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Arbeitstagung Mikromethoden der Proteinchemie München 2011 Synthetic Biology 5.0 Conference Stanford, CA, USA 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 Pôle Bio-Informatique Lyonnais Weizmann Institute Bioinformatics and Biological Computing Baylor College of Medicine HGSC Bioinformatics Software Server Lille San Diego Supercomputer Center Biological Projects Bielefeld University Bioinformatics Server HUSAR Bioinformatics Lab - Biocomputing Services at DKFZ The Genomics and Bioinformatics Group NCI 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 Human Gene and Protein Database (HGPD) Protein Identifier Cross-Reference Service 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 3.0 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 Potato Genome Sequencing Consortium Protein structures RCSB Protein Data Bank Entrez-Structure Conserved Domains 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 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 Software EBI: The BioCatalogue 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 List of Journals Indexed for Medline Scopus Web of Science Google Scholar CiteSeer (Computer and Information Sciences) Scirus Espacenet - Europe's network of patent databases REDI Databases of Baden-Wuerttemberg BIOSIS Previews Medline OVID - Journals DOAJ - Directory of open access journals PLoS Public Library of Science HighWire Press - Stanford University free full papers WorldSciNet Search Engine - World Scientific JSTOR - The Scholarly Journal Archive Electronic Journals Library Subito - German libraries combined paper delivery service Crossref Search - commercial publishers worldwide common paper service Wiley Interscience Springer Link IngentaConnect Literature and Data Mining Compendia Arrowsmith text mining tool compendium Literature mining for the biologist - Review Linking publication, gene and protein data - Review Biomedical language processing - What is beyond PubMed - Review Text-mining and information-retrieval services for molecular biology - Review Text mining in Biology - Martin Krallinger PDG Course Text mining in Biomedical Literature March 2006 BioCreAtIvE Text mining challenge TREC Genomics Track data mining competition BioNLP information portal BLIMP Biomedical Literature Mining Publications Information retrieval and clustering EBIMed Medline information retrieval and extraction GoPubMed - Ontology based literature search HubMed pubmed rewired MyNCBI PubMed updating and alerting PubCrawler PubMed GenBank Update Service eTBlast - related articles to any text CoPub Mapper Gene Co-Publication Text Mining PubMatrix NCBI Esearch Entrez Utility Information Extraction and Mining The Arrowsmith Project BioIE - Extracting informative sentences Chilibot - Mining PubMed for relationships Textpresso PubGene XplorMed: eXploring Medline abstracts iProLink integrated Protein Literature INformation and Knowledge RLIMS-P Rule-based LIterature Mining System for Protein Phosphorylation iHOP - Information Hyperlinked over Proteins String: functional protein association networks BITOLA - Biomedical Discovery Support System ONDEX - Data integration and visualisation Text entity recognition tools AliasServer Protein synonym search ARGH Biomedical Acronym Database Text2Knowledge - Acronym, Gene Name, Synonym, Interaction Database ABNER: A Biomedical Named Entity Recognizer Literature mining software RefViz QUOSA Information Manager TRANSINSIGHT InforSense BioLT Literature Mining Tool (Biomax Informatics AG) FTI Technology e-discovery KNIME - Konstanz Information Miner Ariadne Genomics MEDSCAN BITOLA - Biomedical Discovery Support System ONDEX - Data integration and visualisation HyBrow hypothesis testing software R Text Mining Package Alignment and database searches WWW BLAST Database Searches at NCBI EMBNet QuickGuide BLAST Fasta3 Database Searches at the EBI Sequence similarity 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 Galaxy bioinformatics framework Unipro UGENE: Integrated Bioinformatics 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 MEGA phylogeny software 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 Phylogeny Web Servers List PHYLIP Phylogeny Programs The Tree of Life Home Page Tree of Life Links NCBI Taxonomy Browser 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 Sequence Ontology Project 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 Gene prediction services Glimmer Microbial Gene-Finding System NCBI Glimmer3 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 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 Regulatory Sequence Analysis Tools (RSAT) 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 Phobius - combined TM and signal peptide prediction 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 PRED-TMBB transmembrane beta barrel prediction 3D structures RCSB PDB Protein Data Bank - PDB NCBI Structure Protein Databank in Europe (PDBe) Conserved Domain 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 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 Ressource Parisienne en Bioinformatique Structurale (RPBS) Tutorial Protein Structures (EXPASY) SwissModel 3D software Rosetta foldit - The Protein folding game PyMOL molecular visualization system BALL and BALLView Visualization and Modelling Tools UCSF Chimera TarFisDock identifying drug targets by docking CAVER protein analysis and visulaization - pockets and tunnels DeepView Swiss-PdbViewer GENO3D : Automatic Modeling of Protein Structure PredictProtein Cn3D Home Page Jmol Open Rasmol RasTop - Rasmol Graphical Interface Chime Polyview 3D web server for animated images Biodesigner Molecular Modeling and Visualization VMD - Visual Molecular Dynamics Accelrys Discovery Studio Visualizer (free version) Model building Coot O (Alwyn Jones) Accelrys Discovery Studio ARP/wARP HKL X-ray crystallography package XDS diffraction data processing Mosflm diffraction data processing Phaser crystallographic software SHARP/autoSHARP SHELX Phenix RefMac Solve/Resolve USF Uppsala software factory CCMS XtalView CCP4 Molecular Graphics CCP4 Software for Molecular X-ray crystallography CCP4 Scala - scale together multiple observations of reflections CCP4 Molrep - automated program for molecular replacement CCP4 SOLOMON - density modification (phase improvement) by solvent flipping CNSsolve Crystallography and NMR system EMAN 3D single particle image reconstruction SPIDER and WEB EM 3D single particle image reconstruction Signal peptides and localization SignalP server Phobius - combined TM and signal peptide prediction PSORT WWW Server iPSORT N-terminal protein sorting signals Glycosylation and lipid modifications NetNGlyc Server NetOGlyc server ExPASy - ScanProsite tool LipoP 1.0 server gram negative lipoprotein prediction 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 DSSP Kabsch Sander PDB secondary structure assignment BotDB DSSP analysis DSSPCont Rostlab DomCut prediction of linker regions between functional domains RNA Unafold RNA folding services Integrated DNA Technologies Unafold 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 NCBI Sequence Read Archive 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) 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 TM 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 Mass Search ExPASy MultIdent 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 PROWL protein and MS tools PRIDE - Proteomics Identifications Database PeptideAtlas 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 PhosphoPep Phosphopeptide systems biology database Human Protein Reference Database Proteomics post translational modifications ExPASy - FindMod tool ExPASy - QuickMod - 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) 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 MaxQuant ICPLQuant Scaffold protein identification framework (by Proteome Software) mMass - Open Source Mass Spectrometry Tool PeptideProphet MS proteomics prediction tool ProteinProphet MS proteomics prediction tool MassTRIX Metabolomics mass to pathway mapper Proteomics organisations and standards HUPO - Human Proteome Organisation UniProt Chordata protein annotation program 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 Görg Boston University Biology Proteomics Resource Deutsche Gesellschaft für 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 DIP DLRP Database of Interactiong Proteins BOND - Biomolecular Object Network Database BioGRID - General Repository for Interaction Datasets MINT - Molecular Interactions database GNP Genome Network Platform MIPS MPact Protein Interaction and Complex DB MIPS Mammalian Protein-Protein Interaction Databank The JCB Protein-Protein Interaction Website GeneInfinity's Protein Interaction Analysis page HPRD Human Protein Reference Database Human Protein Interaction Database NCBI HIV Human protein interaction database UniHI MDC Unified Human Interactome MIPS Yeast Protein-Protein-Interaction and Complex Viewer Yeast Protein complex database HomoMINT predicted human interaction network PIPs Human Protein Interaction Prediction Database Domino Domain peptide interaction database VirusMINT OPHID Interologous interaction database PathBlast - Comparison of interaction networks between organisms iHOP - Information Hyperlinked over Proteins String: functional protein association networks 3DID - 3D interacting domains DOMINE Database of Protein Domain Interactions PSI-MI HUPO Standard for interactions BioPAX - data exchange for biologicaql pathway data Graphviz - Open Source Graph Visualization Software Cytoscape - open source software for interaction visualization and integration Osprey - protein interaction viewer Osprey - protein interaction molecular modeling visANT - Visual Analysis Tool for Biological Networks and Pathways aiSee - commercial Graph layout software NAViGaTOR - Network Analysis, Visualization, & Graphing TORonto 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 - 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