Difference between revisions of "ARL/ICB Crash Course in Systems Biology, August 2010"

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(Session 2: Stochastic Modeling and Simulation)
(Session 3: Data Acquisition and Analysis)
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=== Session 3: Data Acquisition and Analysis ===
 
=== Session 3: Data Acquisition and Analysis ===
  
<font color=blue>'''Bernie and Rasha:'''</font> Can you put together a one paragraph summary of your session (abstract-like) that describes the basic areas that you will cover, in words.  Then pick a couple of lecture titles and add a more specific listing of topics below that, as done in the first session,  as well as any references that you think participants might find useful to read.
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<font color=blue>'''Bernie and Rasha:'''</font> Can you put together a one paragraph summary of your session (abstract-like) that describes the basic areas that you will cover, in words.  Then pick a couple of lecture titles and add a more specific listing of topics below that, as done in the first session,  as well as any references that you think participants might find useful to read.  Also, if there is software that can be used by participants (either during the talks or afterwards), it would be great to include a list of programs, source link, and requirements for the software.
  
 
''' Lecture 5: Title (Bernie Daigle, UCSB)'''
 
''' Lecture 5: Title (Bernie Daigle, UCSB)'''

Revision as of 19:13, 15 July 2010

This course is geared toward biologists who want to become familiar with current computational biology software and capabilities, emphasizing quantitative applications for understanding and modeling complex biological systems. The course is taught by researchers from the Army Institute for Collaborative Technology and the Army Research Laboratory.

Schedule

The course will consist of four sessions, each lasting approximately 3.5 hours (including a break in the middle of the session).

Monday, 9 Aug

8:00 am   Continental breakfast
8:45 am   Welcome and introductions (Ed Perkins)
9:00 am   Session 1: Modeling and Analysis using Differential Equations
12:30 pm   Lunch
2:00 pm   Session 2: Stochastic Modeling and Simulation
5:30 pm   Adjourn

Tuesday, 10 Aug

8:30 am   Continental breakfast
9:00 am   Session 3: Data Acquisition and Analysis
12:30 pm   Lunch
2:00 pm   Session 4: Applications
5:30 pm   Adjourn

Lecture Outline

Session 1: Modeling and Analysis using Differential Equations

Elisa and Maria: Please put together a one paragraph summary of your session (abstract-like) that describes the basic areas that you will cover, in words. A more specific listing of topics that you will cover can go below, under the individual lectures. You should update the topics that I listed based on what you will actually cover (probably a more focused list, given the time constraints) and also add any references that you think participants might find useful to read.

Lecture 1: Core Processes in Cells (Elisa Franco, Caltech) This lecture will provide an introduction to modeling of core processes in biology using differential equations. Specific topics to be covered include:

  • The Cell as a Dynamical System
  • Modeling Techniques: reactions, master equation, differential equations
  • Transcription and Translation
  • Transcriptional Regulation
  • Post-Transcriptional and Post-Translational Regulation
  • Cellular Subsystems (?)

Reading list:

Lecture 2: Analysis Methods (Maria Rodriguez Fernandez, UCSB)

  • sensitivity analysis
  • robustness analysis
  • identifiability and design of experiment
  • parameter identification

Reading list:

Session 2: Stochastic Modeling and Simulation

Linda and Min: Can you put together a one paragraph summary of your session (abstract-like) that describes the basic areas that you will cover, in words. A more specific listing of topics that you will cover can go below, under the individual lectures (as done above), as well as any references that you think participants might find useful to read. Also, if you would like to give some hands-on material using computers, can you let Richard know what the requirements are for software that the students would use?

Lecture 3: Discrete stochastic simulation algorithms (Linda Petzold, UCSB)

Lecture 4: Stochkit (Min Roh, UCSB)

Reading list:

Session 3: Data Acquisition and Analysis

Bernie and Rasha: Can you put together a one paragraph summary of your session (abstract-like) that describes the basic areas that you will cover, in words. Then pick a couple of lecture titles and add a more specific listing of topics below that, as done in the first session, as well as any references that you think participants might find useful to read. Also, if there is software that can be used by participants (either during the talks or afterwards), it would be great to include a list of programs, source link, and requirements for the software.

Lecture 5: Title (Bernie Daigle, UCSB)

Reading list:

Lecture 6: Title (Rasha Hammamieh, WRAIR)

Reading list:

Session 4: Applications

Mike, Camilla and Adam: can you send put in a title and abstract for your talk (or send to Richard).

Lecture 7: Polarization in Yeast Mating (Mike Lawson, UCSB)

Lecture 8: Insulin Signaling and Stem Cells (Camilla Luni, UCSB)

Lecture 9: Biofuels (Adam Arkin, LBNL)