Useful links 2Can Support Portal – Bioinformatics educational resource3DID – 3D interacting domainsAccelrys Discovery StudioAccelrys Discovery Studio Visualizer (free version)ActiveState – ActivePerl DownloadsAdvanced PubMed SearchAffymetrix – NetAffx TM Analysis CenterAFGN Arabidopsis Functional Genomics NetworkaiSee – commercial Graph layout softwareAMB Algorithms for Molecular BiologyAmiGO – GO BrowserAnalysis of Affymetrix data using ExcelApacheAraCyc – Pathway Database of Arabidopsis thalianaARP/wARPArrayexpress at the EBIAsiDesigner siRNA design pipelineBabelomics – Systems biology microarray data miningBALL and BALLView Visualization and Modelling ToolsBasis Gillespie Stochastic SimulatorBaylor College of Medicine HGSCBBID-Biological Biochemical Image DatabaseBCM Gene Feature SearchesBCM Search LauncherBCM Search Launcher: Multiple Sequence AlignmentsBCM Sequence UtilitiesBCM Structure Prediction ToolsBingBioBike (LISP)BioConductor Project – Open Source Software for BioinformaticsBioconductor WorkshopsBioCyc Database CollectionBioData MiningBiodesigner Molecular Modeling and VisualizationBioEdit Sequence Alignment Editor for Windows 95/98/NT/XPBioGRID – General Repository for Interaction DatasetsBioinformaticsBioinformatics – Online Courses and TutorialsBioinformatics Links Directory UBiCBioinformatics Open Source Conference BOSC 2011 ViennaBioinformatics Open Source Conference BOSC 2012 Long BeachBioinformatics Software Server LilleBioinformatics.Org – The Open-Access InstituteBioinformatik.deBioJavaBioKnoppixBioLinux – WikipediaBiological NetworksBioMed Central – Systems Biology GatewayBioMed Central BioinformaticsBioModels.NETBioPAX – data exchange for biological pathway dataBioPAX – data exchange for biologicaql pathway dataBioPerlBioPythonBioRubyBioSystemsBiotech Europe Link BaseBLAST FASTA databases downloadBLAST setup procedure for WindowsBLAST standalone documentationBLAST standalone setup for Windows PCBLAST WikipediaBlock SearchBlocks WWW ServerBMC Systems BiologyBOND – Biomolecular Object Network DatabaseBoston University Biology Proteomics ResourceBotDB DSSP analysisBriefings in BioinformaticsBriefings in Functional Genomics and ProteomicsBroad Institute Center for Genome ResearchBroad Institute Genecluster 2.0C.elegans Blast server (Sanger Centre)CADLIVE – network construction systemCaliBayes – Bayesian calibration of biological simulatorsCatalytic Site Atlas – CSA (EBI)CATH database of structural domainsCATH Protein Structure Classification DatabaseCATMA – A complete Arabidopsis Transcriptome MicroArrayCAVER protein analysis and visulaization – pockets and tunnelsCBS Bioinformatics CoursesCBS Genome AtlasCBS Genome atlas databaseCBS HMMgene serverCBS NetGene2 serverCBS NetPlantGene serverCBS NetStart 1.0 server Translation StartCBS Promoter 2.0 serverCCMS XtalViewCCP4 Molecular GraphicsCCP4 Molrep – automated program for molecular replacementCCP4 Scala – scale together multiple observations of reflectionsCCP4 Software for Molecular X-ray crystallographyCCP4 SOLOMON – density modification (phase improvement) by solvent flippingCDD Conserved domains database NCBICellDesigner – a modeling tool for biochemical networksCellware – Modeling and Simulation ToolChEBI – Chemical Entities of Biological InterestChemIDplusCHEMINFO: Chemical Information Sources from Indiana UniversityChimeCiteULike – online reference management sharing serviceClinical ProteomicsClustalXCMBI Courses for protein structureCMS Molecular Biology ResourceCn3D Home PageCNSsolve Crystallography and NMR systemComparison of WAMPsConnotea – online reference and link sharingConserved Domain Database NCBIConserved Domains Database NCBIConTra – identification of conserved transcription factor binding sitesCootCOPASI – Complex Pathway SimulatorCoPub Mapper Gene Co-Publication Text MiningCPAN PERL Script ArchivCPHmodels – Homology modelingCrossref Search – commercial publishers worldwide common paper serviceCurrent ProteomicsCUSI – Suchmoeglichkeiten im InternetCytoscape – open source software for interaction visualization and integrationDAS – Distributed Annotation SystemDAS registry server at Sanger – available DAS serversDasty – DAS clientDBGET/LinkDB Integrated Database Retrieval SystemdChip Software: Gene Expression Microarray and SNP Microarray AnalysisDebian LinuxDeepView Swiss-PdbViewerdel.icio.us social bookmarkingDelta Mass PTM database (ABFR)Deutsche Gesellschaft f�r ProteomforschungDIALIGN – multiple sequence alignments to find conserved regulatory elementsDIP – Database of Interacting ProteinsDIP DLRP Database of Interactiong ProteinsDiRE identification of DIstant Regulatory Elements of co-regulated genesDizzy stochastic simulations toolDOAJ – Directory of open access journalsDocumentation for Expression ProfilerDomCut prediction of linker regions between functional domainsDOMINE Database of Protein Domain InteractionsDomino Domain peptide interaction databaseDotter dot-matrix sequence comparison programDSSP Kabsch Sander PDB secondary structure assignmentDSSPCont RostlabDynetica – a simulator of dynamic networksEBI European Bioinformatics InstituteEBI IntAct ProjectEBI Wise2 matches protein to genomic DNAEBI: The BioCatalogueEBIMed Medline information retrieval and extractionE-Cell projecteFamily Project – Grid integrating of protein database annotationsElectrophoresisELM Eukaryotic Linear Motif Functional Site PredictionEMAN 3D single particle image reconstructionEMBL Dali protein structure comparison serverEMBNet – A Quick Guide to ExpasyEMBNet – A Quick Guide to Swiss-ModelEMBNet A Quick Guide to PHYLIPEMBNet A QuickGuide to UNIXEMBNet Bioinformatics NetworkEMBNet CoursesEmbNet EMBOSS and wEMBOSS Quick GuidesEMBNet QickGuides PERL and Regular ExpressionsEMBNet Quick GuidesEMBNet Quick Guides to phred and phrapEMBNet QuickGuide BLASTEMBNet QuickGuide Swissprot Trembl DatabasesEMBOSSEMBOSS Administrators GuideEMBOSS application wikiEMBOSS applicationsEMBOSS applications program groupsEMBOSS Developers GuideEMBOSS FAQEMBOSS for WindowsEMBOSS mailing listsEMBOSS Main TutorialEMBOSS user documentationEMBOSS Users GuideEMBOSS wikiEMBRACE Network of ExcellenceEnsembl Genome BrowserEnsEMBL Genome Browser DAS clientEntrez Browser NCBIEntrez-Genome NCBIEntrez-StructureEnzyme Database – BRENDAEPD Eukaryotic promotor databaseEspacenet – Europe’s network of patent databasesESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequenceseTBlast – related articles to any textEukaryotic WebGeneMarkEuropean Molecular Biology Open Software Suite EMBOSSExpasyExPASy – Biochemical PathwaysExPASy – FindMod toolExPASy – PROSITEExPASy – QuickMod – MS/MS modified peptide search toolExPASy – ScanProsite toolExPASy – Sulfinator tool Tyr sulfination sites predictorExpasy Life Science DirectoryExPASy Mass SearchExPASy MultIdent Peptide Mass Fingerprinting ToolExPASy Peptide Mass ToolExpasy Proteomics ServerExPASy Swiss 2DpageExpression Profiler at EBIFAF-Drugs: Free ADME/tox FilteringFasta3 Database Searches at the EBIFedora ProjectFlyBase Drosophilafoldit – The Protein folding gameFORESTER phylogenomics software librariesFrog2 format conversion tool for drugsFugu Fish Genome ProjectFungal Genetics Stock Centergabi Arabidopsis Proteomics DataGABI Primary Database ( GabiPD ) – Genomanalyse PflanzeGalaxy bioinformatics frameworkGBM Gesellschaft fuer Biochemie und MolekularbiologieGCB 2011 German Conference on Bioinformatics – WeihenstephanGCB 2012 German Conference on Bioinformatics – JenaGene Expression Atlas – Large Scale Meta-Analysis of Public Microarray DataGene Ontology (GO) ConsortiumGene Ontology Tools for Gene Expression AnalysisGene3D Structural and Functional AnnotationGeneCards WeizmannGeneCAT – Gene Co-expression Analysis ToolboxGeneDoc HomepageGeneInfinity’s Protein Interaction Analysis pageGeneMarkGenetic Association DatabaseGenevestigatorGenMAPP Gene Map Annotator and Pathway ProfilerGENO3D : Automatic Modeling of Protein StructureGenome assembly by phred and phrapGenome Matrix databases information integrationGenomeNet WWW server JapanGENSCAN (C. Burge)GEO Gene Expression Omnibus at NCBIGepasi – Biochemical Kinetics SimulatorGesellschaft fuer Informatik – Fachgruppe BioinformatikGlimmer Microbial Gene-Finding SystemGNP Genome Network PlatformGOA – Gene Ontology Annotation Project at EBIGOLD: Genomes On Line Database v 3.0GoogleGoogle ScholarGoPubMed – Ontology based literature searchGOStat – find statistically overrepresented GO termsGPMDB proteomics databaseGrailExp Grail Experimental Gene Discovery SuiteGraphviz – Open Source Graph Visualization SoftwareGraphWeb: analysis of biological networksHarvard Dept of MCB – Biology LinksHepatoSys – Network Systems BiologyHGP – Human genome project informationHKL X-ray crystallography packageHMMTOP Prediction of transmembrane helices and topologyHomoMINT predicted human interaction networkHPRD Human Protein Reference DatabaseHSLS: Microarray, SAGE and other gene expression data analysis toolsHSLS: OBRC: Online Bioinformatics Resources CollectionHubMed pubmed rewiredHuman Gene and Protein Database (HGPD)Human Genome Resources NCBIHuman GenomicsHuman Metabolome DatabaseHuman Protein AtlasHuman Protein Reference DatabaseHUPO – Human Proteome OrganisationHUPO 2011 10th World Congress GenevaHUPO 2012 11th World Congress BostonHUPO Proteomics Standards InitiativeHUPO PSI Protein Modification DocumentationHypertree large tree displaying toolICPLQuantIET Synthetic BiologyIET Systems BiologyiHOP – Information Hyperlinked over ProteinsIn Silico BiologyInstalling Bioperl on Windows – BioPerlIntegr8 Proteome Analysis at EBIIntegrated DNA Technologies Oligo SciToolsIntegrated DNA Technologies Unafold serverIntEnz EBI Enzyme DatabaseInternational Rice Genome Sequencing ProjectInterpro Domain and Profile DatabaseInterproscanIonSource Proteomics Resource LinksIPI – International Protein Index EBIiPSORT N-terminal protein sorting signalsISB NHLBI Seattle Proteome CenterISCB – International Society for Computational BiologyISMB ECCB 2011 ViennaISMB ECCB 2012 Long BeachISPIDER MS meta protein database searchISREC COILS ServerISREC SAPS serverISREC TMpred ServerIUPHAR receptor databaseJ. Craig Venter Institute (ex TIGR) MD USAJalview – Java alignment editorJarnac biochemical simulation packageJASPAR Transcription factor databaseJASPAR Transcription factor database paperJava Molecular Editor at RPBSJCV Institute GenomicsJDesigner: A Biochemical Network Layout ToolJEMBOSSJ-Express microarray analysis free versionJME Molecular Editor by Peter ErtlJmolJournal of Computational BiologyJournal of Medical Internet ResearchJournal of Proteome ResearchJournal of Proteomics and BioinformaticsJPRED Secondary structure predictionJSim – a Java based simulation systemJUFO neuronal network prediction serverJWS Online – Online Cellular Systems ModellingKDBI – Kinetic Data of Biomolecular InteractionsKEGG Drug DatabaseKEGG Ligand DatabaseKEGG: Kyoto Encyclopedia of Genes and GenomesKinase.com Global kinome analysisKnoppixKomodoLGICD Ligand-gated ion-channel databaseLinnea PathwaysLinux Community (German)Linux Kernel Archiveslinux.deLipoP 1.0 server gram negative lipoprotein predictionLowe Lab tRNAscan-SE Search ServerMacClade Home PageMAGNOLIA advanced RNA sequence and structural alignmentMaize Genetics and Genomic DatabaseMapMan – integrative view of microarray data and metabolic mapsMaRe Microarray RetrieverMASC Arabidopsis Proteomics Standards SubcommitteeMASCOT Peptide Mass FingerprintMass spectrometry data formats – WikipediaMassTRIX Metabolomics mass to pathway mapperMaxQuantMEGA phylogeny softwareMEME MAST motif discovery and searchMetaCyc Encyclopedia of Metabolic PathwaysMetaGerMicroarray Bioinformatics at EBIMicroArray Explorer tool for Data Mining Gene Expression PatternsMicroarray Gene Expression Data SocietyMicroarray Tools at NCImicroRNA.org: A resource for predicted microRNA targets and expressionMINT – Molecular Interactions databaseMIPS Mammalian Protein-Protein Interaction DatabankMIPS MPact Protein Interaction and Complex DBMIPS Yeast Protein-Protein-Interaction and Complex ViewerMIPS: Munich Information Centre for Protein SequencesmiRBASE microRNA database Sanger InstitutemMass – Open Source Mass Spectrometry ToolModBase – Comparative protein structure modelsMolecular and Cellular ProteomicsMolecular Systems BiologyMosflm diffraction data processingMotifMogul – Multiple Transcription Factor Binding Sites AlgorithmsMouse Genome Resources NCBIMPsrch at EBImreps DNA tandem repeat identifierMSD Ligand Chemistry in PDBMyNCBI PubMed updating and alertingMySQLmzML Specification | HUPO Proteomics Standards InitiativeNASC Affymetrix Service: Analysis hintsNature Omics GatewayNature web focus: Systems biology: a user’s guideNAViGaTOR – Network Analysis, Visualization, & Graphing TORontoNCBI BLAST downloadNCBI Esearch Entrez UtilityNCBI Glimmer3NCBI HIV Human protein interaction databaseNCBI Journal databaseNCBI PubChem CompoundNCBI PubChem SubstanceNCBI Sequence Read ArchiveNCBI StructureNCBI Taxonomy BrowserNCBI UniVec and VecScreen Vector contamination searchNCBI US National Center for Biotechnology InformationNCBI VAST structural alignmentsNCI BioCarta – PathwaysNCI Nature Pathway Interaction DatabaseNCI-3D SearchncRNA tools for sequence/structure analyses of non-conding RNAsNetNGlyc ServerNetOGlyc serverNetPath human signal transduction pathwaysNetPhos 2.0 Server STY phosphorylation site predictorNetwork Analysis Tools (NeAT)NetworKIN kinase substrate relationship predictionNeurospora crassa Database (Broad)Neurospora crassa Database (MIPS)NGFN German National Functional Genomics NetworkNIH – DAVID Annotation toolsNIH – Guide to Microarray Data analysisNIH ENCODE Project: ENCyclopedia Of DNA ElementsNIH Histone Sequence DatabaseNLM SIS Chemical InformationNPS : coiled-coils predictionNPS: Consensus secondary structure predictionNPS: GOR4NPS: HNNNPS: MLRCNPS: Network Protein Sequence AnalysisNPS: SOPMANucleic Acids ResearchNucleic Acids Research Database Issue 2011Nucleic Acids Research Database Issue 2012Nucleic Acids Research Database Summary Paper ListNucleic Acids Research Webserver Issue 2010Nucleic Acids Research Webserver Issue 2011O (Alwyn Jones)Oligo Heat Map hybridization analysisOligoWalk Web Server for siRNA designOmics: A Journal of Integrative BiologyOMSSA ms/ms search engineOnline Mendelian Inheritance in ManOntology Lookup Service (OLS)Open Bioinformatics FoundationOpen RasmolOpen Source Initiative OSIOpen SUSE LinuxOpenFreezerOpenMS / TOPP open source MS proteomics pipelineOPHID Interologous interaction databaseORegAnno: Open Regulatory AnnotationOsprey – protein interaction molecular modelingOsprey – protein interaction viewerPaLS Pathway and Literature Strainer (gene set annotation tool)PANDIT Protein and Associated NucleotideDomains with Inferred TreesPANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification SystemPanther Classification Systems – Panther PathwaysPasadena Twain ODE solver of the SWB packagePathAlignerPathBlast – Comparison of interaction networks between organismsPAUPpDraw32 Acaclone Plasmid drawingPeCoP Psi-Blast to find persistently conserved positionsPeptideAtlasPeptideMass – ExpasyPeptideProphet MS proteomics prediction toolPerl documentationPerl DownloadPhaser crystallographic softwarePhenixPhenyx MS protein search engine (GeneBio/SIB)Phobius – combined TM and signal peptide predictionPhospho.ELM Database of phosphorylation sitesPhosphoMotif FinderPhosphoPep Phosphopeptide systems biology databasePHPPHP Labware ProjectphpMyAdminPHYLIPPhylip Online HelpPHYLIP Phylogeny ProgramsPhylip Tutorial (Jarno Tuimala)Phylogeny Web Servers ListPhylogeny.fr – robust phylogenetic analysis for the non-specialistpI/Mw tool – ExpasyPIPs Human Protein Interaction Prediction DatabasePIR – Protein Information ResourcePIR iProClass Protein ClassificationPlant genomes (MIPS)PLoS Computational BiologyPLoS Public Library of SciencePolyview 3D web server for animated imagesPotato Genome Sequencing ConsortiumPredictProteinPRED-TMBB transmembrane beta barrel predictionPRIDE – Proteomics Identifications DatabasePRIDE modification ontology lookup service (OLS)PRIDE Modification SearchPrimer 3PrimerX – mutagenic primer designPRINTS protein fingerprintsProDom conserved protein domainsProdoNet Prokaryotic gene list pathway annotatorPROF – Secondary Structure Prediction SystemProfessional SUSE LinuxProtein Databank in Europe (PDBe)Protein Identifier Cross-Reference ServiceProtein Kinase ResourceProteinProphet MS proteomics prediction toolProteome commonsProteome ScienceProteomicsProteomics – Clinical ApplicationsProtonProtParam tool – ExpasyProtScale – ExpasyPROWL protein and MS toolsPSI-MI HUPO Standard for interactionsPSIPRED Protein Structure Prediction ServerPSORT WWW ServerPub Med CentralPubCrawler PubMed GenBank Update ServicePublic SRS installations | BiowisdomPubMatrixPubMed Single Citation MatcherPubMed/Medline NLM Mesh BrowserPVS: Protein Variability Server – conserved epitope discoveryPyBioS – web server for modeling and simulation of cellular systemsPyMOL molecular visualization systemQuickGO – GO Browser at EBIR and Bioconductor Manual (Thomas Girke)RasTop – Rasmol Graphical InterfaceRat Genome resources NCBIRCSB PDB Protein Data Bank – PDBRCSB Protein Data BankReactome ProjectReadSeqREBASE The Restriction Enzyme DatabaseRedHat LinuxREDI Databases of Baden-WuerttembergRefMacRefSeq Reference Sequence NCBIRegulatory Sequence Analysis Tools (RSAT)RESID Database of protein modificationsRessource Parisienne en Bioinformatique Structurale (RPBS)Reverse Complement of SequenceRfam RNA families database of alignments and CMs Sanger InstituteRibosomal Database ProjectRNA Molecular Biology Tuschl LabRNA-Seq software ERANGERod Page SoftwareRosettaSARSA Structural Alignment of RNA Using a Structural AlphabetSASHIMI MS proteomics pipelineSavvy Plasmid MapsSBGN Systems Biology Graphical Notation StandardizationSBML Systems Biology Markup LanguageSBMLsqueezer: A CellDesigner plug-in to generate kinetic rate equations for biochemical networksScaffold protein identification framework (by Proteome Software)Schizosaccharomyces pombe genome (Sanger Centre)ScirusSCOP: Structural Classification of ProteinsScopusSELFHTMLSELFPHPSequence Analysis with distributed ResourcesSequence Extractor cloning toolboxSequence Manipulation Suite 2Sequence Ontology ProjectSequence similarity searches at the EBISEQUEST MS proteomics search engineSeWeR – Sequence Analysis using Web ResourcesSHARP/autoSHARPSHELXSIB myHits motif scanSignal Transduction – Biochemweb.org virtual librarySignaling Gateway – Cell Signaling Resource NatureSignalP serverSMART – Simple Modular Architecture Research ToolSolve/ResolveSOSUI Structure prediction of membrane proteinsSourceForge.net Open Source ResourceSPICE – DAS ClientSPIDER and WEB EM 3D single particle image reconstructionSplicePredictorSRSWWW EMBL-EBIStandalone BLASTStanford Functional Genomics FacilityStanford Microarray DatabaseSTOCKS – Stochastic kinetic simulationsSTRAP Interactive Structure based Alignment ProgramStrawberry Perl for WindowsString: functional protein association networksStructures by electron microscopy at MSDSuperfamily HMM models SCOPSuperPred Drug Target Prediction ServerSwiss Proteomics SocietySWISS Proteomics Society Proteomics LinksSWISS-MODELSynthetic Biology 5.0 Conference Stanford, CA, USASystems Biology at UC San DiegoSystems Biology in GermanySystems Biology Portal www.systems-biology.orgSystems Biology WikipediaSystems Biology WorkBench SBW packageSystemsX – The Swiss Initiative in Systems Biologytair – The Arabidopsis Information ResourceTarFisDock identifying drug targets by dockingTcoffee DNA, RNA, Protein alignment toolsTFM ExplorerTFM-ScanTFSEARCH – Transcription Factor SearchThe Arabidopsis Information Resource – TAIRThe Comprehensive R archive networkThe DALI databaseThe DALI database Dali Fold ClassificationThe Gibbs Motif SamplerThe International Society for Systems BiologyThe JCB Protein-Protein Interaction WebsiteThe Perl directory at perl.orgThe R project for statistical computingThe Reactome ProjectThe Sanger CentreThe Sanger Centre HMM Pfam SearcherThe Sanger Centre Pfam ServerThe siRNA user guide – Tuschl LabThe Systems Biology Institute – TokyoThe Tree of Life Home PageThe Vim EditorTIGR Microarray SoftwareTIGRFAMs protein families HMMTMAP multiple sequence alignment protein predictionTMHMM Server 2.0Tools from the Eisen LabTopPred – Topology prediction of membrane helicesTPP Trans-Proteomic PipelineTranche – Secure P2P for Scientific Data DisseminationTree of Life LinksTreeViewTutorial Protein Structures (EXPASY) SwissModelUbuntu LinuxUCSF ChimeraUCSF Mass Spectrometry Facility Protein ProspectorUnafold RNA folding servicesUnigene NCBIUnimod – Modification naming guidelinesUnimod database – protein modifications for MSUnipro UGENE: Integrated Bioinformatics ToolsUniProt Chordata protein annotation programUniprot Universal Protein Resource Swiss-Prot/TREMBL/PIRUS National Centers for System BiologyuseR! 2011 R user conference Warwick, UKuseR! 2012 R user conference Nashville, TNUSF Uppsala software factoryVienna RNA secondary structure serversVirtual Cell Internet simulation server at NRCAMVirusMINTvisANT – Visual Analysis Tool for Biological Networks and PathwaysVMD – Visual Molecular DynamicsW3 Search Engines FU BerlinWeb of ScienceWebCrawlerWebcutter 2.0WebGeneMarkWebLogoWebLogo ServerWeizmann Institute Bioinformatics and Biological ComputingwEMBOSSWETLAB: an open source electronic lab notebookWhitehead InstituteWolfram alphaWORLD-2DPAGE Index to 2D-PAGE databases and servicesWormbase C. elegansWWW BLAST Database Searches at NCBIWWW Promotor Scan Pol IIX! Tandem MS search engineXAMPPXDS diffraction data processingYahoo!Yale Microarray DatabaseYASS genomic DNA local alignment similarity search toolYeast Genome Database MIPSYeast Protein complex databaseYSBN The Yeast Systems Biology NetworkZFIN – Zebrafish information network
