NCS: Wed, 2p-3p'''
* Yuxiao
* Meeting may be cancelled

| width=25% |

=== Week 11: 16-20 Mar ===
'''Biocircuits: Tue, 10a-12p'''
* [[http:docs.google.com/presentation/d/1Fe9_7Y9qM6UqJLlByVmxeJ7PPTLwMiFUcbowFfT0Bho|Individual updates]]
* Meeting may be cancelled
'''NCS: Wed, 2p-3p'''
* Apurva
* Meeting may be cancelled


| width=25% |

=== Week 12: 23-27 Mar ===
* Spring break

|}

Sara Molinari, 29 Jan 2019

2019-01-28T18:37:07Z

Xrren: /* Schedule */

Sara Molinari will visit Caltech on 29-30 Jan 2019.

=== Schedule ===

{| width=100% border=1
|- valign=top
| width=50% |
29 Jan (Tue):
* 8:30 am: Richard, 109 Steele Lab
* 9:00 am: seminar
* 10:00 am: Andrey (meet after seminar)
* 10:45 am: Joe (Keck 238)
* 11:30 am: Zoila (Watson courtyard)
* 12:00 pm: Lunch with postdocs John McManus, Leo Green, Chelsea Hu
* 1:00 pm: ELM discussion (Richard, James, Rory, ERDC?)
* 2:00 pm: Andy (meet at Richard's office)
* 2:45 pm: John McManus (133 Keck)
* 3:30 pm: Chelsea (ANB lounge)
* 4:15 pm: Cindy (ANB lounge)
* 5:00 pm: done for the day
* 6:00 pm (or other): dinner with grad students (John Marken, Andy, Joe, Rory) (TBD)

| width=50% |
30 Jan (Wed):
* 9:00 am: Biocircuits group meeting
* 11:00 am: Hold: Niles?
* 11:45 am: open
* 12:30 pm: working lunch with James and Rory
* 1:45 pm: John Marken (103 Steele)
* 2:30 pm: Richard, 109 Steele Lab
* 3:00 pm: depart campus
|}

=== Talk ===

'''Engineering asymmetrical cell division into Escherichia coli'''

Sara Molinari, Rice University 
29 Jan (Tue) @ 9 am, 111 Keck

Multicellularity, in eukaryotic organisms, is ultimately responsible for most of the tissues features, such as controlling its shape and size, distributing biochemical, structural and reproductive tasks. Multicellularity is reached through asymmetrical cell division in which progenitor cells create a differentiated daughter cell while retaining their original phenotype. Here, we describe a synthetic genetic circuit for controlling asymmetrical cell division in Escherichia coli. Specifically, we engineered an inducible system that can bind and segregate plasmid DNA to a single position in the cell. Upon division, the co-localized plasmids are kept by one and only one of the daughter cells. The other daughter cell receives no plasmid DNA and is hence irreversibly differentiated from its sibling. In this way, we achieved asymmetric cell division though asymmetric plasmid partitioning. We used this system to achieve physical separation of genetically different cells. We also characterized an orthogonal inducible circuit that enables the simultaneous asymmetric partitioning of two plasmid species – resulting in pluripotent cells that have four distinct differentiated states. These results point the way towards engineering multicellular systems from prokaryotic hosts.

SURF discussions, Jan 2019

2019-01-27T02:10:25Z

Xrren: /* 29 Jan (Tue) */

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.

{| border=1 width=100%
|- valign=top
| width=25% |
==== 28 Jan (Mon) ====
* 5:00 pm PST: Victoria / Andy
* 5:30 pm PST: open
| width=25% |

==== 29 Jan (Tue) ====
* 12:00 pm PST: Ann / Cindy
| width=25% |

==== 31 Jan (Thu) ====
* 12:00 pm PST: Isabelle / John
| width=25% |

==== 1 Feb (Fri) ====
* 11:00 am PST: Ludvig / Petter
<hr>
* 3:30 pm PST: open
* 4:00 pm 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

SURF discussions, Jan 2019

2019-01-27T02:10:18Z

Xrren: /* 29 Jan (Tue) */

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.

{| border=1 width=100%
|- valign=top
| width=25% |
==== 28 Jan (Mon) ====
* 5:00 pm PST: Victoria / Andy
* 5:30 pm PST: open
| width=25% |

==== 29 Jan (Tue) ====
* 12:00 pm PST: Ann/Cindy
| width=25% |

==== 31 Jan (Thu) ====
* 12:00 pm PST: Isabelle / John
| width=25% |

==== 1 Feb (Fri) ====
* 11:00 am PST: Ludvig / Petter
<hr>
* 3:30 pm PST: open
* 4:00 pm 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

SURF 2019: Modeling and Analysis on Robust Synthetic Consortia with Localized Functions

2018-12-12T01:15:39Z

Xrren:

'''[[SURF 2019|2019 SURF]]: project description'''
* Mentor: Richard M. Murray
* Co-mentor: Xinying (Cindy) Ren

'''Background:'''

Engineering synthetic microbial consortia is an emerging area in synthetic biology. Multiple cell types can interact via cell-cell communications and perform more complex functions. Cooperation and competition are fundamental intercellular interactions, and can shape population level behaviors in consortia. Intercellular interactions can enhance stability of coexistence of multiple cell types and support robust communities by adapting to environmental disturbances. Designing robust synthetic consortia requires in-depth knowledge in cell internal dynamics, cell-cell communication mechanisms and cell growth, division and gene partition rules.

To realize multiple functions, there exist consortia with certain self-organized spatial structures in nature, such as biofilm and gut microbiome. The spatial structures are essential for localized functions and emergent population level behaviors. Designing synthetic consortia with localized functions need understanding of cell-cell and cell-environment interactions and cell movements caused by motility and division.

Building models and running simulations for synthetic consortia help to predict population levels. Analysis on system dynamics provide conditions for stability and robustness of the system. Combining models for intracellular chemical reactions, intercellular communications and cell growth, we can characterize multiscale dynamics and provide control principles for robust and spatially organized consortia.

'''Project Goals:'''

The aim of this SURF project is to provide theoretical insights to biological design using model predictions and analysis. There will be several potential modules and mechanisms to use in circuits design, so the modeling and analysis should include certain biology details.
Specific interesting questions to think about:

*What are the differences of cell population behaviors when using different intracellular regulatory modules (growth gene, self lysis gene, antibiotics resistant genes, etc.)?
*How do cells switch cell-cell interactions (cooperation <-> competition) to adapt to environmental perturbations?
* What drives spatial patterning of microbial consortia (heterogeneity in environment, intercellular interactions, etc.)?
*How to avoid interference between cells that conduct localized functions (orthogonal signaling, growth/death competition, etc.)?

In this SURF project, you will learn:

*Modeling for synthetic consortia across multiple scales
*Deterministic and stochastic simulation algorithms
*Feedback control in synthetic biology, analysis and estimation for dynamical systems

'''Prerequisite Skills'''

You need to be familiar with:

*Synthetic biology and genetic circuit design
*ODEs and PDEs
*Probability and stochastic processes
*Programming in Python (preferred) or Matlab

'''References'''

#Del Vecchio, D., & Murray, R. M. (2015). Biomolecular feedback systems. Princeton, NJ: Princeton University Press.
#Johns, N. I., Blazejewski, T., Gomes, A. L., & Wang, H. H. (2016). Principles for designing synthetic microbial communities. Current opinion in microbiology, 31, 146-153.
#Coyte, K. Z., Schluter, J., & Foster, K. R. (2015). The ecology of the microbiome: networks, competition, and stability. Science, 350(6261), 663-666.
#Nadell, C. D., Drescher, K., & Foster, K. R. (2016). Spatial structure, cooperation and competition in biofilms. Nature Reviews Microbiology, 14(9), 589.

SURF 2019: Modeling and Analysis on Robust Synthetic Consortia with Localized Functions

2018-12-12T01:15:12Z

Xrren:

'''[[SURF 2018|2018 SURF]]: project description'''
* Mentor: Richard M. Murray
* Co-mentor: Xinying (Cindy) Ren

'''Background:'''

Engineering synthetic microbial consortia is an emerging area in synthetic biology. Multiple cell types can interact via cell-cell communications and perform more complex functions. Cooperation and competition are fundamental intercellular interactions, and can shape population level behaviors in consortia. Intercellular interactions can enhance stability of coexistence of multiple cell types and support robust communities by adapting to environmental disturbances. Designing robust synthetic consortia requires in-depth knowledge in cell internal dynamics, cell-cell communication mechanisms and cell growth, division and gene partition rules.

To realize multiple functions, there exist consortia with certain self-organized spatial structures in nature, such as biofilm and gut microbiome. The spatial structures are essential for localized functions and emergent population level behaviors. Designing synthetic consortia with localized functions need understanding of cell-cell and cell-environment interactions and cell movements caused by motility and division.

Building models and running simulations for synthetic consortia help to predict population levels. Analysis on system dynamics provide conditions for stability and robustness of the system. Combining models for intracellular chemical reactions, intercellular communications and cell growth, we can characterize multiscale dynamics and provide control principles for robust and spatially organized consortia.

'''Project Goals:'''

The aim of this SURF project is to provide theoretical insights to biological design using model predictions and analysis. There will be several potential modules and mechanisms to use in circuits design, so the modeling and analysis should include certain biology details.
Specific interesting questions to think about:

*What are the differences of cell population behaviors when using different intracellular regulatory modules (growth gene, self lysis gene, antibiotics resistant genes, etc.)?
*How do cells switch cell-cell interactions (cooperation <-> competition) to adapt to environmental perturbations?
* What drives spatial patterning of microbial consortia (heterogeneity in environment, intercellular interactions, etc.)?
*How to avoid interference between cells that conduct localized functions (orthogonal signaling, growth/death competition, etc.)?

In this SURF project, you will learn:

*Modeling for synthetic consortia across multiple scales
*Deterministic and stochastic simulation algorithms
*Feedback control in synthetic biology, analysis and estimation for dynamical systems

'''Prerequisite Skills'''

You need to be familiar with:

*Synthetic biology and genetic circuit design
*ODEs and PDEs
*Probability and stochastic processes
*Programming in Python (preferred) or Matlab

'''References'''

#Del Vecchio, D., & Murray, R. M. (2015). Biomolecular feedback systems. Princeton, NJ: Princeton University Press.
#Johns, N. I., Blazejewski, T., Gomes, A. L., & Wang, H. H. (2016). Principles for designing synthetic microbial communities. Current opinion in microbiology, 31, 146-153.
#Coyte, K. Z., Schluter, J., & Foster, K. R. (2015). The ecology of the microbiome: networks, competition, and stability. Science, 350(6261), 663-666.
#Nadell, C. D., Drescher, K., & Foster, K. R. (2016). Spatial structure, cooperation and competition in biofilms. Nature Reviews Microbiology, 14(9), 589.

SURF 2019: Modeling and Analysis on Robust Synthetic Consortia with Localized Functions

2018-12-12T01:15:01Z

Xrren:

'''[[SURF 2018|2018 SURF]]: project description'''
* Mentor: Richard M. Murray
* Co-mentor: Xinying (Cindy) Ren

'''Background:'''

Engineering synthetic microbial consortia is an emerging area in synthetic biology. Multiple cell types can interact via cell-cell communications and perform more complex functions. Cooperation and competition are fundamental intercellular interactions, and can shape population level behaviors in consortia. Intercellular interactions can enhance stability of coexistence of multiple cell types and support robust communities by adapting to environmental disturbances. Designing robust synthetic consortia requires in-depth knowledge in cell internal dynamics, cell-cell communication mechanisms and cell growth, division and gene partition rules.

To realize multiple functions, there exist consortia with certain self-organized spatial structures in nature, such as biofilm and gut microbiome. The spatial structures are essential for localized functions and emergent population level behaviors. Designing synthetic consortia with localized functions need understanding of cell-cell and cell-environment interactions and cell movements caused by motility and division.

Building models and running simulations for synthetic consortia help to predict population levels. Analysis on system dynamics provide conditions for stability and robustness of the system. Combining models for intracellular chemical reactions, intercellular communications and cell growth, we can characterize multiscale dynamics and provide control principles for robust and spatially organized consortia.

'''Project Goals:'''

The aim of this SURF project is to provide theoretical insights to biological design using model predictions and analysis. There will be several potential modules and mechanisms to use in circuits design, so the modeling and analysis should include certain biology details.
Specific interesting questions to think about:

*What are the differences of cell population behaviors when using different intracellular regulatory modules (growth gene, self lysis gene, antibiotics resistant genes, etc.)?
*How do cells switch cell-cell interactions (cooperation <-> competition) to adapt to environmental perturbations?
* What drives spatial patterning of microbial consortia (heterogeneity in environment, intercellular interactions, etc.)?
*How to avoid interference between cells that conduct localized functions (orthogonal signaling, growth/death competition, etc.)?

In this SURF project, you will learn:

*Modeling for synthetic consortia across multiple scales
*Deterministic and stochastic simulation algorithms
*Feedback control in synthetic biology, analysis and estimation for dynamical systems

'''Prerequisite Skills'''
You need to be familiar with:

*Synthetic biology and genetic circuit design
*ODEs and PDEs
*Probability and stochastic processes
*Programming in Python (preferred) or Matlab

'''References'''

#Del Vecchio, D., & Murray, R. M. (2015). Biomolecular feedback systems. Princeton, NJ: Princeton University Press.
#Johns, N. I., Blazejewski, T., Gomes, A. L., & Wang, H. H. (2016). Principles for designing synthetic microbial communities. Current opinion in microbiology, 31, 146-153.
#Coyte, K. Z., Schluter, J., & Foster, K. R. (2015). The ecology of the microbiome: networks, competition, and stability. Science, 350(6261), 663-666.
#Nadell, C. D., Drescher, K., & Foster, K. R. (2016). Spatial structure, cooperation and competition in biofilms. Nature Reviews Microbiology, 14(9), 589.

SURF 2019: Modeling and Analysis on Robust Synthetic Consortia with Localized Functions

2018-12-12T01:14:50Z

Xrren:

'''[[SURF 2018|2018 SURF]]: project description'''
* Mentor: Richard M. Murray
* Co-mentor: Xinying (Cindy) Ren

'''Background:'''

Engineering synthetic microbial consortia is an emerging area in synthetic biology. Multiple cell types can interact via cell-cell communications and perform more complex functions. Cooperation and competition are fundamental intercellular interactions, and can shape population level behaviors in consortia. Intercellular interactions can enhance stability of coexistence of multiple cell types and support robust communities by adapting to environmental disturbances. Designing robust synthetic consortia requires in-depth knowledge in cell internal dynamics, cell-cell communication mechanisms and cell growth, division and gene partition rules.

To realize multiple functions, there exist consortia with certain self-organized spatial structures in nature, such as biofilm and gut microbiome. The spatial structures are essential for localized functions and emergent population level behaviors. Designing synthetic consortia with localized functions need understanding of cell-cell and cell-environment interactions and cell movements caused by motility and division.

Building models and running simulations for synthetic consortia help to predict population levels. Analysis on system dynamics provide conditions for stability and robustness of the system. Combining models for intracellular chemical reactions, intercellular communications and cell growth, we can characterize multiscale dynamics and provide control principles for robust and spatially organized consortia.

'''Project Goals:'''

The aim of this SURF project is to provide theoretical insights to biological design using model predictions and analysis. There will be several potential modules and mechanisms to use in circuits design, so the modeling and analysis should include certain biology details.
Specific interesting questions to think about:

*What are the differences of cell population behaviors when using different intracellular regulatory modules (growth gene, self lysis gene, antibiotics resistant genes, etc.)?
*How do cells switch cell-cell interactions (cooperation <-> competition) to adapt to environmental perturbations?
* What drives spatial patterning of microbial consortia (heterogeneity in environment, intercellular interactions, etc.)?
*How to avoid interference between cells that conduct localized functions (orthogonal signaling, growth/death competition, etc.)?

In this SURF project, you will learn:

*Modeling for synthetic consortia across multiple scales
*Deterministic and stochastic simulation algorithms
*Feedback control in synthetic biology, analysis and estimation for dynamical systems

'''Prerequisite Skills'''
You need to be familiar with:

*Synthetic biology and genetic circuit design
*ODEs and PDEs
*Probability and stochastic processes
*Programming in Python (preferred) or Matlab

'''References'''

#Del Vecchio, D., & Murray, R. M. (2015). Biomolecular feedback systems. Princeton, NJ: Princeton University Press.
#Johns, N. I., Blazejewski, T., Gomes, A. L., & Wang, H. H. (2016). Principles for designing synthetic microbial communities. Current opinion in microbiology, 31, 146-153.
#Coyte, K. Z., Schluter, J., & Foster, K. R. (2015). The ecology of the microbiome: networks, competition, and stability. Science, 350(6261), 663-666.
#Nadell, C. D., Drescher, K., & Foster, K. R. (2016). Spatial structure, cooperation and competition in biofilms. Nature Reviews Microbiology, 14(9), 589.

SURF 2019: Modeling and Analysis on Robust Synthetic Consortia with Localized Functions

2018-12-12T01:13:56Z

Xrren:

'''[[SURF 2018|2018 SURF]]: project description'''
* Mentor: Richard M. Murray
* Co-mentor: Xinying (Cindy) Ren

'''Background:'''

Engineering synthetic microbial consortia is an emerging area in synthetic biology. Multiple cell types can interact via cell-cell communications and perform more complex functions. Cooperation and competition are fundamental intercellular interactions, and can shape population level behaviors in consortia. Intercellular interactions can enhance stability of coexistence of multiple cell types and support robust communities by adapting to environmental disturbances. Designing robust synthetic consortia requires in-depth knowledge in cell internal dynamics, cell-cell communication mechanisms and cell growth, division and gene partition rules.

To realize multiple functions, there exist consortia with certain self-organized spatial structures in nature, such as biofilm and gut microbiome. The spatial structures are essential for localized functions and emergent population level behaviors. Designing synthetic consortia with localized functions need understanding of cell-cell and cell-environment interactions and cell movements caused by motility and division.

Building models and running simulations for synthetic consortia help to predict population levels. Analysis on system dynamics provide conditions for stability and robustness of the system. Combining models for intracellular chemical reactions, intercellular communications and cell growth, we can characterize multiscale dynamics and provide control principles for robust and spatially organized consortia.

'''Project Goals:'''

The aim of this SURF project is to provide theoretical insights to biological design using model predictions and analysis. There will be several potential modules and mechanisms to use in circuits design, so the modeling and analysis should include certain biology details.
Specific interesting questions to think about:

*What are the differences of cell population behaviors when using different intracellular regulatory modules (growth gene, self lysis gene, antibiotics resistant genes, etc.)?
*How do cells switch cell-cell interactions (cooperation <-> competition) to adapt to environmental perturbations?
* What drives spatial patterning of microbial consortia (heterogeneity in environment, intercellular interactions, etc.)?
*How to avoid interference between cells that conduct localized functions (orthogonal signaling, growth/death competition, etc.)?

In this SURF project, you will learn:

*Modeling for synthetic consortia across multiple scales
*Deterministic and stochastic simulation algorithms
*Feedback control in synthetic biology, analysis and estimation for dynamical systems

You need to be familiar with:

*Synthetic biology and genetic circuit design
*ODEs and PDEs
*Probability and stochastic processes
*Programming in Python (preferred) or Matlab

'''References'''

#Del Vecchio, D., & Murray, R. M. (2015). Biomolecular feedback systems. Princeton, NJ: Princeton University Press.
#Johns, N. I., Blazejewski, T., Gomes, A. L., & Wang, H. H. (2016). Principles for designing synthetic microbial communities. Current opinion in microbiology, 31, 146-153.
#Coyte, K. Z., Schluter, J., & Foster, K. R. (2015). The ecology of the microbiome: networks, competition, and stability. Science, 350(6261), 663-666.
#Nadell, C. D., Drescher, K., & Foster, K. R. (2016). Spatial structure, cooperation and competition in biofilms. Nature Reviews Microbiology, 14(9), 589.

SURF 2019: Modeling and Analysis on Robust Synthetic Consortia with Localized Functions

2018-12-12T01:08:28Z

Xrren: Created page with "'''Background:''' Engineering synthetic microbial consortia is an emerging area in synthetic biology. Multiple cell types can interact via cell-cell communications and perfor..."

'''Background:'''

Engineering synthetic microbial consortia is an emerging area in synthetic biology. Multiple cell types can interact via cell-cell communications and perform more complex functions. Cooperation and competition are fundamental intercellular interactions, and can shape population level behaviors in consortia. Intercellular interactions can enhance stability of coexistence of multiple cell types and support robust communities by adapting to environmental disturbances. Designing robust synthetic consortia requires in-depth knowledge in cell internal dynamics, cell-cell communication mechanisms and cell growth, division and gene partition rules.

To realize multiple functions, there exist consortia with certain self-organized spatial structures in nature, such as biofilm and gut microbiome. The spatial structures are essential for localized functions and emergent population level behaviors. Designing synthetic consortia with localized functions need understanding of cell-cell and cell-environment interactions and cell movements caused by motility and division.

Building models and running simulations for synthetic consortia help to predict population levels. Analysis on system dynamics provide conditions for stability and robustness of the system. Combining models for intracellular chemical reactions, intercellular communications and cell growth, we can characterize multiscale dynamics and provide control principles for robust and spatially organized consortia.

'''Project Goals:'''

The aim of this SURF project is to provide theoretical insights to biological design using model predictions and analysis. There will be several potential modules and mechanisms to use in circuits design, so the modeling and analysis should include certain biology details.
Specific interesting questions to think about:

1. What are the differences of cell population behaviors when using different intracellular regulatory modules (growth gene, self lysis gene, antibiotics resistant genes, etc.)?
2. How do cells switch cell-cell interactions (cooperation <-> competition) to adapt to environmental perturbations?
3. What drives spatial patterning of microbial consortia (heterogeneity in environment, intercellular interactions, etc.)?
4. How to avoid interference between cells that conduct localized functions (orthogonal signaling, growth/death competition, etc.)?

In this SURF project, you will learn:

1. Modeling for synthetic consortia across multiple scales
2. Deterministic and stochastic simulation algorithms
3. Feedback control in synthetic biology, analysis and estimation for dynamical systems

You need to be familiar with:

1. Synthetic biology and genetic circuit design
2. ODEs and PDEs
3. Probability and stochastic processes
4. Programming in Python (preferred) or Matlab

'''References'''

Del Vecchio, D., & Murray, R. M. (2015). Biomolecular feedback systems. Princeton, NJ: Princeton University Press.
Johns, N. I., Blazejewski, T., Gomes, A. L., & Wang, H. H. (2016). Principles for designing synthetic microbial communities. Current opinion in microbiology, 31, 146-153.
Coyte, K. Z., Schluter, J., & Foster, K. R. (2015). The ecology of the microbiome: networks, competition, and stability. Science, 350(6261), 663-666.
Nadell, C. D., Drescher, K., & Foster, K. R. (2016). Spatial structure, cooperation and competition in biofilms. Nature Reviews Microbiology, 14(9), 589.

SURF 2019

2018-12-12T01:02:35Z

Xrren: /* List of available projects */

{{righttoc}}
This page is intended for students interested in working on SURF projects in the Summer of 2019. It contains information about how to apply for a SURF project in my group along with a list of project areas.

'''Note:''' Projects will be posted here starting after finals week. Please check back after that time for more information.

=== 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 10 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 11 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 19 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. 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|2019|Geometry of Control-Invariant Sets}}
| TBD
| Petter Nilsson
|
|-
| {{SURF|2019|Engineering a synthetic high-bandwidth intercellular communication system through plasmid conjugation}}
| [[ICB Microbial]]
| John Marken
|
|-
| {{SURF|2019|Modeling and Analysis on Robust Synthetic Consortia with Localized Functions}}
| [[DARPA]]
| Xinying(Cindy) Ren
|
|-
| {{SURF|2018|Genetically-Programmed Synthetic Cells and Multi-Cellular Machines}}
| [[GBMF PMTI]], [[NSF MPP2]]
| TBD
| Multiple projects may be available; competitive selection
|}

May 2017 meeting schedule

2017-05-08T15:44:41Z

Xrren: /* 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: Open
* 3:00 pm: Open
* 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: Open
* 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

2017-04-13T03:58:19Z

Xrren: /* 23 Apr (Sun) */

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: 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)
* 5:15 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: Reed (if NOT 19 Apr Wed 1700)
* 6:45 pm: Open (if needed)
* 7:30 pm: Done for the day

| width=25% |

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

| width=25% |

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

Michaëlle Mayalu, Jan 2017

2017-01-20T20:49:52Z

Xrren: /* 24 Jan (Tue) */

Michaëlle Mayalu from MIT will visit on 23-24 January. __NOTOC__

=== Schedule ===
{| border=1
|- valign=top
| width=50% |
==== 23 Jan (Mon) ====
* 8 am: Breakfast with Richard (Ath)
* 9 am: Anandh (103 Steele?)
* 10 am: DARPA Biological Control program meeting, 168 Broad (walk over with Richard)
<hr>
* 12 pm: Seminar, 121 Annenberg (abtract below)
* 1 pm: lunch with TBD
<hr>
* 2 pm: Open
* 2:45 pm: Open
* 3:30 pm: Open
* 4:15 pm: Aaron Ames, 266 Gates-Thomas
<hr>
* 5:30 pm: Meet Richard in 107 Steele. Walk to dinner.

| width=50% |

==== 24 Jan (Tue) ====
* 9:00 am: Open
* 9:45 am: Open
* 10:30 am: Cindy (2nd floor lounge, Annenberg)
* 11:15 am: Ania (2nd floor lounge, Annenberg)
<hr>
* 12 pm: Henrike Niederholtmeyer seminar, 121 Annenberg
<hr>
* 1:00 pm: Open
* 1:45 pm: [[Jan 2017 meeting schedule|Richard]]
* 2:30 pm: John Doyle
* 3:15 pm: Vipul (Keck 222)
* 4:00 pm: Open
* 4:45 pm: Open
* 5:30 pm: Done for the day
|}

=== Seminar info ===
<center>
'''Reduced-order Systems Approach to Prediction of Emergent Behaviors'''

Michaëlle N. Mayalu 
Massachusetts Institute of Technology

Monday, January 23, 2017 
12-1 pm, 121 Annenberg
</center>

Increased understanding of the physical and chemical principles that drive a biological process has led to the development of mathematical formulations that are used to simulate a rich variety of responses. As a result, a vast amount of simulation data can be created for analyzing single cell behavior numerically. However complex and extensive mechanisms involved in emergent behavior of multiple interacting cells may become intractable due to mathematical and computational complexity. This talk will address how we can exploit simulation data describing the nonlinear dynamics of single cell behavior to create a reduced- order linear state equation in latent variable space. Furthermore, the linearity of the reduced-order latent variable state equation allows for the superposition of multiple solutions to predict emergent behaviors of interacting cells.
The linear latent state equation describing the nonlinear dynamics of single cell is created in two steps. First the original independent state variables are augmented by adding auxiliary variables necessary to “sufficiently inform” the single cell nonlinear dynamics. This creates a high-dimensional state space where a linear description of the nonlinear system can be found. Second, latent variables extracted from the high-dimensional state space and used to create the reduced-order linear equation. While the resultant latent state equation is linear, complex nonlinearities are embedded in the compact model, leading to precise and global linearization of nonlinear dynamics. Furthermore, in order to predict multi-cell emergent behavior, the reduced-order linear models of single cells are used as agents in a comprehensive agent-based framework based on linear superposition of mutually shared variables. The approach is motivated by emergent behaviors in collective cell migration in order to gain insight for the study and control cancer metastasis and wound healing. However, the general approach may be applied to systems of interacting nonlinear agents, which would otherwise be prohibitively complex to compute.

Michaëlle N. Mayalu is a Ph.D. student at the Brit and Alex d’Arbeloff Laboratory for Information Systems and Technology in the Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge MA. She received the B.S., and M.S., degrees in Mechanical Engineering in 2010 and 2012 from Massachusetts Institute of Technology. Her thesis work is focused on modeling and predicting biological systems behavior by drawing on aspects of dynamic modeling and simulation, data analysis, statistical learning and control theory. Her thesis supervisor is Professor H. Harry Asada in the Department of Mechanical Engineering at MIT.

Jan 2017 meeting schedule

2017-01-13T17:54:53Z

Xrren: /* 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: Open
* 4:00 pm: Miki
* 4:45 pm: Break
* 5:00 pm: Cindy
* 5:45 pm: Open
* 6:30 pm: Done for the day

| width=25% |

==== 22 Jan (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=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: Open
* 2:30 pm: CDS faculty meeting
* 4:15 pm: Tony Fragoso
* 5:00 pm: Open
* 5:45 pm: Open
* 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
|}

Nov 2016 meeting schedule

2016-11-03T19:26:48Z

Xrren: /* 15 Nov (Tue) */

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) ====
 
 
<hr>
* 2 pm: Hold until needed
* 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: Open
* 11:15 am: Tung
<hr>
* 1:30 pm: Open
* 2:15 pm: Andrey Shur
* 3:00 pm: Shaobin
* 3:45 pm: Break
* 4:00 pm: Open
* 4:45 pm: Open
* 5:30 pm: Anu
* 6:15 pm: Done for the day
| width=25% |

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

==== 16 Nov (Wed) ====
* 10:30 am: Open
* 11:15 am: Open
<hr>
* 1:30 pm: Open
* 2:15 pm: Open
* 3:00 pm: CDS tea
* Depart for airport at ~4 pm
|}

Sep/Oct 2016 meeting schedule

2016-09-17T19:34:08Z

Xrren: /* 2 Oct (Sun) */

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% |
==== 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: Open
* 5:00 pm: Open
* 5:45 pm: Break
* 6:00 pm: Open
* 6:45 pm: Open
* 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: Hold: Miki
* 4:30 pm: break
* 4:45 pm: Open
* 5:30 pm: Open
* 6:15 pm: Done for the day
| width=25% |

==== 2 Oct (Sun) ====
* 1:45 pm: Open
* 2:30 pm: Open
* 3:15 pm: Open
* 4:00 pm: Break
* 4:15 pm: Cindy
* 5:00 pm: Open
* 5:45 pm: Open
* 6:30 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: Open
* 4:15 pm: Victoria
* 5:00 pm: Break
* 5:15 pm: Hold: Daniel N
* 6:00 pm: Open
* 6:45 pm: Open
* 7:30 pm: Done for the day
|}

Aug 2016 meeting schedule

2016-08-04T08:51:53Z

Xrren: /* 7 Aug (Sun) */

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: Hold: 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
|}