Bookmarks

bioinfo2 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 - 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 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 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 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 Databases 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 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 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 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 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 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 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 2011 Nucleic Acids Research Database Issue 2010 Nucleic Acids Research Webserver Issue 2011 Nucleic Acids Research Webserver Issue 2010 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 Professional SUSE Linux Fedora Project RedHat Linux Linux Kernel Archives BioLinux - Wikipedia Knoppix BioKnoppix EMBNet A QuickGuide to UNIX Linux Community (German) linux.de WAMP Apache SELFHTML MySQL PHP SELFPHP phpMyAdmin Comparison of WAMPs XAMPP Perl Perl The Perl directory at perl.org Perl documentation Perl Download ActiveState - ActivePerl Downloads Strawberry Perl for Windows 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! 2011 R user conference Warwick, UK useR! 2010 R user conference Gaithersburg, Maryland Editors The Vim Editor Proton Komodo Laboratory tools WETLAB: an open source electronic lab notebook PHP Labware Project OpenFreezer EMBOSS EMBOSS EMBOSS wiki EMBOSS application wiki EMBOSS applications EMBOSS applications program groups EMBOSS for Windows EMBOSS Users Guide EMBOSS Developers Guide EMBOSS Administrators Guide 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 Open Source Bioinformatics Platforms Galaxy bioinformatics framework myGRID - Open Source Middleware Environment for Bioinformatics Workflows TAVERNA Open Source Bioinformatics Workbench eFamily Project - Grid integrating of protein database annotations Bioclipse - visual platform for structural chemo- and bioinformatics Systems Biology WorkBench SWB package Mobyle web environment for bioinformatics workflows Chinook P2P Bioinformatics Platform Gaggle data management framework