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Computational Systems Biology
 
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ETH Zurich - D-BSSE - csb -  

csb-tools

polco — Polyhedral Computations Tool

polco

Java tool to compute extreme rays of polyhedral cones. It can also be used to enumerate vertices of polytopes, and for the dual problem, the enumeration of facets given the extreme points (aka convex hull).

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efmtool — Elementary Flux Mode Tool

efmtool

MATLAB/Java tool to compute elementary flux modes of metabolic networks.

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Mapping Tool

Java tool which maps different nomenclatures.

Features:

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Convert2Sbml / Convert2Matlab

Java tool to convert various metabolic network source files into sbml/matlab files.

Read more & download ...

Java libraries

odeSD

A Specialized ODE Integrator for Efficient Computation of Parameter Sensitivities:
odeSD_files

HYPERSPACE

A matlab implementation of the algorithm for exploration and charaterization of parameter spaces as described in BMC Systems Biology 2011, 5:142. Download: HYPERSPACE.

SDE evaluation package

Matlab package for evaluation of parameter points in models based on stochastic differential equations and examples: SDEeval.zip.

Image segmentation package

Matlab package for segmentation of cells in microscopy images with membrane patterns. The implementation also includes examples: cellSegmPackage.zip


 

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© 2014 ETH Zurich | Imprint | Disclaimer | 22 May 2014
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