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Bioinfo1 Courses and lectures Bioinformatics - Online Courses and Tutorials The European School In Bioinformatics (Biosapiens) 4ESB The Fourth Biosapiens Eurropean School in Bioinformatics VSNS Biocomputing Division EMBNet Quick Guides EMBNet Courses EMBNet Biocomputing Tutorials - Introduction Sequence Analysis with distributed Resources BioComputing Hypertext Coursebook Tutorial Protein Structures (EXPASY) SwissModel CMBI Course Homology Modelling BioInformatics Glossary 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 2006 German Conference on Bioinformatics - Tuebingen SBMC Conference on Systems Biology of Mammalian Cells 2006 Journals Applied Bioinformatics Bioinformatics BioMed Central Bioinformatics In Silico Biology Nucleic Acids Research Omics: A Journal of Integrative Biology PLoS Computational Biology Nature Omics Gateway Proteomics Electrophoresis BioMed Central - Systems Biology Gateway Molecular Systems Biology BioSystems 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 Databases Sequences Entrez Browser NCBI SRSWWW EMBL-EBI DBGET/LinkDB Integrated Database Retrieval System SRSWWW at Expasy 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 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 The Institute for Genomic Research The Sanger Centre Broad Institute Center for Genome Research HGP - Human genome project information DHGP - German human genome project Human Genome Resources NCBI Mouse Genome Resources NCBI Rat Genome resources NCBI Fugu Fish Genomics Project QMUL ZFIN - Zebrafish information network Wormbase C. elegans FlyBase Drosophila Yeast Genome Database MIPS tair - The Arabidopsis Information Resource GABI Primary Database ( GabiPD ) - Genomanalyse Pflanze Plant genomes (MIPS) Protein structures RCSB Protein Data Bank Entrez-Structure MSD Macromolecular Structure Database at EBI SWISS-MODEL EMBNet - A Quick Guide to Swiss-Model SCOP: Structural Classification of Proteins CATH database of structural domains Gene3D Structural and Functional Annotation The DALI database Domain Structure Database NCBI ModBase - Comparative protein structure models 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 The Sanger Centre Pfam Server ProDom conserved protein domains CDD Conserved domains database NCBI PIR iProClass Protein Classification Superfamily HMM models SCOP Gene3D Structural and Functional Annotation Pathways KEGG: Kyoto Encyclopedia of Genes and Genomes ExPASy - Biochemical Pathways BioCarta - Pathways PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System Reactome Project Pathway Knowledge Base BioCyc Database Collection MetaCyc Encyclopedia of Metabolic Pathways IUPHAR receptor database LGICD Ligand-gated ion-channel database AraCyc - Pathway Database of Arabidopsis thaliana Invitrogen iPath Human Biological Pathways biodirectory - biochemical and metabolic pathways Signal Transduction - Biochemweb.org virtual library MapMan - integrative view of microarray data and metabolic maps GenMAPP Gene Map Annotator and Pathway Profiler Enzymes Enzyme Database - BRENDA REBASE The Restriction Enzyme Database Protein Kinase Resource Kinase.com Global kinome analysis IntEnz EBI Enzyme Database Catalytic Site Atlas - CSA (EBI) Software EBI: The BioCatalog Bioperl Open Source Initiative OSI SourceForge.net Open Source Resource 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 WorldSciNet Search Engine - World Scientific 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 PubFinder - finds related articles in PubMed eTBlast - related articles to any text MedBlast - sequence-based literature retrieval CoPub Mapper Gene Co-Publication Text Mining PubMatrix Vivisimo PubMed Clustering Search 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 Nucleic Acids Research Database Summary Paper List Nucleic Acids Research Database Issue 2006 Nucleic Acids Research Webserver Issue 2006 CMS Molecular Biology Resource Harvard Dept of MCB - Biology Links Institute Pasteur Bio NetBook CiteULike - online reference management sharing service Connotea - online reference and link sharing The bioinformatics bench Linux Novell SUSE Linux Linux Online RedHat Linux Debian Linux Ubuntu Linux Linux Kernel Archives Knoppix BioKnoppix BioLinux EMBNet A QuickGuide to UNIX Linux Community (German) linux.de Linux user group Tuebingen WAMP Apache SELFHTML MySQL PHP SELFPHP phpMyAdmin Perl and R PERL The Perl directory at perl.org Perl documentation ActiveState - ActivePerl Downloads CPAN PERL Script Archiv Bioperl BioConductor Project - Open Source Software for Bioinformatics EMBNet QickGuides PERL and Regular Expressions The R project for statistical computing The Comprehensive R archive network Editors The Vim Editor Proton EMBOSS European Molecular Biology Open Software Suite EMBOSS EMBNet Quick Guides EMBOSS and wEMBOSS Ready-to-install EMBOSS at BioLinux wEMBOSS BioKNOPPIX with JEMBOSS and EMBOSS Bioinformatic System Management Workshop 2005 Alignment WWW BLAST Database Searches at NCBI EMBNet QuickGuide BLAST Fasta3 Database Searches at the EBI BCM Search Launcher: Multiple Sequence Alignments The Sequence and Structure Searching Site Berkeley PeCoP Psi-Blast to find persistently conserved positions Directory of /pub/ClustalX GeneDoc Homepage ReadSeq Sequence tools BCM Sequence Utilities SeWeR - Sequence Analysis using Web Resources 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 Protein tools NPS: Network Protein Sequence Analysis pI/Mw tool - Expasy PeptideMass - Expasy ProtParam tool - Expasy ProtScale - Expasy ISREC SAPS server Phylogenetics PHYLIP BIOBOX / Phylip Online Server Phylip Online Help EMBNet A Quick Guide to PHYLIP PAUP TreeView PANDIT Protein and Associated NucleotideDomains with Inferred Trees PeCoP Psi-Blast to find persistently conserved positions PHYLIP Phylogeny Programs Phylogenetics Resources Berkeley The Tree of Life Home Page Tree of Life Links NCBI Taxonomy Browser The Mathematical Basis of Molecular Phylogenetics 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 TMPred - Prediction of transmembrane regions and orientation TopPred - Topology prediction of membrane helices 3D structures RCSB PDB Protein Data Bank - PDB NCBI Structure MSD Macromolecular Structure Database at EBI Domain Structure Database NCBI 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 BALL and BALLView Visualization and Modelling Tools DeepView Swiss-PdbViewer Protein Explorer RasMol RasTop - Rasmol Graphical Interface Chime Principals of protein structure Genetic algorithms on proteins Signal peptides and glycosylation sites SignalP server PSORT WWW Server WWW Signal Scan NetOGlyc server ExPASy - ScanProsite tool Secondary structures NNPredict PredictProtein PredictProtein Help JPRED Secondary structure prediction JUFO neuronal network prediction server PSIPRED Protein Structure Prediction Server NIH: GOR4 secondary structure prediction 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 RNA BiC RNA folding services Vienna RNA secondary structure servers Small molecules 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 Annotation Gene Function Resources Gene Ontology (GO) Consortium QuickGO - GO Browser at EBI AmiGO - GO Browser GOA - Gene Ontology Annotation Project at EBI GOStat - find statistically overrepresented GO terms Online Mendelian Inheritance in Man GeneCards Weizmann Integrated annotation services 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 AAT Server - Analysis and Annotation Tool 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 GENSCAN (C. Burge) SplicePredictor 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 TFSEARCH - Transcription Factor Search ORegAnno: Open Regulatory Annotation cisRED: cis-regulatory element database Functional genomics Microarrays Microarray Bioinformatics at EBI Arrayexpress at the EBI Expression Profiler at EBI Documentation for Expression Profiler GEO Gene Expression Omnibus at NCBI Stanford Microarray Database TIGR functional genomics NGFN German National Functional Genomics Network Genevestigator The Arabidopsis Information Resource - TAIR AFGN Arabidopsis Functional Genomics Network Microarray Gene Expression Data Society Microarray.Org - Microarray protocols and software NIH - Guide to Microarray Data analysis Microarray Tools at NCI Mesher - TIGR MeSH terms overrepresented in microarray data J-Express microarray analysis free version MicroArray Explorer tool for Data Mining Gene Expression Patterns Cluster and Treeview from the Eisen Lab BioConductor Project - Open Source Software for Bioinformatics TIGR TM4 Microarray Software Suite 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 EXPASY Swiss 2Dpage WORLD-2DPAGE Index to 2D-PAGE databases and services EXPASY Peptide Mass Tool EXPASY PeptIdent Tool MASCOT Peptide Mass Fingerprint UCSF Protein Prospector PROWL protein and MS tools RESID Database of protein modifications HUPO - Human Proteome Organisation HPI - Human Proteomics Initiative gabi Arabidopsis Proteomics Data Proteomics from Angelika G�rg Boston University Biology Proteomics Resource Deutsche Gesellschaft f�r Proteomforschung SWISS Proteomics Society Proteomics Links IonSource Proteomics Resource Links Protein-Protein Interactions EBI IntAct Project DIP - Database of Interacting Proteins BOND - Biomolecular Object Network Databank MIPS Mammalian Protein-Protein Interaction Database 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 SPIES - Scientific-literature-based protein interaction extraction system Graphviz - Open Source Graph Visualization Software Cytoscape - open source software for interaction visualization and integration 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 Systems Biology System Biology Information Resources BioModels.NET The Reactome Project Panther Classification Systems - Panther Pathways KDBI - Kinetic Data of Biomolecular Interactions SBML Systems Biology Markup Language The International Society for Systems Biology Systems Biology Portal www.systems-biology.org HepatoSys - Network Systems Biology SystemsX - The Swiss Initiative in Systems Biology Systems Biology Modeling Tools Systems Biology WorkBench SWB package JDesigner: A Biochemical Network Layout Tool CADLIVE - network construction system Dizzy stochastic simulations tool CellDesigner - a modeling tool for biochemical networks CellWare - building computational chassis for systems and synthetic biology E-Cell project COPASI - Complex Pathway Simulator Gepasi - Biochemical Kinetics Simulator JSim - a Java based simulation system STOCKS - Stochastic kinetic simulations JWS Online - Online Cellular Systems Modelling PyBioS - web server for modeling and simulation of cellular systems Virtual Cell Internet simulation server at NRCAM