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bioinfo1 Courses and lectures Bioinformatics - Online Courses and Tutorials The European School In Bioinformatics (Biosapiens) 9th Biosapiens European School in Bioinformatics 2009 Brussels Belgium VSNS Biocomputing Division EMBNet Quick Guides EMBNet Courses Sequence Analysis with distributed Resources BioComputing Hypertext Coursebook Tutorial Protein Structures (EXPASY) SwissModel CMBI Courses for protein structure Nycomed Chair for Applied Computer Science - Data Mining (Berthold) 2Can Support Portal - Bioinformatics educational resource Bioconductor Workshops CBS Bioinformatics Courses Organizations Conferences Bioinformatik.de Bioinformatics.Org - The Open-Access Institute EMBNet Bioinformatics Network Gesellschaft fuer Informatik - Fachgruppe Bioinformatik GBM Gesellschaft fuer Biochemie und Molekularbiologie ISCB - International Society for Computational Biology GCB 2009 German Conference on Bioinformatics - Braunschweig GCB 2009 German Conference on Bioinformatics - Halle Bioinformatics Open Source Conference BOSC 2010 Bioinformatics Open Source Conference BOSC 2009 ECCB 2010 ISMB 2010 ISMB + ECCB 2009 Stockholm 7th International Workshop on Data Integration in the Life Sciences 2010 6th International Workshop on Data Integration in the Life Sciences 2009 SBMC Conference on Systems Biology of Mammalian Cells 2010 Freiburg 11th International Conference on Systems Biology ICSB 2010, Edinburgh, UK 10th International Conference on Systems Biology ICSB 2009, Stanford, CA HUPO 2010 9th World Congress Sydney HUPO 2009 8th World Congress Toronto 17. Arbeitstagung Mikromethoden der Proteinchemie M�nchen 2010 Synthetic Biology 4.0 Conference Hongkong Biofine 2010, Synthetic Biology in Pharma Conference, Cambridge, UK Biofine 2009, Applied Industrial Synthetic Biology in Europe, Freiburg, Germany Journals Bioinformatics BioMed Central Bioinformatics AMB Algorithms for Molecular Biology BioData Mining Briefings in Bioinformatics Human Genomics In Silico Biology Journal of Computational Biology Journal of Medical Internet Research Nucleic Acids Research Omics: A Journal of Integrative Biology PLoS Computational Biology Nature Omics Gateway Proteomics Molecular and Cellular Proteomics Journal of Proteome Research Clinical Proteomics Proteomics - Clinical Applications Current Proteomics Journal of Proteomics and Bioinformatics Briefings in Functional Genomics and Proteomics Proteome Science Electrophoresis BioMed Central - Systems Biology Gateway BMC Systems Biology Molecular Systems Biology BioSystems IET Systems Biology IET Synthetic Biology Bioinformatics server EBI European Bioinformatics Institute NCBI US National Center for Biotechnology Information GenomeNet WWW server Japan Expasy Proteomics Server EMBNet - A Quick Guide to Expasy P�le Bio-Informatique Lyonnais Weizmann Institute Bioinformatics and Biological Computing Baylor College of Medicine HGSC Bioinformatics Software Server Lille Databases Sequences Entrez Browser NCBI SRSWWW EMBL-EBI DBGET/LinkDB Integrated Database Retrieval System BCM Search Launcher GeneCards Weizmann Genome Matrix databases information integration RefSeq Reference Sequence NCBI Unigene NCBI Uniprot Universal Protein Resource Swiss-Prot/TREMBL/PIR EMBNet QuickGuide Swissprot Trembl Databases PIR - Protein Information Resource IPI - International Protein Index EBI Protein Identifier Cross-Reference Service Vector Database NCBI UniVec and VecScreen Vector contamination search Public SRS installations | Biowisdom Genomes Ensembl Genome Browser Entrez-Genome NCBI Integr8 Proteome Analysis at EBI GOLD: Genomes On Line Database v 2.0 CBS Genome atlas database MIPS: Munich Information Centre for Protein Sequences J. Craig Venter Institute (ex TIGR) MD USA The Sanger Centre Whitehead Institute Broad Institute Center for Genome Research GeneCards Weizmann HGP - Human genome project information Human Genome Resources NCBI Mouse Genome Resources NCBI Rat Genome resources NCBI Fugu Fish Genome Project ZFIN - Zebrafish information network Wormbase C. elegans C.elegans Blast server (Sanger Centre) FlyBase Drosophila Yeast Genome Database MIPS Schizosaccharomyces pombe genome (Sanger Centre) Neurospora crassa Database (Broad) Neurospora crassa Database (MIPS) Fungal Genetics Stock Center tair - The Arabidopsis Information Resource GABI Primary Database ( GabiPD ) - Genomanalyse Pflanze Plant genomes (MIPS) Maize Genetics and Genomic Database International Rice Genome Sequencing Project Protein structures RCSB Protein Data Bank Entrez-Structure Domain Structure Database NCBI Protein Databank in Europe (PDBe) Structures by electron microscopy at MSD SWISS-MODEL EMBNet - A Quick Guide to Swiss-Model SCOP: Structural Classification of Proteins Superfamily HMM models SCOP CATH database of structural domains Gene3D Structural and Functional Annotation The DALI database NCBI VAST structural alignments ModBase - Comparative protein structure models BALL and BALLView Visualization and Modelling Tools Motifs Profiles Domains Interpro Domain and Profile Database ExPASy - PROSITE ExPASy - ScanProsite tool SIB myHits motif scan PRINTS protein fingerprints SMART - Simple Modular Architecture Research Tool Blocks WWW Server Block Search The Sanger Centre Pfam Server The Sanger Centre HMM Pfam Searcher TIGRFAMs protein families HMM ProDom conserved protein domains CDD Conserved domains database NCBI DomCut prediction of linker regions between functional domains PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System PIR iProClass Protein Classification Superfamily HMM models SCOP Gene3D Structural and Functional Annotation ModBase - Comparative protein structure models Interproscan WebLogo WebLogo Server Human Protein Reference Database PhosphoMotif Finder ELM Eukaryotic Linear Motif Functional Site Prediction Phospho.ELM Database of phosphorylation sites NetworKIN kinase substrate relationship prediction Footprinter 3 phylogenetic conserved motif extraction - Web server Footprinter phylogenetic conserved motif extraction - Manual AlignACE yeast cis-regulatory element search DIALIGN - multiple sequence alignments to find conserved regulatory elements The Gibbs Motif Sampler MEME MAST motif discovery and search Pathways KEGG: Kyoto Encyclopedia of Genes and Genomes ExPASy - Biochemical Pathways NCI BioCarta - Pathways PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System Signaling Gateway - Cell Signaling Resource Nature Reactome Project BioCyc Database Collection MetaCyc Encyclopedia of Metabolic Pathways NCI Nature Pathway Interaction Database IUPHAR receptor database LGICD Ligand-gated ion-channel database AraCyc - Pathway Database of Arabidopsis thaliana Invitrogen Pathways NetPath human signal transduction pathways BBID-Biological Biochemical Image Database Signal Transduction - Biochemweb.org virtual library BioPAX - data exchange for biological pathway data visANT - Visual Analysis Tool for Biological Networks and Pathways MapMan - integrative view of microarray data and metabolic maps GenMAPP Gene Map Annotator and Pathway Profiler Biological Networks Comparative Pathway Analyzer PaLS Pathway and Literature Strainer (gene set annotation tool) ProdoNet Prokaryotic gene list pathway annotator GraphWeb: analysis of biological networks Network Analysis Tools (NeAT) Enzymes Enzyme Database - BRENDA IntEnz EBI Enzyme Database Catalytic Site Atlas - CSA (EBI) REBASE The Restriction Enzyme Database Protein Kinase Resource Kinase.com Global kinome analysis NetworKIN kinase substrate relationship prediction PRIME Developed Kinase Pathway Database Software EBI: The BioCatalog Open Source Initiative OSI Open Bioinformatics Foundation SourceForge.net Open Source Resource Bioinformatics.Org - The Open-Access Institute BioPerl BioPython BioJava BioRuby BioBike (LISP) Literature Pub Med Central Advanced PubMed Search PubMed/Medline NLM Mesh Browser PubMed Single Citation Matcher NCBI Journal database Scopus Web of Science Google Scholar Scirus Espacenet - Europe's network of patent databases REDI Databases of Baden-Wuerttemberg DOAJ - Directory of open access journals PLoS Public Library of Science Crossref Search - commercial publishers worldwide common paper service Information retrieval and clustering EBIMed Medline information retrieval and extraction GoPubMed - Ontology based literature search HubMed pubmed rewired MyNCBI PubMed updating and alerting BioMail Pubmed Mail Update Service PubCrawler PubMed GenBank Update Service eTBlast - related articles to any text CoPub Mapper Gene Co-Publication Text Mining PubMatrix Vivisimo PubMed Clustering Search NCBI Esearch Entrez Utility Internet search Search engines Google Clusty the Clustering Engine AltaVista Yahoo! WebCrawler MetaGer CUSI - Suchmoeglichkeiten im Internet W3 Search Engines FU Berlin Link lists Expasy Expasy Life Science Directory Bioinformatics Links Directory UBiC HSLS: OBRC: Online Bioinformatics Resources Collection Nucleic Acids Research Database Summary Paper List Nucleic Acids Research Database Issue 2010 Nucleic Acids Research Database Issue 2009 Nucleic Acids Research Webserver Issue 2009 Nucleic Acids Research Webserver Issue 2008 CMS Molecular Biology Resource Harvard Dept of MCB - Biology Links CiteULike - online reference management sharing service Connotea - online reference and link sharing del.icio.us social bookmarking Biotech Europe Link Base The bioinformatics bench Linux Ubuntu Linux Debian Linux Open SUSE Linux Novell SUSE Linux Fedora Project RedHat Linux Linux Kernel Archives BioLinux - Wikipedia Knoppix BioKnoppix EMBNet A QuickGuide to UNIX Linux Online Linux Community (German) linux.de Linux user group Tuebingen WAMP Apache SELFHTML MySQL PHP SELFPHP phpMyAdmin Comparison of WAMPs XAMPP Perl PERL The Perl directory at perl.org Perl documentation ActiveState - ActivePerl Downloads CPAN PERL Script Archiv Bioperl Installing Bioperl on Windows - BioPerl EMBNet QickGuides PERL and Regular Expressions R and BioConductor The R project for statistical computing The Comprehensive R archive network BioConductor Project - Open Source Software for Bioinformatics R and Bioconductor Manual (Thomas Girke) useR! 2010 R user conference Gaithersburg, Maryland useR! 2009 R user conference Rennes, France Editors The Vim Editor Proton Komodo Laboratory tools DOE 2000 Electronic Notebook Project ORNL DOE 2000 Electronic Notebook Project Main WETLAB: an open source electronic lab notebook PHP Labware Project EMBOSS EMBOSS EMBOSS wiki EMBOSS application wiki EMBOSS applications EMBOSS applications program groups EMBOSS for Windows EMBOSS user documentation EMBOSS FAQ EMBOSS Main Tutorial EMBOSS mailing lists EmbNet EMBOSS and wEMBOSS Quick Guides JEMBOSS wEMBOSS Public SRS installations | Biowisdom NCBI BLAST software BLAST Wikipedia BLAST setup procedure for Windows NCBI BLAST download BLAST FASTA databases download BLAST standalone documentation Alignment and database searches WWW BLAST Database Searches at NCBI EMBNet QuickGuide BLAST Fasta3 Database Searches at the EBI BLITZ searches at the EBI MPsrch at EBI BCM Search Launcher: Multiple Sequence Alignments PeCoP Psi-Blast to find persistently conserved positions PVS: Protein Variability Server - conserved epitope discovery Dotter dot-matrix sequence comparison program ClustalX Tcoffee DNA, RNA, Protein alignment tools mreps DNA tandem repeat identifier YASS genomic DNA local alignment similarity search tool Standalone BLAST BLAST standalone setup for Windows PC STRAP Interactive Structure based Alignment Program GeneDoc Homepage Jalview - Java alignment editor BioEdit Sequence Alignment Editor for Windows 95/98/NT/XP Sequence tools BCM Sequence Utilities SeWeR - Sequence Analysis using Web Resources Sequence Manipulation Suite 2 Sequence Extractor cloning toolbox ReadSeq Webcutter 2.0 Reverse Complement of Sequence Primer 3 PrimerX - mutagenic primer design pDraw32 Acaclone Plasmid drawing Savvy Plasmid Maps European Molecular Biology Open Software Suite EMBOSS Genome assembly by phred and phrap EMBNet Quick Guides to phred and phrap Oligo Heat Map hybridization analysis Integrated DNA Technologies Oligo SciTools Protein tools NPS: Network Protein Sequence Analysis pI/Mw tool - Expasy PeptideMass - Expasy ProtParam tool - Expasy ProtScale - Expasy ISREC SAPS server Phylogenetics PHYLIP Inst. Pasteur Pylip Online Server Phylip Online Help Phylip Tutorial (Jarno Tuimala) EMBNet A Quick Guide to PHYLIP Phylogeny.fr - robust phylogenetic analysis for the non-specialist MacClade Home Page PAUP FORESTER phylogenomics software libraries TreeView Rod Page Software Hypertree large tree displaying tool PANDIT Protein and Associated NucleotideDomains with Inferred Trees PeCoP Psi-Blast to find persistently conserved positions Ribosomal Database Project II Phylogeny Web Servers List PHYLIP Phylogeny Programs The Tree of Life Home Page Tree of Life Links NCBI Taxonomy Browser The Mathematical Basis of Molecular Phylogenetics Annotation Gene Function Resources Gene Ontology (GO) Consortium QuickGO - GO Browser at EBI AmiGO - GO Browser Ontology Lookup Service (OLS) GOA - Gene Ontology Annotation Project at EBI GOStat - find statistically overrepresented GO terms Gene Ontology Tools for Gene Expression Analysis Online Mendelian Inheritance in Man GeneCards Weizmann Genetic Association Database Integrated annotation services NIH - DAVID Annotation tools eFamily Project - Grid integrating of protein database annotations DAS - Distributed Annotation System DAS registry server at Sanger - available DAS servers SPICE - DAS Client EnsEMBL Genome Browser DAS client Dasty - DAS client Protein Information and Property Explorer (FEWB) Gene prediction services Glimmer Microbial Gene-Finding System GrailExp Grail Experimental Gene Discovery Suite BCM Gene Feature Searches CBS HMMgene server CBS NetGene2 server CBS NetPlantGene server CBS Genome Atlas GeneMark WebGeneMark Eukaryotic WebGeneMark GENSCAN (C. Burge) SplicePredictor ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences EBI Wise2 matches protein to genomic DNA Lowe Lab tRNAscan-SE Search Server Promotor prediction services CBS NetStart 1.0 server Translation Start CBS Promoter 2.0 server WWW Promotor Scan Pol II EPD Eukaryotic promotor database TRADAT Transcription Databases and Analysis Tool TFM Explorer TFM-Scan TFSEARCH - Transcription Factor Search TRANSFAC database at Biobase Biological Databases ORegAnno: Open Regulatory Annotation JASPAR Transcription factor database JASPAR Transcription factor database paper MotifMogul - Multiple Transcription Factor Binding Sites Algorithms TiffIn Fly genome motif database Regulatory Sequence Analysis Tools (RSAT) Footprinter 3 phylogenetic conserved motif extraction - Web server Footprinter phylogenetic conserved motif extraction - Manual AlignACE yeast cis-regulatory element search DIALIGN - multiple sequence alignments to find conserved regulatory elements The Gibbs Motif Sampler MEME MAST motif discovery and search DiRE identification of DIstant Regulatory Elements of co-regulated genes ConTra - identification of conserved transcription factor binding sites Structures Transmembrane features TMHMM Server 2.0 ISREC TMpred Server SOSUI Structure prediction of membrane proteins HMMTOP Prediction of transmembrane helices and topology TMAP multiple sequence alignment protein prediction TopPred - Topology prediction of membrane helices 3D structures RCSB PDB Protein Data Bank - PDB NCBI Structure Protein Databank in Europe (PDBe) Domain Structure Database NCBI Structures by electron microscopy at MSD NCBI VAST structural alignments SWISS-MODEL EMBNet - A Quick Guide to Swiss-Model EMBL Dali protein structure comparison server The DALI database Dali Fold Classification GENO3D : Automatic Modeling of Protein Structure CPHmodels - Homology modeling ModBase - Comparative protein structure models SCOP: Structural Classification of Proteins Superfamily HMM models SCOP CATH Protein Structure Classification Database Gene3D Structural and Functional Annotation PredictProtein Cn3D Home Page Ressource Parisienne en Bioinformatique Structurale (RPBS) PyMOL molecular visualization system BALL and BALLView Visualization and Modelling Tools TarFisDock identifying drug targets by docking DeepView Swiss-PdbViewer Protein Explorer Open Rasmol RasTop - Rasmol Graphical Interface Chime Polyview 3D web server for animated images Simulation Dynamischer Molekuele (DKFZ) Biodesigner Molecular Modeling and Visualization VMD - Visual Molecular Dynamics Accelrys Discovery Studio Visualizer (free version) CNSsolve Crystallography and NMR system Principals of protein structure Genetic Algorithms and Protein Folding Signal peptides and glycosylation sites SignalP server PSORT WWW Server iPSORT N-terminal protein sorting signals NetNGlyc Server NetOGlyc server ExPASy - ScanProsite tool Secondary structures BCM Structure Prediction Tools PredictProtein JPRED Secondary structure prediction JUFO neuronal network prediction server PSIPRED Protein Structure Prediction Server PROF - Secondary Structure Prediction System ISREC COILS Server NPS: Consensus secondary structure prediction NPS : coiled-coils prediction NPS: MLRC NPS: HNN NPS: SOPMA NPS: GOR4 DomCut prediction of linker regions between functional domains RNA BiC RNA folding services Integrated DNA Technologies mfold server Vienna RNA secondary structure servers ncRNA tools for sequence/structure analyses of non-conding RNAs SARSA Structural Alignment of RNA Using a Structural Alphabet MAGNOLIA advanced RNA sequence and structural alignment Small molecules Human Metabolome Database KEGG Drug Database KEGG Ligand Database ChEBI - Chemical Entities of Biological Interest MSD Ligand Chemistry in PDB NCBI PubChem Compound NCBI PubChem Substance NLM SIS Chemical Information NCI-3D Search ChemIDplus CHEMINFO: Chemical Information Sources from Indiana University FAF-Drugs: Free ADME/tox Filtering OpenBabel format conversion tool for drugs Java Molecular Editor at RPBS JME Molecular Editor by Peter Ertl SuperPred Drug Target Prediction Server Functional genomics Transcriptomics databases Microarray Bioinformatics at EBI Arrayexpress at the EBI Expression Profiler at EBI Documentation for Expression Profiler Gene Expression Atlas - Large Scale Meta-Analysis of Public Microarray Data GEO Gene Expression Omnibus at NCBI MaRe Microarray Retriever Stanford Microarray Database Yale Microarray Database JCV Institute Genomics NIH ENCODE Project: ENCyclopedia Of DNA Elements NGFN German National Functional Genomics Network Genevestigator GeneCAT - Gene Co-expression Analysis Toolbox CATMA - A complete Arabidopsis Transcriptome MicroArray The Arabidopsis Information Resource - TAIR AFGN Arabidopsis Functional Genomics Network Microarray Gene Expression Data Society Stanford Functional Genomics Facility Transcriptomics tools NIH - Guide to Microarray Data analysis Microarray Tools at NCI HSLS: Microarray, SAGE and other gene expression data analysis tools J-Express microarray analysis free version MicroArray Explorer tool for Data Mining Gene Expression Patterns Tools from the Eisen Lab BioConductor Project - Open Source Software for Bioinformatics R and Bioconductor Manual (Thomas Girke) GEPAS microarray analysis pipeline Babelomics - Systems biology microarray data mining TIGR Microarray Software RNA-Seq software ERANGE Broad Institute Genecluster 2.0 dChip Software: Gene Expression Microarray and SNP Microarray Analysis NASC Affymetrix Service: Analysis hints Analysis of Affymetrix data using Excel Affymetrix - NetAffx? Analysis Center MapMan - integrative view of microarray data and metabolic maps GenMAPP Gene Map Annotator and Pathway Profiler Proteomics databases and search engines EXPASY Swiss 2Dpage WORLD-2DPAGE Index to 2D-PAGE databases and services EXPASY Peptide Mass Tool EXPASY Aldente Peptide Mass Fingerprinting Tool MASCOT Peptide Mass Fingerprint SEQUEST MS proteomics search engine Phenyx MS protein search engine (GeneBio/SIB) X! Tandem MS search engine OMSSA ms/ms search engine UCSF Mass Spectrometry Facility Protein Prospector Protein Prospector Server at Joint Proteomics Laboratory Melbourne PROWL protein and MS tools PRIDE - Proteomics Identifications Database PeptideAtlas OPD: Open Proteomics Database (MS) GPMDB proteomics database Human Protein Atlas Tranche - Secure P2P for Scientific Data Dissemination ISPIDER MS meta protein database search Protein Identifier Cross-Reference Service NIH Histone Sequence Database Phospho.ELM Database of phosphorylation sites Human Protein Reference Database Proteomics post translational modifications ExPASy - FindMod tool ExPASy - Popitam - MS/MS modified peptide search tool RESID Database of protein modifications Delta Mass PTM database (ABFR) Unimod database - protein modifications for MS Unimod - Modification naming guidelines PRIDE Modification Search PRIDE modification ontology lookup service (OLS) AutoMotif Server - Modification site prediction ExPASy - Sulfinator tool Tyr sulfination sites predictor NetPhos 2.0 Server STY phosphorylation site predictor HUPO PSI Protein Modification Documentation Proteomics software TPP Trans-Proteomic Pipeline SASHIMI MS proteomics pipeline OpenMS / TOPP open source MS proteomics pipeline TOPP-the OpenMS proteomics pipeline MaxQuant Scaffold protein identification framework (by Proteome Software) mMass - Open Source Mass Spectrometry Tool PeptideProphet MS proteomics prediction tool ProteinProphet MS proteomics prediction tool MassNET MS proteomics annotation server MassTRIX Metabolomics mass to pathway mapper Proteomics organisations and standards HUPO - Human Proteome Organisation SwissProt HPI - Human Proteome Initiative HUPO Proteomics Standards Initiative MASC Arabidopsis Proteomics Standards Subcommittee mzML Specification | HUPO Proteomics Standards Initiative Mass spectrometry data formats - Wikipedia gabi Arabidopsis Proteomics Data Proteomics from Angelika G�rg Boston University Biology Proteomics Resource Deutsche Gesellschaft f�r Proteomforschung Swiss Proteomics Society SWISS Proteomics Society Proteomics Links Proteome commons ISB NHLBI Seattle Proteome Center IonSource Proteomics Resource Links Protein-Protein Interactions EBI IntAct Project DIP - Database of Interacting Proteins BOND - Biomolecular Object Network Database MIPS Mammalian Protein-Protein Interaction Databank BioGRID - General Repository for Interaction Datasets HPID Human Protein Interaction Database The JCB Protein-Protein Interaction Website MIPS Yeast Protein-Protein-Interaction and Complex Viewer Yeast Protein complex database MINT - Molecular Interactions database Complexpander - Predicting protein complexes PathBlast - Comparison of interaction networks between organisms iHOP - Information Hyperlinked over Proteins String: functional protein association networks BioPAX - data exchange for biologicaql pathway data Graphviz - Open Source Graph Visualization Software Cytoscape - open source software for interaction visualization and integration visANT - Visual Analysis Tool for Biological Networks and Pathways aiSee - commercial Graph layout software miRNA RNA Molecular Biology Tuschl Lab miRBASE microRNA database Sanger Institute Rfam RNA families database of alignments and CMs Sanger Institute The siRNA user guide - Tuschl Lab microRNA.org: A resource for predicted microRNA targets and expression OligoWalk Web Server for siRNA design AsiDesigner siRNA design pipeline Systems Biology System Biology Information Resources BioModels.NET The Reactome Project Panther Classification Systems - Panther Pathways Human Metabolome Database KDBI - Kinetic Data of Biomolecular Interactions SBML Systems Biology Markup Language SBGN Systems Biology Graphical Notation Standardization The International Society for Systems Biology Systems Biology Portal www.systems-biology.org The Systems Biology Institute - Tokyo US National Centers for System Biology Systems Biology at UC San Diego Systems Biology in Germany HepatoSys - Network Systems Biology SystemsX - The Swiss Initiative in Systems Biology YSBN The Yeast Systems Biology Network Nature web focus: Systems biology: a user's guide Systems Biology Wikipedia Systems Biology Modeling Tools Systems Biology WorkBench SBW package JDesigner: A Biochemical Network Layout Tool Jarnac biochemical simulation package Pasadena Twain ODE solver of the SWB package CADLIVE - network construction system Dizzy stochastic simulations tool CellDesigner - a modeling tool for biochemical networks SBMLsqueezer: A CellDesigner plug-in to generate kinetic rate equations for biochemical networks Cellware - Modeling and Simulation Tool E-Cell project COPASI - Complex Pathway Simulator Gepasi - Biochemical Kinetics Simulator Dynetica - a simulator of dynamic networks PLAS Power Law Analysis and Simulation tool JSim - a Java based simulation system STOCKS - Stochastic kinetic simulations Basis Gillespie Stochastic Simulator CaliBayes - Bayesian calibration of biological simulators JWS Online - Online Cellular Systems Modelling PyBioS - web server for modeling and simulation of cellular systems Virtual Cell Internet simulation server at NRCAM