Bioinformatics

 
Bio-Ontologies

Computational Analysis Tools

ResourceDeveloper
AmiGO (Gene Ontology database search)AmiGO development team
Bioconductor ("provides tools for the analysis and comprehension of high-throughput genomic data" using R)Bioconductor development team
FunDO ("Exploring Genes Using Functional Disease Ontology Annotations")Northwestern University Biomedical Informatics Center
GOFFA - Gene Ontology for Functional AnalysisUSFDA

Information Portals and Databases

ResourceDeveloper
CharProtDB - Characterized Protein DatabaseJ. Craig Venter Institute
ChEBI - Chemical Entities of Biological InterestEMBL-EBI
FlyMine - "integrated database for Drosophila and Anopheles genomics"University of Cambridge, Cambridge, UK
Gene WeaverJackson Laboratory, ME and collaborators
GFBio - German Federation for the curation of Biological dataGFBio
GO Database - Gene Ontology DatabaseGene Ontology Consortium
MouseMine MGI at The Jackson Laboratory and InterMine project at Cambridge Systems Biology Centre, UK
RatMineUniversity of Cambridge, Cambridge, UK
YeastMine ("Search and retrieve S. cerevisiae data")SGD and Intermine project at Cambridge Systems Biology Centre, UK
ZebrafishMineZFIN at University of Oregon and InterMine project at Cambridge Systems Biology Centre, UK
Biomolecular Sequences/Structures

Characterizations and comparisons of biomolecular sequences and structures

Computational Analysis Tools

ResourceDeveloper
7TMRmine ("hierarchical mining tool for 7TMRs")University of Nebraska
ABySS - Assembly By Short SequencesMichael Smith Genome Sciences Centre, Canada and BC Cancer Research Centre
ABySS-Explorer - Assembly By Short Sequences ExplorerMichael Smith Genome Sciences Centre, Canada and BC Cancer Research Centre
Affymetrix GeneChip Sequence Analysis SoftwareAffymetrix
Affymetrix Transcriptome Analysis ConsoleAffymetrix
ALLPATHS-LG ("genome assembly from low cost data")Broad Institute
Alscript ("program to format multiple sequence alignments in PostScript")University of Oxford
Antigenicity PlotLuca Toldo
ARAGORN (tRNA and tmRNA detection)ARAGORN development team
AUGUSTUS ("predicts genes in eukaryotic genomic sequences")University of Göttingen and University of Greifswald, Germany
AutoDock (docking tools suite)The Scripps Research Institute
BicAT - Biclustering Analysis ToolboxETH, Zurich
Bioclipse ("workbench for the life sciences" based on Eclipse Rich Client Platform)Bioclipse development team
Bioconductor ("provides tools for the analysis and comprehension of high-throughput genomic data" using R)Bioconductor development team
Biopython ("tools for biological computation written in Python")Biopython development team
BiQ Analyzer ("software tool for DNA methylation analysis")Max Planck Institute for Informatics, Germany
Bismark (tool to map bisulfite converted sequence reads and determine cytosine methylation states)Babraham Bioinformatics
BLAST - Basic Local Alignment Search Tool (see also PSI-BLAST for Protein Similarity Search)National Center for Biotechnology Information, NLM, NIH
BLAT - BLAST-like Alignment ToolJim Kent
Bowtie (DNA sequence alignment tool)Bowtie development team
Bowtie 2 (sequencing reads to long reference sequences aligner)Bowtie 2 development team
BWA - Burrows-Wheeler AlignerBWA development team
CD-HIT - Cluster Database at High Identity with ToleranceLi group, University of California, San Diego (developed at Burnham Institute)
Chipster ("analysis software for high-throughput data")Kallio, M. A. and Tuimala, J. T. et al., CSC - IT Center for Science, Finland, Finnish Red Cross Blood Service, Finland
CLC Sequence ViewerCLC bio
CLCbio Genomics Workbench (analysis, comparison and visualization of next generation sequencing data)CLCbio
Clustal Omega (Multiple DNA, RNA and protein sequence alignment program)Conway Institute, UCD Dublin
ClustalW2 (see Clustal Omega)EMBL-EBI
CMARRT (A tool for the analysis of ChIP-chip data from tiling arrays by incorporating the correlation structure)Keles Research Group, University of Wisconsin
CNVFinder - Copy Number Variant FinderWellcome Trust Sanger Institute, UK
CompMoby ("detect over-represented motifs in the upstream or 3' UTR sequences of co-expressed genes")QB3 and UCSF
Contrail - To assemble large genomes in the cloudUniversity of MD
CSEM - Multi-read Allocation for ChIP-seqKeles Research Group, University of Wisconsin
Cufflinks - Transcript assembly, differential expression and regulation for RNA-Seq samplesUC Berkeley, JHU, and Caltech
CummeRbund - To analyze Cufflinks RNA-Seq outputMIT and Harvard
DAVID - Database for Annotation, Visualization and Integrated DiscoveryNational Institute of Allergy and Infectious Diseases, NIH
DBChIP - program to detect differentially bound sharp binding sites across multiple conditionsKeles Research Group, University of Wisconsin
DISCOVAR - genome assembler and variant callerBroad Institute
DISCOVAR de novo - Assembler for large genomes up to human sizeBroad Institute
DisEBML ("Intrinsic Protein Disorder Prediction")DisEBML development team, EMBL
EIGENSOFT ("combines functionality from our population genetics methods [...] and our EIGENSTRAT stratification correction method")EIGENSOFT development team, Harvard School of Public Health
EMBOSS - European Molecular Biology Open Software SuiteEMBOSS development team (P. Rice and A. Bleasby et al.)
EpiGRAPH - for advanced (epi-) genome analysis and predictionEpiGRAPH development team
FASTA - DNA and protein sequence alignment software packageEMBL-EBI
FastQC - Quality control tool for high throughput sequence dataBabraham Bioinformatics
FGENESH - "Program for predicting multiple genes in genomic DNA sequences"Softberry, Inc. and The Sanger Centre, Cambridge, UK
FoundationOneFoundation Medicine
Galaxy - web-based platform for data intensive biomedical research ("Online bioinformatics analysis for everyone")Penn State and Emory U.
GATK - Genome Analysis ToolkitBroad Institute
GeneMANIA - "predict the function of [...] genes and gene sets"Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Canada
GeneSpringAgilent Technologies
GeneTalk - "Analyze human sequence variants"GeneTalk development team
GenMAPP - Gene Map Annotator and Pathway ProfilerGladstone Institutes, UCSF
Genotyping ConsoleAffymetrix Inc
GENSCANStanford University (C. Burge and S. Karlin)
Geospiza GeneSifter Analysis EditionPerkin Elmer
geWorkBench - Genomics WorkbenchNCI (National Cancer Institute), NIH
GlimmerHMMCenter for Bioinformatics and Computational Biology, University of Maryland
GMAP - Genomic Mapping and Alignment Program for mRNA and EST SequencesGenentech, Inc., CA
GoMinerNCI (National Cancer Institute), NIH
GPCRHMM - "GPCR detection method"Stockholm Bioinformatics Centre
GPCRTree - "hierarchical classification of GPCR function"University of Oxford, UK
GPUFRAGFOLD - Protein Structure Prediction toolBioinformatics Group, University College London
GRAM - Genetic RegulAtory ModulesGifford Laboratory, MIT
GSNAP - Genomic Short-read Nucleotide Alignment ProgramGenentech, Inc., CA
HDMFinder ("Methylation prediction software")Zhang Lab, Cold Spring Harbor Laboratory, NY
HMMER ("biosequence analysis using profile hidden Markov models")HMMER development team
HMMTOP ("Prediction of transmembrane helices and topology of proteins")HMMTOP team, Institute of Enzymology, Hungary
IDBA-UD - iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing DepthThe Bioinformatics Research Group, University of Hong Kong
IGV - Integrative Genomics ViewerBroad Institute
Illumina GenomeStudioIllumina Software
Infernal - INFERence of RNA ALignmentEddy group, HHMI Janelia Farm Research Campus, VA
Ingenuity Variant AnalysisQiagen
InterProEMBL-EBI
jMOSAiCS - Joint Analysis of Multiple ChIP-seq DatasetsKeles Research Group, University of Wisconsin
JPredBarton Group, University of Dundee
KalignEMBL-EBI
KELVINBattelle Center for Mathematical Medicine, Nationwide Children's Hospital, Ohio
KelvizBattelle Center for Mathematical Medicine, Nationwide Children's Hospital, Ohio
MACS - Model-based Analysis of ChIP-Seq dataHarvard University
MAExplorer - Microarray ExplorerMAExplorer development team
MAKER ("portable and [...] configurable genome annotation pipeline")Yandell Laboratory, University of Utah
Maq - Mapping and Assembly with QualityMaq development team
Maqview - graphical read alignment viewerMaqview development team (Ruan et al.)
MascotMatrix Science
MATLAB Bioinformatics ToolboxThe Mathworks, Inc.
MATLAB Toolboxes (Optimization; Direct Search; Genetic Algorithms)The Mathworks, Inc.
MDscan - Motif Discovery scanStanford Medical Informatics, Stanford University
MEGA - Molecular Evolutionary Genetics AnalysisMEGA team
MEMSAT3 - MEMbrane protein Structure And TopologyMEMSAT team, University College London, UK
MetaQTLMetaQTL development team
Methylator ("An SVM Based Method for DNA Methylation Prediction")Methylator Development Team
MeV - MultiExperiment ViewerMeV development team
Microarray Center cDNA Clone SearchNIEHS
MIDAS - Multi Instance Data Acquisition SystemScience and Technology Facilities Council, UK
MIRA - Whole Genome Shotgun and EST Sequence AssemblerBastien Chevreux
MISO - Mixture of Isoforms ("Probabilistic analysis and design of RNA-Seq experiments for identifying isoform regulation")Burge and Airoldi lab, MIT and Harvard University
MOABS - MOdel based Analysis of Bisulfite Sequencing dataDeqiang Sun, Baylor College of Medicine
MobyDickThe Rockefeller University
modMine ("data warehouse for the modENCODE project")University of Cambridge, Cambridge, UK
Mold2USFDA
MOSAiCS - MOdel-based one and two Sample Analysis and Inference for ChIP-Seq DataKeles Research Group, University of Wisconsin
MrBayesMrBayes development team
mrsFAST (short-read mapper)mrsFAST development team
MUSCLE - MUltiple Sequence Comparison by Log- ExpectationEMBL-EBI
NCBI/ Primer-BLASTNational Center for Biotechnology Information, NLM, NIH
NetRecodonNetRecodon development team
Newbler ("software package for de novo DNA sequence assembly")454 Life Sciences, Roche Diagnostics Corporation
NovoalignNovocraft Technologies
NucDe - A non-homogeneous hidden-state model on first order differences for automatic detection of nucleosome positions from MNase-chip and MNase-seq dataKeles Research Group, University of Wisconsin
NuPoP - Nucleosome Positioning Prediction EngineNorthwestern University (J.-P. Wang)
OptiRNAUniversity of Nebraska
PaGE - Patterns from Gene ExpressionPaGE development team, University of Pennsylvania
PAM - Prediction Analysis for MicroarraysStanford University
pepgrepUniversity of Essex
Persephone ("Genome Visualization & Exploration Software")Ceres, Inc.
PFAAT - Protein Family Alignment Annotation ToolPFAAT development team
PhyMLS. Guindon, et al., CNRS
PhyreStructural Bioinformatics Group, Imperial College, London
picard ("A set of Java command line tools for manipulating high-throughput sequencing data (HTS) data and formats")Broad Institute and picard development team
PLINK ("Whole genome association analysis toolset")PLINK development team, CHGR - Massachusetts General Hospital, Boston, MA
PolyBayes ("automated analysis of single-nucleotide polymorphism (SNP) discovery in redundant DNA sequences")Washington University Genome Sequencing Center
Polyphred (single nucleotide substitution identification)University of Washington (Brent Ewing, Phil Green, David Gordon et al.)
PRED-GPCRUniversity of Athens, Greece
PredictProteinROSTLAB
Protein ProspectorUCSF
PSI-BLAST - Protein Similarity Search BLASTEMBL-EBI
QTDT (Linkage Disequilibrium Analyses for Quantitative and Discrete Traits)Abecasis Lab, University of Michigan
QTXQTX development team
QuEST - Quantitative Enrichment of Sequence TagsStanford University
Ray (Assembly of reads obtained with sequencing technologies) S. Boisvert, F. Laviolette, J. Corbeil
Reaxys system (Search substances, reactions, citations, patents, etc.)Reaxys development team
REDUCEHarmen Bussemaker Laboratory, Columbia University
RMAP (next-generation sequencing read mapper)Cold Spring Harbor Laboratory, NY and USC, CA
RNA CoMPASS - RNA Comprehensive Multi-Processor Analysis System for SequencingGuorong Xu and RNA CoMPASS development team
SAMBAShamir Laboratory, Tel Aviv University
SAMtools - Sequence Alignment/MapLi et al., Wellcome Trust Sanger Institute, UK and Broad Institute of MIT and Harvard, USA
SANDYGerstein Laboratory, Yale University
SCAMPI ("Prediction of membrane protein topology")Stockholm Bioinformatics Center, Stockholm University
SCOP - Structural Classification of ProteinsMRC Laboratory of Molecular Biology
SEQUESTYates Laboratory, University of Washington
Shape SignaturesWelsh Laboratory, RWJMS
SICER ("clustering approach for identification of enriched domains from histone modification ChIP-Seq data")W. Peng lab, George Washington University
SMART-BS-Seq - Specific Methylation Analysis and Report Tool for BS-Seq dataPython Software Foundation
SNAP - Screening for Non-Acceptable PolymorphismsRost Lab, Columbia University, New York
SNAP - SNP Annotation and Proxy SearchSNAP Development Team
SNP-o-matic (analysis of Solexa reads and comparison with reference)Sanger Institute
SNPTrackUSFDA
SOAP - Short Oligonucleotide Analysis PackageBeijing Genomics Institute
SOAPdenovo2 (Large-size genome de-novo assembler)Ruibang Luo, et al., Tai Po Industrial Estate
SOPRA - Scaffolding algorithm for paired reads via statistical optimizationA. Sengupta lab, Rutgers University
SOSUI ("predicts a part of the secondary structure of proteins from a given amino acid sequence")Tokyo University
SSEARCH (sequence similarity search)SSEARCH team
STRING - Search Tool for the Retrieval of Interacting Genes/ProteinsSTRING Team
SUCcESS (Integration of quantitative information from ChIP-chip experiments into motif finding)Keles Research Group, University of Wisconsin
SYBYL ("Molecular Modeling from Sequence through Lead Optimization")Certara, L.P. and Tripos
T-CoffeeEMBL-EBI
THREADER (Protein Structure Prediction tool)Bioinformatics Group, University College London
TileHGMM (Mixture modeling for genome-wide localization of transcription factors)Keles Research Group, University of Wisconsin
TMFinder ("Trans-Membrane protein prediction tool")TM-Finder development team and The Hospital for Sick Children (SickKids)
TopHat (spliced read mapper for RNA-Seq)JHU Center for Computational Biology
TopPred ("Topology prediction of membrane proteins")TopPred development team
TopSpin (NMR data analysis and acquisition and processing of NMR spectra)Bruker Corporation
ToxmatchJoint Research Centre, IHCP
Trinity RNA-Seq Assembly Broad Institute, Hebrew University of Jerusalem and Trinity Developers Group
Trinotate ("Transcriptome Functional Annotation and Analysis")Trinotate development team
Tute ("web application [...] in the cloud and [...] analyze and annotate entire human genomes")Tute Genomics
Twinscan/N-SCAN ("gene-structure prediction")Brent Lab, Washington University in St. Louis
VEGAS - Versatile Gene-based Association StudyVEGAS development team, Queensland Institute of Medical Research, Australia
Velvet ("Sequence assembler for very short reads")EMBL-EBI
X!TandemThe Global Proteome Machine Organization

Information Portals and Databases

ResourceDeveloper
Alu Pairs DatabaseNIEHS
ASAP - A Systematic Annotation Package For Community Analysis of GenomesUniversity of Wisconsin, Madison
Berkeley Drosophila Genome ProjectBerkeley Drosophila Genome Project Consortium
BioGPS ("gene annotation portal")BioGPS development team
Blocks Database ("sequence analysis"; no longer updated)Fred Hutchinson Cancer Research Center
BOND - Biomolecular Object Network DatabankThomson
BRENDA - BRaunschweig ENzyme DAtabaseD. Schomburg, Technische Universität Braunschweig, Germany
Cambridge Structural DatabaseCambridge Crystallographic Data Centre
CATH ("Protein Structure Classification Database")University College, London
CharProtDB - Characterized Protein DatabaseJ. Craig Venter Institute
ChemBankBroad Institute
ChromDB - The Chromatin DatabaseBIO5 Institute
CluSTrEMBL-EBI
CNV Project Data - Copy Number Variation Project DataWellcome Trust Sanger Institute, UK
COG - Clusters of Orthologous Groups of proteinsNational Center for Biotechnology Information, NLM, NIH
CpGislandEVO (A database for comparing evolutionary genomics of CpG islands)Computational Genomics and Bioinformatics Group, University of Granada and Inst. of Biotechnology, Granada, Spain (Barturen et al.)
Database of Macromolecular MovementMark Gerstein, et al., Yale University
DBCAT - DataBase of CpG islands and Analytical ToolResearch Center for Medical Excellence National Taiwan University
dbGaP - Database of Genotypes and PhenotypesNational Center for Biotechnology Information, NLM, NIH
dbSNPNational Center for Biotechnology Information, NLM, NIH
DiseaseMeth - human disease methylation databaseCollege of Bioinformatics Sci. and Tech., Harbin Medical U., China
EMDataBank ("Unified Data Resource for 3-Dimensional Electron Microscopy")Protein Databank in Europe (PDBe), European Bioinformatics Institute; Research Collaboratory for Structural Bioinformatics (RCSB), Rutgers, and National Center for Macromolecular Imaging (NCMI), Baylor College of Medicine
ENA - European Nucleotide ArchiveEMBL-EBI
ENCODE - Encyclopedia Of DNA ElementsNHGRI, NIH
Ensembl Genome BrowserEMBL-EBI and Wellcome Trust Sanger Institute, UK
GBrowse (Generic Genome Browser)GBrowse development team
GenBankNational Center for Biotechnology Information, NLM, NIH
Genetic Association DatabaseGAD development team and NIH
Genomatix SuiteGenomatix Software GmbH
GLIDA - GPCR-Ligand DatabaseKyoto University
GOLD - Genomes Online DatabaseGOLD Team
GPCR NaVa database - G Protein-Coupled Receptors Natural Variants databaseLeiden/Amsterdam Center for Drug Research and Leiden Institute of Advanced Computer Science
GPCR SARfari ("integrated chemogenomics research and discovery workbench for Class A G Protein Coupled Receptors")EMBL-EBI
GPCRDB - G Protein-Coupled Receptor Data BaseGPCRDB development team
GPCR-OKB - G Protein Coupled Receptor - Oligomer Knowledge BaseGPCR-OKB development team
GPCR-PD ("database for G protein-coupled receptors")Incyte Genomics
GVS - Genome Variation ServerUniversity of Washington
HapMapInternational HapMap Project
HGMD - Human Gene Mutation Database (integrated with Ingenuity Variant Analysis) BIOBASE
Histone DatabaseNHGRI Division of Intramural Research, NIH
HIV Sequence databaseLos Alamos National Laboratory
HomoloGeneNational Center for Biotechnology Information, NLM, NIH
Human DNA Polymerase Gamma Mutation DatabaseNIEHS
Human Genome BrowserGenome Bioinformatics Group, UC Santa Cruz.
HuRef Genome Browser (Individual Human Genome Browser)J. Craig Venter Institute
IMGT - ImMunoGeneTics information systemMarie-Paule Lefranc
IMGT/3Dstructure-DB - ImMunoGeneTicsMarie-Paule Lefranc
Integr8EMBL-EBI
InterProEMBL-EBI
iProClassPIR - Protein Information Resource
IRD - Influenza Research DatabaseIRD Project Team
JSNP - Japanese Single Nucleotide PolymorphismsUniversity of Tokyo and the Japan Science and Technology Agency (JST)
KEGG GENES databaseKanehisa Laboratories, Japan
LMPD - LIPID MAPS Proteome DatabaseUniversity of California, San Diego
LMSD - LIPID MAPS Structure DatabaseUniversity of California, San Diego
MethBase - a reference methylome databaseSmith lab, Molecular and Computational Biology, U. of Southern California
MethylomeDB - Brain Methylome DatabaseHaghighi lab, Columbia University
MGI - Mouse Genome InformaticsThe Jackson Laboratory, Maine and MGI team
MINT - Molecular INTeraction databaseUniversity of Rome Tor Vergata, Italy
miRBase - microRNA databaseGriffiths-Jones lab, U. of Manchester and Wellcome Trust Sanger Institute
miRBase ("the microRNA database")University of Manchester, UK
MMDB - Molecular Modeling Database (NCBI Structure)National Center for Biotechnology Information, NLM, NIH
modENCODE - Model Organism ENCyclopedia Of DNA ElementsmodENCODE Project Consortium
Mouse Genome Resequencing ProjectNIEHS
NCBI GeneNational Center for Biotechnology Information, NLM, NIH
NCBI Model Organisms GuideNational Center for Biotechnology Information, NLM, NIH
NCBI Nucleotide Sequence DatabaseNational Center for Biotechnology Information, NLM, NIH
NCI DIS 3D - National Cancer Institute Drug Information System 3D structure databaseNCI (National Cancer Institute), NIH
NDB - Nucleic Acid Database ("A Portal for Three-dimensional Structural Information about Nucleic Acids")The Nucleic Acid Database Project, Rutgers University
NGSmethDB - A database for next-generation sequencing single-cytosine-resolution DNA methylation databaseComputational Genomics and Bioinformatics Group, U. Granada, Spain
NIEHS SNPs Exome Variant ServerNIEHS and University of Washington
OChem - Online Chemical databaseeADMET GmbH, Germany
ORDB - Olfactory Receptor DataBaseYale University
Pan Asian SNP DatabasePan-Asian SNP Consortium
PDB - Protein Data BankRCSB PDB (Rutgers University, UCSD)
Peptide AtlasPeptideAtlas team, Institute for Systems Biology
Persephone ("Genome Visualization & Exploration Software")Ceres, Inc.
Pfam ("collection of protein families, each represented by multiple sequence alignments and hidden Markov models")Wellcome Trust Sanger Institute, UK and Howard Hughes Janelia Farm Research Campus, US
RefSeq - NCBI Reference Sequence DatabaseNational Center for Biotechnology Information, NLM, NIH
RGD - Rat Genome DatabaseMedical College of Wisconsin
RNA World ("collection of links to RNA-related information")Leibniz Institute for Age Research, FLI, Germany and RNA World team
SBKB - Structural Biology KnowledgebaseProtein Structure Initiative and Nature Publishing Group
SCAN ("SNP and CNV Annotation Database")The University of Chicago
SEVENS database ("summarizes GPCR (G-protein coupled receptor) genes that are identified [...] from [...] eukaryote genomes")Computational Biology Research Center, AIST, Japan
SGD - Saccharomyces Genome DatabaseStanford University
SNP500CancerSAIC-Frederick, NCI-FCRDC, MD
SNPinfo Web ServerNIEHS
SpringerProtocolsSpringer-Verlag
Structural Biology Software DatabaseTheoretical and Computational Biophysics Group, University of Illinois
TransFacGene Regulation
UniSTS ("database of sequence tagged sites")National Center for Biotechnology Information, NLM, NIH
VEGA - Vertebrate Genome AnnotationHAVANA group, Wellcome Trust Sanger Institute, UK
ViPR - Virus Pathogen ResourceViPR Project team
WormBaseWormBase development team
wwPDB - Worldwide Protein Data BankRCSB PDB, USA, PDBe, Europe, PDBj, Japan and BMRB, USA
ZebrafishMineZFIN at University of Oregon and InterMine project at Cambridge Systems Biology Centre, UK
Interactions/Biopathways/Bionetworks

Characterization of biomolecular interactions, pathways, and networks

Computational Analysis Tools

ResourceDeveloper
Accelerated Stochastic Simulation Algorithm for Reaction NetworksUniversity of California, Irvine
atBioNet ("an Integrated Network Analysis Tool […] in Genomics and Proteomics")USFDA
BioLayout Express3D ("visualization and analysis of network graphs")BioLayout Express3D Team
BioPAX - Biological Pathway ExchangeBioPAX development team
Bio-PEPA WorkbenchBio-PEPA development team
BioTapestry ("tool for building, visualizing, and simulating [...] networks")Institute for Systems Biology, Davidson Laboratory at Caltech
bsim-bccs ("Models the stochastic interactions of bacteria and particles in a fluid based environment")bsim-bccs development team
Cain ("Stochastic Simulations for Chemical Kinetics")Cain development team (Sean Mauch et al.)
CellDesignerSystems Biology Institute, Japan
CellNetAnalyzer / FluxAnalyzerMax Planck Institute
CellNetOptimizerCellNOpt development team
Cognoscente ("database and visualization tool for biomolecular interactions [...] in the literature")VanBuren laboratory, Texas A&M Health Science Center
COPASI - Complex Pathway Simulator ("successor of Gepasi")Virginia Bioinformatics Institute, Virginia Tech
CySBGN ("SBGN diagrams in Cytoscape")CySBGN development team, Saez-Rodriguez Group, EMBL-EBI
Discrete Dynamics Lab ("Tools for researching Cellular Automata, Random Boolean Networks, multi-value Discrete Dynamical Networks, and beyond")DDLab development team
DisEBML ("Intrinsic Protein Disorder Prediction")DisEBML development team, EMBL
Dynamic Signaling MapsHippron Physiomics Inc
DyneticaDuke University
Ecolab ("software package [...] looking at the dynamics of evolution")Ecolab development team
Edinburgh Pathway EditorEPE development team
EMBOSS - European Molecular Biology Open Software SuiteEMBOSS development team (P. Rice and A. Bleasby et al.)
EPPIC - Evolutionary Protein-Protein Interface Classifier (interface classification in protein crystal lattice to determine biological relevance)Paul Scherrer Institut & SyBIT, Zurich (G. Capitani)
FluxMap - "VANTED add-on for the visual exploration of flux distributions in biological networks"Plant Bioinformatics Group, Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben, Germany
Gene Network Inference ToolUniversity of California, Irvine
Genes2FANsSBCNY and Mount Sinai School of Medicine
GenMAPP - Gene Map Annotator and Pathway ProfilerGladstone Institutes, UCSF
Gepasi (see COPASI)Virginia Bioinformatics Institute, Virginia Tech
geWorkBench - Genomics WorkbenchNCI (National Cancer Institute), NIH
GNA - Genetic Network AnalyzerIbis
GRAM - Genetic RegulAtory ModulesGifford Laboratory, MIT
IPA - Ingenuity Pathway AnalysisQiagen N.V.
iPathwayGuideAdvaita Corporation
iPathwaysThe Systems Biology Institute, Japan
iTOL - Interactive Tree Of LifeEMBL, Germany
Maximally Informative GenesAndroulakis Laboratory, Rutgers University
MetaCoreThomson Reuters
MetaMerge (reconcile differences in existing metabolic network models)MetaMerge development team
MeteorLhasa Limited
MetNetGEIowa State University
MgenomeGu Laboratory, Iowa State University
MONGOOSE - MetabOlic Network GrOwth Optimization Solved ExactlyMONGOOSE development team, MIT
Moose - Multiscale Neuroscience and Systems Biology SimulatorMoose team
NetworkFluxus Technology Ltd.
NEURON ("for empirically-based simulations of neurons and networks of neurons")NEURON development team
NSL - Neural Simulation LanguageNSL Development Team
OmixPeter Droste
OpenFLUX ("MATLAB-based modelling software for 13C metabolic flux analysis")OpenFLUX development team
OspreySamuel Lunenfeld Research Institute, Canada
PathVisio ("a tool to edit and analyze biological pathways")PathVisio development team
Pathway CommonsMemorial Sloan-Kettering Cancer Center and University of Toronto
Pathway Map CreatorThomson Reuters
Pathway ProcessorIstituto Agrario di San Michele all’Adige, Italy
Pathway StudioPathway Studio
Pathway ToolsPathway Tools development team
PathwayLab - in silico pathway analysis toolInnetics
PHYLIP - PHYLogeny Inference PackageUniversity of Washington
REDUCEHarmen Bussemaker Laboratory, Columbia University
SAMBAShamir Laboratory, Tel Aviv University
SANDYGerstein Laboratory, Yale University
SBGN-ED ("Edit, translation and validation of SBGN Maps")Plant Bioinformatics Group, Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben, Germany
Sets2NetworksSBCNY and Mount Sinai School of Medicine
SimBiology app for MATLAB ("Model, simulate, and analyze biological systems")The MathWorks, Inc.
SMBioNetUniversity of Nice, France
SNIP - S-Space Network Inference ProcedureRabitz Laboratory, Princeton University
StarNet 2 ("query and visualization tool for precomputed correlation data derived from [...] published microarray data")VanBuren laboratory, Texas A&M Health Science Center
STITCH - Search Tool for Interactions of ChemicalsSTITCH development team
SubMAP - Subnetwork Mappings in Alignment of PathwaysBioinformatics Lab, University of Florida
TargetPCenter for Biological Sequence Analysis, Technical University of Denmark
VANTED - Visualization and Analysis of Networks containing Experimental DataPlant Bioinformatics Group, Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben, Germany
visANTBoston University

Information Portals and Databases

ResourceDeveloper
BBID - Biological Biochemical Image DatabaseNIA, Intramural Research Program
BIND - Biomolecular Interaction Network DatabaseChristopher Hogue's Research Laboratory
BioCartaBioCarta LLC
Biocatalysis/ Biodegradation DatabaseUniversity of Minnesota
BioGRID - Biological General Repository for Interaction DatasetsBioGRID Team
Cognoscente ("database and visualization tool for biomolecular interactions [...] in the literature")VanBuren laboratory, Texas A&M Health Science Center
eggNOG - evolutionary genealogy of genes: Non-supervised Orthologous GroupsEMBL, Germany
FlyMine - "integrated database for Drosophila and Anopheles genomics"University of Cambridge, Cambridge, UK
gpDB - "database of GPCRs, G-proteins, effectors and their interactions"University of Athens, Greece
HumanCycSRI International
Human-gpDB ("database of human GPCRs, G-proteins, Effectors and their interactions")Human-gpDB team
KEGG - Kyoto Encyclopedia of Genes and GenomesKanehisa Laboratories, Japan
KEGG GENES databaseKanehisa Laboratories, Japan
KUPKB - The Kidney and Urinary Pathway Knowledge BaseINSERM, France and University of Manchester, UK
MetaCycSRI International
MetNetDB - MetNet DatabaseIowa State University
MGI - Mouse Genome InformaticsThe Jackson Laboratory, Maine and MGI team
MINT - Molecular INTeraction databaseUniversity of Rome Tor Vergata, Italy
MouseMine MGI at The Jackson Laboratory and InterMine project at Cambridge Systems Biology Centre, UK
OrthoDBUniversity of Geneva Medical School, Switzerland
PANTHER - Protein ANalysis THrough Evolutionary RelationshipsPANTHER development team (Paul Thomas)
PathArtJubilant Biosys
PathCase Pathways Database SystemCase Western Reserve University
Pathway DatabaseProtein Lounge
PD map - Parkinson’s disease mapLCSB and Hiroaki Kitano team at SBI, Tokyo
PID - Pathway Interaction DatabaseNCI (National Cancer Institute), NIH
RatMineUniversity of Cambridge, Cambridge, UK
ReactomeReactome team
RGD - Rat Genome DatabaseMedical College of Wisconsin
SGD - Saccharomyces Genome DatabaseStanford University
SPAD - Signaling Pathway DatabaseKyushu University
SpringerProtocolsSpringer-Verlag
TransFacGene Regulation
TransPathGene Regulation
YeastMine ("Search and retrieve S. cerevisiae data")SGD and Intermine project at Cambridge Systems Biology Centre, UK
YEASTNET ("A consensus reconstruction of yeast metabolism")Yeastnet development team
Biological Dose-Response

Characterization of biological dose-response to internal and external physical, chemical, and biological stimuli (including energy, nutrients, food additives, pharmaceuticals, allergens, pathogens, etc.) in genomic/transcriptomic, epigenomic, proteomic, metabolomic, cytomic, and histomic systems [see also Toxicoinformatics, for tools characterizing dose-response to environmental toxics]

Computational Analysis Tools

ResourceDeveloper
ADME Workbench ("pharmacokinetic modeling by integrating [...] absorption, distribution, metabolism and excretion methods")The AEgis Technologies Group
Affymetrix Expression ConsoleAffymetrix
Affymetrix Transcriptome Analysis ConsoleAffymetrix
ArrayTrack/ebTrackUSFDA and ebCTC
Automated Particle Tracking and Analysis SoftwareUniversity of California, Irvine
Bismark (tool to map bisulfite converted sequence reads and determine cytosine methylation states)Babraham Bioinformatics
BMDExpress ("analyze microarray dose-response data")BMDExpress team
BRB-ArrayToolsDr. Richard Simon and BRB-ArrayTools Development Team
Chipster ("analysis software for high-throughput data")Kallio, M. A. and Tuimala, J. T. et al., CSC - IT Center for Science, Finland, Finnish Red Cross Blood Service, Finland
Cloe PredictCyprotex
CMARRT (A tool for the analysis of ChIP-chip data from tiling arrays by incorporating the correlation structure)Keles Research Group, University of Wisconsin
CombiToolLeibniz Institute for Age Research - FLI, Germany
CSEM - Multi-read Allocation for ChIP-seqKeles Research Group, University of Wisconsin
Cufflinks - Transcript assembly, differential expression and regulation for RNA-Seq samplesUC Berkeley, JHU, and Caltech
CVSimCVSim development team
DBChIP - program to detect differentially bound sharp binding sites across multiple conditionsKeles Research Group, University of Wisconsin
dChip - DNA-Chip AnalyzerHarvard University and Stanford University
Decision ForestUSFDA
Disease/ Phenotype web-PAGE ("disease based gene set analysis of microarray gene expression")Gene Expression and Genomics Unit, NIA, NIH
DORIAN - DOse-Response Information ANalysis systemComputational Chemodynamics Laboratory
ELECANS - A Computational Cancer Systems Biology Simulation StudioDepartment of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Korea
EMBERUniversity of Chicago
EpiGRAPH - for advanced (epi-) genome analysis and predictionEpiGRAPH development team
EpiSIM PlatformTIGA Center Heidelberg, Germany
Galaxy - web-based platform for data intensive biomedical research ("Online bioinformatics analysis for everyone")Penn State and Emory U.
GMC impute - Gaussian mixture clustering imputeComputational Chemodynamics Laboratory
GSEA - Gene Set Enrichment AnalysisBroad Institute
IGV - Integrative Genomics ViewerBroad Institute
IPA - Ingenuity Pathway AnalysisQiagen N.V.
J/maanovaChurchill Group, Jackson Laboratory
Java Treeview ("Viewer for Microarray Data in the PCL or CDT format")Stanford University School of Medicine (A. J. Saldanha) and Java Treeview development team
jMOSAiCS - Joint Analysis of Multiple ChIP-seq DatasetsKeles Research Group, University of Wisconsin
MAQC - MicroArray Quality ControlUSFDA
MATLAB Bioinformatics ToolboxThe Mathworks, Inc.
maxdViewManchester Bioinformatics
MethToolsLeibniz Institute for Age Research - Fritz Lipmann Institute, Germany
MOABS - MOdel based Analysis of Bisulfite Sequencing dataDeqiang Sun, Baylor College of Medicine
Monocle - toolkit for analyzing single-cell gene expression experimentsCole Trapnell
MOSAiCS - MOdel-based one and two Sample Analysis and Inference for ChIP-Seq DataKeles Research Group, University of Wisconsin
NucDe - A non-homogeneous hidden-state model on first order differences for automatic detection of nucleosome positions from MNase-chip and MNase-seq dataKeles Research Group, University of Wisconsin
OmicsOffice for MicroarraysIntegromics
Pathway StudioPathway Studio
Persephone ("Genome Visualization & Exploration Software")Ceres, Inc.
ProteoIQ ("qualitative and quantitative suite for proteomics")Premier Biosoft
R/maanovaChurchill Group, Jackson Laboratory
RealTimeDesign SoftwareBiosearch Technologies
SBPOP Package ("Support for Model Based Drug Development – From Mechanistic Models to Complex Trial Simulation")SBPOP Package development team at Novartis Pharma AG Modeling & Simulation
SimBiology app for MATLAB ("Model, simulate, and analyze biological systems")The MathWorks, Inc.
SMART-BS-Seq - Specific Methylation Analysis and Report Tool for BS-Seq dataPython Software Foundation
SPELL - Serial Pattern of Expression Levels LocatorPrinceton University
SPLS - Sparse partial least squaresKeles Research Group, University of Wisconsin
SUCcESS (Integration of quantitative information from ChIP-chip experiments into motif finding)Keles Research Group, University of Wisconsin
TileHGMM (Mixture modeling for genome-wide localization of transcription factors)Keles Research Group, University of Wisconsin
ToxFXNIEHS
WebArrayWebArray project team

Information Portals and Databases

ResourceDeveloper
ACToR - Aggregated Computational Toxicology ResourceUSEPA
AHEAD - Alliance for Human Epigenomics and DiseaseAHEAD Task Force
AOPWiki - Adverse Outcome Pathway WikiAOPWiki team (includes European Commission JRC, USEPA ORD and OECD)
ArrayExpressEMBL-EBI
Berkeley Drosophila Genome ProjectBerkeley Drosophila Genome Project Consortium
Biomarkers Database (last updated in August 2004)USEPA
BioNumbers ("The Database of Useful Biological Numbers")Weizmann Institute, Israel
BOSS - Biomarkers of Oxidative Stress StudyNIEHS
CEBS - Chemical Effects in Biological SystemsNIEHS
CGAP - Cancer Genome Anatomy ProjectNCI (National Cancer Institute), NIH
ChIPBase ("decoding transcription factor binding maps [...] and transcriptional regulation [...] from ChIP-Seq data")Qu lab at Sun Yat-sen University (J. Yang)
Comparative Toxicogenomics DatabaseMount Desert Island Biological Laboratory
CREMOFAC - Chromatin Remodeling FactorsChromatin Biology Lab, Jawaharlal Nehru Centre for Advanced Scientific Research, India
DrugMatrixNIEHS
EADB - Estrogenic Activity DatabaseUSFDA
EDKB - Endocrine Disruptor Knowledge BaseUSFDA
EMAGE - e-Mouse Atlas of Gene ExpressionEMAGE team
FDALabel - Full-Text Search of Drug Label DatabaseUSFDA
FlyMine - "integrated database for Drosophila and Anopheles genomics"University of Cambridge, Cambridge, UK
GAC - Genetic Alterations in CancerNIEHS
GeMDBJ - Genome Medicine Database of JapanSGMGP (The Study Groups of Millennium Genome Project for Alzheimer's disease, Cancer, Diabetes Mellitus, Hypertension, Asthma and Pharmacogenetics)
Gene Expression AtlasEMBL-EBI
Gene WeaverJackson Laboratory, ME and collaborators
GeneToxNLM
Genomatix SuiteGenomatix Software GmbH
GENSAT - Gene Expression Nervous System ATlas databaseRockefeller University
HEP - Human Epigenome ProjectHEP Consortium
HEROIC - High-Throughput Epigenetic Regulatory Organization in Chromatin ProjectHEROIC Project Consortium
HGMD - Human Gene Mutation Database (integrated with Ingenuity Variant Analysis) BIOBASE
Human Epigenome AtlasBioinformatics Research Laboratory, Baylor College of Medicine
ICRP - International Commission on Radiological Protection - Database of Dose CoefficientsICRP
IRIS - Integrated Risk Information SystemUSEPA
LIVERTOX™NIDDK and NLM
LTKB - Liver Toxicity Knowledge BaseUSFDA
Mammalian Protein-Protein Interaction DatabaseMunich Information Center for Protein Sequences (MIPS), Institute of Bioinformatics and Systems Biology (IBIS), Germany
MeInfoTextNational Taiwan University
MethDB - database for DNA methylation and environmental epigenetic effectsMethDB team
MethPrimerDBGhent University, Belgium
MethyCancer - Database for studying human DNA Methylation and CancerChinese Academy of Sciences
MethyLogiX DNA methylation databaseEpigenetics Group, Technical University of Munich, Germany (A. Schumacher)
MGI - Mouse Genome InformaticsThe Jackson Laboratory, Maine and MGI team
microRNA.org
MouseMine MGI at The Jackson Laboratory and InterMine project at Cambridge Systems Biology Centre, UK
NCBI EpigenomicsNational Center for Biotechnology Information, NLM, NIH
NCBI GEO - NCBI Gene Expression Omnibus databaseNational Center for Biotechnology Information, NLM, NIH
NIH Roadmap Epigenomics Project DataNational Center for Biotechnology Information, NLM, NIH
OncomineLife Technologies Corporation
Persephone ("Genome Visualization & Exploration Software")Ceres, Inc.
Personalized Medicine Research Project population-based bio-bankMarshfield Clinic Research Foundation
PubMedNational Center for Biotechnology Information, NLM, NIH
PubMethBioBix, Laboratory for Bioinformatics and Computational Genomics, Ghent University, Belgium
PUMAdb - Princeton University MicroArray database (supersedes SMD)Princeton University
RatMineUniversity of Cambridge, Cambridge, UK
REBASE - The Restriction Enzyme dataBASENew England Biolabs, Inc. (Roberts, R.J., Macelis, D.)
RNAi databaseNYU's Center for Genomics & Systems Biology
Roadmap Epigenomics Project DataNIEHS
RUCDR - Rutgers University Cell and DNA RepositoryRUCDR Team
SGD - Saccharomyces Genome DatabaseStanford University
SMD - Stanford Microarray Database (see PUMAdb)Stanford University
SpringerProtocolsSpringer-Verlag
StemBase (gene expression data obtained from stem cells)Canadian Stem Cell Network
TissueDistributionDBsGerman Cancer Research Center, DKFZ, Heidelberg
ToxCast - Toxicity ForecasterUSEPA
UCSC Genome BrowserGenome Bioinformatics Group, UC Santa Cruz
WashU Epigenome BrowserWashington University
YeastMine ("Search and retrieve S. cerevisiae data")SGD and Intermine project at Cambridge Systems Biology Centre, UK
Data Integration

Data integration across biological scales

Computational Analysis Tools

ResourceDeveloper
ADZE - Allelic Diversity AnalyZErStanford University
AFLP-SURV ("estimates genetic diversity and population genetic structure from population samples analysed with AFLP or RAPD methods")Xavier Vekemans
atBioNet ("an Integrated Network Analysis Tool […] in Genomics and Proteomics")USFDA
Automated Particle Tracking and Analysis SoftwareUniversity of California, Irvine
Biopython ("tools for biological computation written in Python")Biopython development team
CellSysInterdisciplinary Centre for Bioinformatics, University of Leipzig, Germany
Chaste ("general purpose simulation package [...] in biology and physiology")Computational Biology Group, Dept. of Computer Science, University of Oxford
DAVID - Database for Annotation, Visualization and Integrated DiscoveryNational Institute of Allergy and Infectious Diseases, NIH
ELECANS - A Computational Cancer Systems Biology Simulation StudioDepartment of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Korea
EpiSIM PlatformTIGA Center Heidelberg, Germany
FoundationOneFoundation Medicine
Gene Network Inference ToolUniversity of California, Irvine
Gwyddion ("a modular program for SPM (scanning probe microscopy) data visualization and analysis")Gwyddion development team
KELVINBattelle Center for Mathematical Medicine, Nationwide Children's Hospital, Ohio
KelvizBattelle Center for Mathematical Medicine, Nationwide Children's Hospital, Ohio
Literature LabAcumenta Biotech
Morpheus ("modeling and simulation environment for the study of multiscale and multicellular systems")Center for Information Services and High Performance Computing, Technische Universität Dresden, Germany
Nemo - "forward-time, individual-based, genetically explicit, and stochastic simulation program"Nemo development team (F. Guillaume et al.)
NewHybridsNewHybrids development team
QTDT (Linkage Disequilibrium Analyses for Quantitative and Discrete Traits)Abecasis Lab, University of Michigan
TavernamyGrid, University of Manchester
Tute ("web application [...] in the cloud and [...] analyze and annotate entire human genomes")Tute Genomics
X-TileYale University

Information Portals and Databases

ResourceDeveloper
Biocatalysis/ Biodegradation DatabaseUniversity of Minnesota
BioGRID - Biological General Repository for Interaction DatasetsBioGRID Team
BioNumbers ("The Database of Useful Biological Numbers")Weizmann Institute, Israel
CEBS - Chemical Effects in Biological SystemsNIEHS
ChIPBase ("decoding transcription factor binding maps [...] and transcriptional regulation [...] from ChIP-Seq data")Qu lab at Sun Yat-sen University (J. Yang)
ChromDB - The Chromatin DatabaseBIO5 Institute
COG - Clusters of Orthologous Groups of proteinsNational Center for Biotechnology Information, NLM, NIH
CREMOFAC - Chromatin Remodeling FactorsChromatin Biology Lab, Jawaharlal Nehru Centre for Advanced Scientific Research, India
dbGaP - Database of Genotypes and PhenotypesNational Center for Biotechnology Information, NLM, NIH
DiseaseMeth - human disease methylation databaseCollege of Bioinformatics Sci. and Tech., Harbin Medical U., China
EMA - e-Mouse AtlasEMA team
ESCAPE - Embryonic Stem Cells Atlas of Pluripotency EvidenceSBCNY and Mount Sinai School of Medicine
gpDB - "database of GPCRs, G-proteins, effectors and their interactions"University of Athens, Greece
GWAS Catalog - Genome-Wide Association Studies CatalogNHGRI Division of Genomic Medicine, NIH
GWASdbGWASdb team
Histone DatabaseNHGRI Division of Intramural Research, NIH
Human Epigenome AtlasBioinformatics Research Laboratory, Baylor College of Medicine
Human-gpDB ("database of human GPCRs, G-proteins, Effectors and their interactions")Human-gpDB team
IUPHAR-DB - International Union of Basic and Clinical Pharmacology DatabaseIUPHAR-DB development team
KEGG - Kyoto Encyclopedia of Genes and GenomesKanehisa Laboratories, Japan
KUPKB - The Kidney and Urinary Pathway Knowledge BaseINSERM, France and University of Manchester, UK
LMPD - LIPID MAPS Proteome DatabaseUniversity of California, San Diego
LMSD - LIPID MAPS Structure DatabaseUniversity of California, San Diego
MeInfoTextNational Taiwan University
MethDB - database for DNA methylation and environmental epigenetic effectsMethDB team
MethPrimerDBGhent University, Belgium
MGI - Mouse Genome InformaticsThe Jackson Laboratory, Maine and MGI team
microBEnet - microbiology of the Built Environment networkEisen Lab at University of California, Davis and Building Ecology Research Group
NCBI EpigenomicsNational Center for Biotechnology Information, NLM, NIH
NIMH-RGR Data ExplorerNIMH Center for Collaborative Genomic Studies on Mental Disorders
OmicBrowseGenome-Phenome Superbrain Project
OMIM - Online Mendelian Inheritance in Man ("Online Catalog of Human Genes and Genetic Disorders")Johns Hopkins University and NCBI, NLM, NIH
PANTHER - Protein ANalysis THrough Evolutionary RelationshipsPANTHER development team (Paul Thomas)
PATRIC - Pathosystems Resource Integration CenterPATRIC Project Team
Personalized Medicine Research Project population-based bio-bankMarshfield Clinic Research Foundation
PharmGKB - Pharmacogenomics KnowledgebaseUS Dept of Health and Human Services
PubMethBioBix, Laboratory for Bioinformatics and Computational Genomics, Ghent University, Belgium
REBASE - The Restriction Enzyme dataBASENew England Biolabs, Inc. (Roberts, R.J., Macelis, D.)
RGD - Rat Genome DatabaseMedical College of Wisconsin
RNAi databaseNYU's Center for Genomics & Systems Biology
Roadmap Epigenomics Project DataNIEHS
RUCDR - Rutgers University Cell and DNA RepositoryRUCDR Team
SBKB - Structural Biology KnowledgebaseProtein Structure Initiative and Nature Publishing Group
SKY/M-FISH and CGH DatabaseNational Center for Biotechnology Information, NLM, NIH and National Cancer Institute, NIH
SpringerProtocolsSpringer-Verlag
VectorBase ("Bioinformatics Resource for Invertebrate Vectors of Human Pathogens")VectorBase Project team
ViPR - Virus Pathogen ResourceViPR Project team
WashU Epigenome BrowserWashington University
Yeast GFP Fusion Localization DatabaseUniversity of California, San Francisco and SGD