ARL/ICB Crash Course in Systems Biology, August 2010

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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)

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 (?)

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

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

Session 2: Stochastic Modeling and Simulation

Linda and Min: 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 (as done above)

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

Lecture 4: Stochkit (Min Roh, UCSB)

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.

Lecture 5: Title (Bernie Daigle, UCSB)

Lecture 6: Title (Rasha Hammamieh, WRAIR)

Session 4: Applications

Lecture 7:

Lecture 8:

Lecture 9: