Computational Systems Biology
Sauro Lab
University of Washington
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What is SBW 
Research Impact 
Published Papers 
Lab Members 
Available Positions 
CSB Links 
Student Projects 
Software Downloads:

1. SBW
2. JDesigner
3. Jarnac
5. Matlab Interface
6. Optimization
6. Bifurcation
maintained by Frank Bergmann

CSB Links

The first site to check out is: Enzymes and MCA in Marseilles: Lots of useful material here and always up to date.

Software Sites

BioKin Enzyme kinetic software.

BioQuest Metabolic Simulation

E-Cell From a Japanese group who have a modeling and simulation environment for biochemical and genetic processes for the Linux platform.

MetaModel Modeling Metabolic Pathways under MS-DOS

Pedro Mendes' Gepasi site, a popular bio/chemical simulator for Windows 32.

netBuilder A Windows based gene circuit simulator


DBSolve UK site Software for metabolic, enzymatic and receptor-ligand binding simulation.

Online Modeling System A web-based modeling system

JigCell Java based pathway simulator at Virginia tech (I know, two simulators in one university!)

bioSPICE DARPA funded biochemical pathway simulation software project.

Research Sites

Adam Arkin BioSpice etc

BioPathways “Supporting the Transformation of Genomic Information into a Web of Knowledge for the Life Sciences”

David Fell's Research Group Details of the research carried out by the group and links to software.

Princeton Integrative Genomics New institute dedicated to integrative genomics Published StandardsCellML A corporate standard for storing metabolic type data destined for numerical simulation

BioPathways Consortium Corporate Sites

Entelos Company which specializes in physiological modelling.

KineCyte by Daniel Cook, a visual pathway simulator for the Mac (Commercial, but nice)

Gene Network Sciences Claims to be able to model very large systems


Information Sites

Quantitative Modeling of Metabolic Networks This paper discusses the theory of Petrinets and how they might be useful for the quantitative modeling of biochemical networks.


sysbio/csblinks.txt · Last modified: 2007/08/02 10:18 by mallain

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