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Information on SB Activities on European Level 
European Funding initiatives for Systems Biology 
SB Centres, Institutes, Networks and Initiatives in Europe 
Working Groups active in Systems Biology 
  
?Database?, ?Modelling tools? and ?Standards and Ontologies? 
Database 
CellML repository (Auckland, NZ): http://www.cellml.org/examples/repository/ 
Human Metabolome Database : http://www.hmdb.ca/ 
Panther Classification Systems - Panther Pathways: http://www.pantherdb.org/pathway/ 
KDBI - Kinetic Data of Biomolecular Interactions : http://xin.cz3.nus.edu.sg/group/kdbi/kdbi.asp 
The Systems Biology Researcher Database: http://emb1.bcc.univie.ac.at/cgi-bin/SYSBIOL/Welcome.cgi 
Standards and Ontologies 
Systems Biology Markup Language: http://sbml.org/ 
Systems Biology Graphical Notation: http://www.sbgn.org/  
Systems Biology Ontology:: http://www.biomodels.net/sbo/  
Minimum Information Requested In the Annotation of Models:: http://www.biomodels.net/...  
BioPAX: http://www.biopax.org/ 
CellML: http://www.cellml.org/ 
Modelling tools 
Cytoscape: http://www.cytoscape.org/ 
Database of Quantitative Cellular Signalling (Bangalore, India), Models: http://doqcs.ncbs.res.in/ 
E-Cell Project University Keio, Models: http://ecell.sourceforge.net/ 
The Harvey Project, Models: http://harveyproject.science.wayne.edu/development/ 
C. elegans, DKFZ, Models: http://mbi.dkfz-heidelberg.de/projects/cellsim/ 
Modelling Tools, Models: http://mmtsb.scripps.edu/ 
Virtual Cell Portal, Models: http://nrcam.uchc.edu/servlets/VCellPortal 
Molecular Simulation Virtual Lab, Models: http://polymer.bu.edu/vmdl/ 
ModelDB, Models: http://senselab.med.yale.edu/senselab/modeldb/ 
The yeast silicon cell, Models: http://www.bio.vu.nl/hwconf/FP6/ysic/ysicab.html 
BioModels Database (Cambridge, UK), Models: http://www.ebi.ac.uk/biomodels/ 
GENESIS, Models: http://www.faqs.org/faqs/ai-faq/general/part6/section-11.html 
Silicon Cell ready to use, Models: http://www.jjj.bio.vu.nl/ 
Virtual Cell Plant, Models: http://www.life.uiuc.edu/plantbio/cell/ 
M-Cell, Models: http://www.mcell.cnl.salk.edu/ 
  
JWS Online - Online Cellular Systems Modelling: http://jjj.biochem.sun.ac.za/ 
Dizzy stochastic simulations tool : http://magnet.systemsbiology.net/software/Dizzy/ 
JSim - a Java based simulation system: http://nsr.bioeng.washington.edu/PLN/Software/ 
PyBioS - web server for modeling and simulation of cellular systems : http://pybios.molgen.mpg.de/ 
Pasadena Twain ODE solver of the SWB package: http://sbw.sourceforge.net/sbw/software/ 
Basis Gillespie Stochastic Simulator : http://www.basis.ncl.ac.uk/software.html 
CADLIVE - network construction system : http://www.cadlive.jp/ 
CaliBayes - Bayesian calibration of biological simulators: http://www.calibayes.ncl.ac.uk/ 
CellDesigner - a modeling tool for biochemical networks: http://www.celldesigner.org/ 
CellWare - building computational chassis for systems and synthetic biology : http://www.cellware.org/ 
COPASI - Complex Pathway Simulator: http://www.copasi.org/tiki-index.php 
PLAS Power Law Analysis and Simulation tool: http://www.dqb.fc.ul.pt/docentes/aferreira/plas.html 
Dynetica - a simulator of dynamic networks : http://www.duke.edu/~you/Dynetica_page.htm 
E-Cell project: http://www.e-cell.org/ 
Gepasi - Biochemical Kinetics Simulator : http://www.gepasi.org/ 
STOCKS - Stochastic kinetic simulations: http://www.sysbio.pl/stocks/index.html 
Virtual Cell Internet simulation server at NRCAM : http://www.nrcam.uchc.edu/ 
  
Training Systems Biology 
Seasonal Schools, Workshops, Symposia in Systems Biology 
Meetings and conferences 
SB world-wide