MODELS

This page will present cell models of Saccharomyces cerevisiae.

YSBN will present or link to two types of models:

1. Whole cell network (connectivity) models, which are based on protein-protein or genetic interactions or global expression data (and more).

2. Software-implemented and in the long-run also animated models (simulations) of processes in yeast cell. Initially it will present modules (such as metabolic pathways, signalling pathways, cell biological pathways etc).

One of the main goals will be building reference models for specific modules (based on several existing models) and eventually generating whole cell models on cellular processes.

The Model Working group is in charge of the content of this page. Present members are (underlined: responsible persons): Hans Westerhoff, Jacky Snoep, Pedro Mendes (vice-chair), Hiraoki Kitano (vice-chair), Edda Klipp (chair), Mats Jirstrand, Matthias Reuss, Bela Novak, Bernard Palsson, Matej Oresic.

Links to simulation sites (please submit further links) and other useful places:

BioModels Database at EBI.

JWS Online by one of our members, Jacky Snoep.

Cyberyeast - cell cycle model by our members Bela Novak/John Tyson

UCSD yeast model - metabolic model by Bernard Palsson

Models from the YSBN Community

Stoichiometric network of yeast metabolism (termed iLL672). Intended as supplementary material for an upcoming Genome Research article (Kuepfer, Sauer, Blank: "Metabolic Functions of Duplicate Genes in Saccharomyces cerevisiae", Genome Res. 2005 15: 1421-1430). Download as Excel file.

Links to Systems Biology Tools

Bioperl - provides an online resource for modules, scripts, and web links for developers of Perl-based software for life science research - open source Bioperl course at: http://www.pasteur.fr/recherche/unites/sis/formation/bioperl/

Biopython - freely available Python tools for computational molecular biology

BioSPICE - open source framework and toolset for modeling dynamic cellular network functions

Cytoscape - open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data

Gepasi - developed for the modeling of biochemical reaction systems by Pedro Mendes - provides several analysis tools (MCA, Parameter scan, Optimization & Fitting) - SBML compatible

E-cell - E-Cell is a concept of constructing virtual cells on computers.

INA – Integrated Net Analyzer - a tool package supporting the analysis of Place/Transition Nets (Petri Nets) and Coloured Petri nets

CPN Tools - actively developed Colored Petri Net tool of the university of Aarhus, Denmark

JCell - a Java based framework to reconstruct genetic interactions from microarray data

SBW - SBML-based software system that enables different tools to communicate with each other - supports tools like - Jdesigner, a program for the graphical creation of reaction networks - Jarnac, a tool for the numerical simulation of such networks - CellDesigner, graphical creation and simulation of networks - Metatool, analysis tool for detection of elementary modes

STOCKS - software for stochastic simulations of biochemical processes with Gillespie algorithm - developed by Andrzej M. Kierzek

Model exchange languages

SBML – The Systems Biology Markup Language (SBML) is a computer-readable format for representing models of biochemical reaction networks. SBML is applicable to metabolic networks, cell-signaling pathways, regulatory networks, and many others.

CellML – Cell Markup Language The CellML language is an open standard based on the XML markup language. CellML is being developed by the Bioengineering Institute at the University of Auckland and affiliated research groups. The purpose of CellML is to store and exchange computer-based mathematical models. CellML allows scientists to share models even if they are using different model-building software. It also enables them to reuse components from one model in another, thus accelerating model building