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bioinfo2 Functional genomics Microarrays Microarray Bioinformatics at EBI Arrayexpress at the EBI Expression Profiler at EBI Documentation for Expression Profiler NCBI GEO Gene Expression Omnibus Stanford Microarray Database Microarray Gene Expression Data Society Yale Microarray Database TIGR functional genomics NGFN German National Functional Genomics Network Genevestigator CATMA � A complete Arabidopsis Transcriptome MicroArray The Arabidopsis Information Resource - TAIR AFGN Arabidopsis Functional Genomics Network 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 Aldente Peptide Mass Fingerprinting Tool MASCOT Peptide Mass Fingerprint UCSF Protein Prospector PROWL protein and MS tools PRIDE - Proteomics Identifications Database RESID Database of protein modifications Scaffold protein identification framework (by Proteome Software) Proteomics Society 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 PreBIND literature protein interaction extractor 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 Stratagene PathwayArchitect 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 Systems Biology System Biology Information Resources The Systems Biology Institute - Tokyo BioModels.NET The Reactome Project Panther Classification Systems - Panther Pathways KDBI - Kinetic Data of Biomolecular Interactions SBML Systems Biology Markup Language Systems Biology at UC San Diego The International Society for Systems Biology Systems Biology Portal www.systems-biology.org HepatoSys - Network Systems Biology SystemsX - The Swiss Initiative in Systems Biology YSBN The Yeast Systems Biology Network Systems Biology Modeling Tools Systems Biology WorkBench SWB 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 CellWare - building computational chassis for systems and synthetic biology 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 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 NCI-3D Search ChemIDplus ChemFinder Searching CHEMINFO: Chemical Information Sources from Indiana University Acronymfinder 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 Genetic Association Database Integrated annotation services NIH - DAVID 2006 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 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 WebGeneMark Eukaryotic WebGeneMark GENSCAN (C. Burge) SplicePredictor Lowe Lab tRNAscan-SE Search Server Rat Genome Database METAGENE Annotation Tool Promotor prediction services CBS NetStart 1.0 server Translation Start CBS Promoter 2.0 server WWW Promotor Scan Pol II EPD Eukaryotic promotor database JASPAR Transcription factor binding profile database TRADAT Transcription Databases and Analysis Tool TFSEARCH - Transcription Factor Search ORegAnno: Open Regulatory Annotation cisRED: cis-regulatory element database MotifMogul - Multiple Transcription Factor Bindin Sites Algorithms Pathways KEGG: Kyoto Encyclopedia of Genes and Genomes ExPASy - Biochemical Pathways BioCarta - Pathways PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System Signaling Gateway - Cell Signaling Resource Nature Reactome Project Pathway Knowledge Base BioCyc Database Collection MetaCyc Encyclopedia of Metabolic Pathways MIM Molecular Interaction Maps at NCI IUPHAR receptor database LGICD Ligand-gated ion-channel database SPAD: Signaling PAthways Database AraCyc - Pathway Database of Arabidopsis thaliana DRASTIC- Database resource for analysis of signal transduction in plant cells Invitrogen iPath Human Biological Pathways BBID-Biological Biochemical Image Database biodirectory - biochemical and metabolic pathways 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 Enzymes Enzyme Database - BRENDA REBASE The Restriction Enzyme Database PRIME Developed Kinase Pathway Database Kinase.com Global kinome analysis IntEnz EBI Enzyme Database Catalytic Site Atlas - CSA (EBI) 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 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 WebLogo Server for Sequence Logos Protein structures RCSB Protein Data Bank Entrez-Structure MSD Macromolecular Structure Database at EBI 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 Domain Structure Database NCBI 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 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 Vector Database 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 Whitehead Institute Broad Institute Center for Genome Research GeneCards Weizmann 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 C.elegans Blast server (Sanger Centre) FlyBase Drosophila Yeast Genome Database MIPS Yeast Protein complex database 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 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 San Diego Supercomputer Center Biological Projects Bielefeld University Bioinformatics Server HUSAR Bioinformatics Lab - Biocomputing Services at DKFZ The Genomics and Bioinformatics Group NCI 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 Apache and HTML Apache SELFHTML MySQL MySQL PHP PHP SELFPHP PHP FAQ phpMyAdmin php-homepage.de - Resource fuer PHP und MySQL PHP-Archiv - PHP Scripts phpwelt Perl and R PERL The Perl directory at perl.org Perl documentation ActiveState - ActivePerl Downloads CPAN PERL Script Archiv Bioperl EMBNet QickGuides PERL and Regular Expressions BioConductor Project - Open Source Software for Bioinformatics BioConductor Course CSAMA June 2007 Brixen The R project for statistical computing The Comprehensive R archive network Open Source Initiative OSI SourceForge.net Open Source Resource Editors The Vim Editor Proton Enote DOE 2000 Electronic Notebook Project ORNL DOE 2000 Electronic Notebook Project Main WETLAB: an open source electronic lab notebook EMBOSS European Molecular Biology Open Software Suite EMBOSS EMBNet Quick Guides EMBOSS and wEMBOSS mEMBOSS for Microsoft Windows Ready-to-install EMBOSS at BioLinux wEMBOSS BioKNOPPIX with JEMBOSS and EMBOSS Bioinformatic System Management Workshop 2005 Open Source Bioinformatics Platforms 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 Bioinformatics Web APIs (nodalpoint wiki)