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| Name | Modified | Size | Downloads / Week |
|---|---|---|---|
| Parent folder | |||
| 0.1 | 2010-09-14 | ||
| Totals: 1 Item | 0 | ||
bioSDP Toolbox: A Matlab Toolbox for uncertainty analysis of biochemical
networks via semidefinite programming.
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Document Outline:
1. Overview
2. Installation Instructions
3. Usage
================================================================================
1. Overview
The BioSDP Toolbox is a MATLAB Toolbox which uses semidefinite programming
methods for the analysis of biochemical reaction networks with uncertain
parameters and/or measurements. In particular, it features the following general
analysis tasks:
- uncertainty analysis for steady states in biochemical reaction networks with
uncertain parameters
- approximation of the set of consistent parameters from uncertain measurements
- robustness analysis of biochemical reaction networks with respect to uncertain
parameters
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2. Installation Instructions
Requirements:
- Matlab Release R2007b or later
http://www.mathworks.com/products/matlab/
- SeDuMi Version 1.1 or later
http://sedumi.ie.lehigh.edu/
Installation:
a) Make sure that SeDuMi is installed correctly (refer to the SeDuMi instructions).
b) Add the 'toolbox' subdirectory to the Matlab path:
e.g., if the toolbox is installed in HOME/biosdp, then put the line
addpath(genpath('HOME/biosdp/toolbox'));
to the Matlab startup script startup.m, where HOME is your home directory.
For more information on the startup script, refer to the Matlab help
>> doc startup
in the Matlab command window.
c) Check the installation by running the examples in the 'examples' directory.
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3. Usage
The tutorial in the 'doc/tutorial' directory contains a walkthrough for two simple
examples, one for the stationary uncertainty analysis, the other for set based
parameter estimation.
Several examples with extensive documentation in code comments are located in the
'examples' directory.