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

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=== Session 2: Stochastic Modeling and Simulation ===
 
=== Session 2: Stochastic Modeling and Simulation ===
  
<font color=blue>'''Linda and Min:'''</font> In this session, we will discuss various stochastic simulation methods in details. The latter half of the session focuses on StochKit, a software package for simulating stochastic models. We will give a comprehensive review of the available algorithms and illustrate how to use Matlab functions in StochKit to process output files.
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In this session, we will discuss various stochastic simulation methods in details. The latter half of the session focuses on StochKit, a software package for simulation of stochastic models. StochKit provides command-line executable for running stochastic simulations using variants of Gillespie’s Stochastic Simulation Algorithm (SSA) and Tau-leaping. Among the numerous implementations of the SSA, we provide solvers for the most well used and efficient methods: SSA Direct Method, Optimized Direct Method [Cao et al. 2004], Logarithmic Direct Method, and a Constant-Time Algorithm [Slepoy et al. 2008]. As for the Tau-leaping algorithm, we provide a solver for an Adaptive Explicit Tau-leaping method. To further increase the computational efficiency, StochKit provides automatic parallelization and a converter for SBML files. We will give a comprehensive review of the available algorithms and illustrate how to use Matlab functions in StochKit to process output files. For advanced developers, we will briefly illustrate how to build a custom solver for specific needs.
  
 
''' Lecture 3: Discrete stochastic simulation algorithms (Linda Petzold, UCSB)'''
 
''' Lecture 3: Discrete stochastic simulation algorithms (Linda Petzold, UCSB)'''

Revision as of 02:19, 23 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   Registration open
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

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

This session will provide an introduction to modeling of core processes in biology using differential equations. The first lecture will focus on the cell as a multi-layered feedback system. Scientists need to build ad hoc models to analyze the cellular complexity in a quantitative manner. Ordinary differential equations (ODEs) are a good choice when considering high copy number molecules in a well mixed environment. Several transcriptional regulation pathways in bacteria, for instance, have been successfully modeled with ODEs. We will overview the general methods to build macroscopic deterministic models of biological processes, referring to the trp operon and the iron starvation pathways as application examples. Classical control and dynamical systems analysis tools (equilibria, bifurcations and frequency analysis) will also be reviewed. Finally, we will provide some fundamental notions from the theory of chemical reaction networks. The second lecture will close the modeling process cycle by covering the model identification theory and practice. Once a model structure (system of equations) is proposed, the validity of this structure should be tested by means of an identifiability analysis, e.g. making use of sensitivity analysis tools that can help to identify critical and negligible parameters and to establish a parameter ranking. If experimental data are available, parameter estimation is then carried out, leading to a first model. Otherwise a set of experiments must be devised by means of optimal experimental design and performed before the parameter estimation. The quality of these estimators should be assessed by checking the correlation between them and computing their confidence intervals. This initial model must be validated with new experiments, which in most cases will reveal a number of deficiencies. Thus, a new model structure and/or a new experimental design must be planned, and the process is repeated iteratively until the validation step is considered satisfactory.

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 with different layers of feedback
  • Modeling techniques and ordinary differential equations
  • Examples: transcriptional and post-transcriptional regulation
  • Control and dynamical systems analysis tools (equilibria, bifurcations, frequency analysis)
  • Basic notions of chemical reaction networks theory

Reading list:

  • H. de Jong (2002). "Modeling and simulation of genetic regulatory systems: a literature review", J Comput Biol, 9(1):67-103
  • M. Santillán and M. C. Mackey (2001). "Dynamic regulation of the tryptophan operon: A modeling study and comparison with experimental data", Proc. Natl. Acad. Sci. USA. 98(4):1364-1369
  • E. Levine, Z. Zhang, T. Kuhlman and T. Hwa (2007). "Quantitative Characteristics of Gene Regulation by Small RNA", PLoS Biol, 5(9):e229
  • M. Feinberg (1987). "Chemical reaction network structure and the stability of complex isothermal reactors-I. The deficiency zero and deficiency one theorems", Chemical Engineering Science, 42(10):2229-2268


Lecture 2: Model analysis and identification (Maria Rodriguez Fernandez, UCSB) This lecture will provide an introduction to model identification theory and practice. Specific topics to be covered include:

  • Global and local sensitivity analysis
  • Identifiability analysis
  • Optimal experimental design
  • Robust parameter identification
  • Confidence intervals of the estimated parameters
  • Model identification tools

Reading list:

  • M. Joshi, A. Seidel-Morgenstern, and A. Kremling (2006). "Exploiting the bootstrap method for quantifying parameter confidence intervals in dynamical systems", Metabolic Engineering, 8:447–455
  • A. Saltelli, M. Ratto, T. Andres, F. Campolongo, J. Cariboni, D. Gatelli, M. Saisana, and S. Tarantola (2008). "Global Sensitivity Analysis: The Primer", John Wiley & Sons Ltd.
  • M. Rodriguez-Fernandez and J. R. Banga (2010). "SensSB: a software toolbox for the development and sensitivity analysis of systems biology models", Bioinformatics, 26(13):1675-1676
  • E. Walter and L. Pronzato (1997). "Identification of Parametric Models from Experimental Data", Springer
  • D. E. Zak, G. E. Gonye, J. S. Schwaber, and F. J. Doyle III (2003). "Importance of input perturbations and stochastic gene expression in the reverse engineering of genetic regulatory networks: Insights from an identifiability analysis of an in silico network", Genome Research, 13:2396–2405

Session 2: Stochastic Modeling and Simulation

In this session, we will discuss various stochastic simulation methods in details. The latter half of the session focuses on StochKit, a software package for simulation of stochastic models. StochKit provides command-line executable for running stochastic simulations using variants of Gillespie’s Stochastic Simulation Algorithm (SSA) and Tau-leaping. Among the numerous implementations of the SSA, we provide solvers for the most well used and efficient methods: SSA Direct Method, Optimized Direct Method [Cao et al. 2004], Logarithmic Direct Method, and a Constant-Time Algorithm [Slepoy et al. 2008]. As for the Tau-leaping algorithm, we provide a solver for an Adaptive Explicit Tau-leaping method. To further increase the computational efficiency, StochKit provides automatic parallelization and a converter for SBML files. We will give a comprehensive review of the available algorithms and illustrate how to use Matlab functions in StochKit to process output files. For advanced developers, we will briefly illustrate how to build a custom solver for specific needs.

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

Reading list:

Lecture 4: Stochkit (Min Roh, UCSB)

  • Presentation on StochKit
    • available stochastic solvers
    • creating a model
    • SBML conversion
    • output processing
    • examples

Reading list:

Available software:

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)

We have developed a spatial stochastic model of polarisome formation in mating yeast, focusing on the tight localization of proteins on the membrane. This new model is built on simple mechanistic components, but is able to achieve a highly polarized phenotype even in relatively shallow input gradients. Preliminary results highlight the need for spatial stochastic modeling because deterministic simulation fails to achieve a sharp break in symmetry.

Lecture 8: Biological variability and model uncertainty: issues for stem cell expansion and therapy development (Camilla Luni, UCSB)

  • Dissecting cell population heterogeneity
  • Case study: input dynamics affects population heterogeneity during stem cell expansion
  • Developing multi-drug therapies from ODE models in presence of uncertainty (patient-patient variability, dosage uncertainty, measurement uncertainty ...)
  • Case study: adipocyte cell response to insulin

Lecture 9: Biofuels (Adam Arkin, LBNL)