Bioinformatics-new

 
Bio-Ontologies

Tools

ResourceDeveloperProprietary or Public Domain?
AmiGO (Gene Ontology database search)AmiGO development teampublic domain
Bioconductor ("provides tools for the analysis and comprehension of high-throughput genomic data" using R)Bioconductor development teampublic domain
FunDO ("Exploring Genes Using Functional Disease Ontology Annotations")Northwestern University Biomedical Informatics Centerpublic domain
GOFFA - Gene Ontology for Functional AnalysisUSFDApublic domain

Databases

ResourceDeveloperProprietary or Public Domain?
CharProtDB - Characterized Protein DatabaseJ. Craig Venter Institutepublic domain
ChEBI - Chemical Entities of Biological InterestEMBL-EBIpublic domain
FlyMine - "integrated database for Drosophila and Anopheles genomics"University of Cambridge, Cambridge, UKpublic domain
Gene WeaverJackson Laboratory, ME and collaboratorspublic domain
GFBio - German Federation for the curation of Biological dataGFBiopublic domain
GO Database - Gene Ontology DatabaseGene Ontology Consortiumpublic domain
MouseMine MGI at The Jackson Laboratory and InterMine project at Cambridge Systems Biology Centre, UKpublic domain
RatMineUniversity of Cambridge, Cambridge, UKpublic domain
YeastMine ("Search and retrieve S. cerevisiae data")SGD and Intermine project at Cambridge Systems Biology Centre, UKpublic domain
ZebrafishMineZFIN at University of Oregon and InterMine project at Cambridge Systems Biology Centre, UKpublic domain
Biomolecular Sequences/Structures

Characterizations and comparisons of biomolecular sequences and structures

Tools

ResourceDeveloperProprietary or Public Domain?
7TMRmine ("hierarchical mining tool for 7TMRs")University of Nebraskapublic domain
ABySS - Assembly By Short SequencesMichael Smith Genome Sciences Centre, Canada and BC Cancer Research Centrepublic domain
ABySS-Explorer - Assembly By Short Sequences ExplorerMichael Smith Genome Sciences Centre, Canada and BC Cancer Research Centrepublic domain
Affymetrix GeneChip Sequence Analysis SoftwareAffymetrixproprietary
Affymetrix Transcriptome Analysis ConsoleAffymetrixproprietary
ALLPATHS-LG ("genome assembly from low cost data")Broad Institutepublic domain
Alscript ("program to format multiple sequence alignments in PostScript")University of Oxfordpublic domain
Antigenicity PlotLuca Toldopublic domain
ARAGORN (tRNA and tmRNA detection)ARAGORN development teampublic domain
AUGUSTUS ("predicts genes in eukaryotic genomic sequences")University of Göttingen and University of Greifswald, Germanypublic domain
AutoDock (docking tools suite)The Scripps Research Institutepublic domain
BicAT - Biclustering Analysis ToolboxETH, Zurichpublic domain
Bioclipse ("workbench for the life sciences" based on Eclipse Rich Client Platform)Bioclipse development teampublic domain
Bioconductor ("provides tools for the analysis and comprehension of high-throughput genomic data" using R)Bioconductor development teampublic domain
Biopython ("tools for biological computation written in Python")Biopython development teampublic domain
BiQ Analyzer ("software tool for DNA methylation analysis")Max Planck Institute for Informatics, Germanypublic domain
Bismark (tool to map bisulfite converted sequence reads and determine cytosine methylation states)Babraham Bioinformaticspublic domain
BLAST - Basic Local Alignment Search Tool (see also PSI-BLAST for Protein Similarity Search)National Center for Biotechnology Information, NLM, NIHpublic domain
BLAT - BLAST-like Alignment ToolJim Kentpublic domain
Bowtie (DNA sequence alignment tool)Bowtie development teampublic domain
Bowtie 2 (sequencing reads to long reference sequences aligner)Bowtie 2 development teampublic domain
BWA - Burrows-Wheeler AlignerBWA development teampublic domain
CD-HIT - Cluster Database at High Identity with ToleranceLi group, University of California, San Diego (developed at Burnham Institute)public domain
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 public domain
CLC Sequence ViewerCLC biopublic domain
CLCbio Genomics Workbench (analysis, comparison and visualization of next generation sequencing data)CLCbioproprietary
Clustal Omega (Multiple DNA, RNA and protein sequence alignment program)Conway Institute, UCD Dublinpublic domain
ClustalW2 (see Clustal Omega)EMBL-EBIpublic domain
CMARRT (A tool for the analysis of ChIP-chip data from tiling arrays by incorporating the correlation structure)Keles Research Group, University of Wisconsinpublic domain
CNVFinder - Copy Number Variant FinderWellcome Trust Sanger Institute, UKpublic domain
CompMoby ("detect over-represented motifs in the upstream or 3' UTR sequences of co-expressed genes")QB3 and UCSFpublic domain
Contrail - To assemble large genomes in the cloudUniversity of MDpublic domain
CSEM - Multi-read Allocation for ChIP-seqKeles Research Group, University of Wisconsinpublic domain
Cufflinks - Transcript assembly, differential expression and regulation for RNA-Seq samplesUC Berkeley, JHU, and Caltechpublic domain
CummeRbund - To analyze Cufflinks RNA-Seq outputMIT and Harvardpublic domain
DAVID - Database for Annotation, Visualization and Integrated DiscoveryNational Institute of Allergy and Infectious Diseases, NIHpublic domain
DBChIP - program to detect differentially bound sharp binding sites across multiple conditionsKeles Research Group, University of Wisconsinpublic domain
DISCOVAR - genome assembler and variant callerBroad Institutepublic domain
DISCOVAR de novo - Assembler for large genomes up to human sizeBroad Institutepublic domain
DisEBML ("Intrinsic Protein Disorder Prediction")DisEBML development team, EMBLpublic domain
EIGENSOFT ("combines functionality from our population genetics methods [...] and our EIGENSTRAT stratification correction method")EIGENSOFT development team, Harvard School of Public Healthpublic domain
EMBOSS - European Molecular Biology Open Software SuiteEMBOSS development team (P. Rice and A. Bleasby et al.)public domain
EpiGRAPH - for advanced (epi-) genome analysis and predictionEpiGRAPH development teampublic domain
FASTA - DNA and protein sequence alignment software packageEMBL-EBIpublic domain
FastQC - Quality control tool for high throughput sequence dataBabraham Bioinformaticspublic domain
FGENESH - "Program for predicting multiple genes in genomic DNA sequences"Softberry, Inc. and The Sanger Centre, Cambridge, UKpublic domain
FoundationOneFoundation Medicineproprietary
Galaxy - web-based platform for data intensive biomedical research ("Online bioinformatics analysis for everyone")Penn State and Emory U.public domain
GATK - Genome Analysis ToolkitBroad Institutepublic domain
GeneMANIA - "predict the function of [...] genes and gene sets"Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Canadapublic domain
GeneSpringAgilent Technologiesproprietary
GeneTalk - "Analyze human sequence variants"GeneTalk development teampublic domain
GenMAPP - Gene Map Annotator and Pathway ProfilerGladstone Institutes, UCSFpublic domain
Genotyping ConsoleAffymetrix Incproprietary
GENSCANStanford University (C. Burge and S. Karlin)public domain
Geospiza GeneSifter Analysis EditionPerkin Elmerproprietary
geWorkBench - Genomics WorkbenchNCI (National Cancer Institute), NIHpublic domain
GlimmerHMMCenter for Bioinformatics and Computational Biology, University of Marylandpublic domain
GMAP - Genomic Mapping and Alignment Program for mRNA and EST SequencesGenentech, Inc., CApublic domain
GoMinerNCI (National Cancer Institute), NIHpublic domain
GPCRHMM - "GPCR detection method"Stockholm Bioinformatics Centrepublic domain
GPCRTree - "hierarchical classification of GPCR function"University of Oxford, UKpublic domain
GPUFRAGFOLD - Protein Structure Prediction toolBioinformatics Group, University College Londonpublic domain
GRAM - Genetic RegulAtory ModulesGifford Laboratory, MITpublic domain
GSNAP - Genomic Short-read Nucleotide Alignment ProgramGenentech, Inc., CApublic domain
HDMFinder ("Methylation prediction software")Zhang Lab, Cold Spring Harbor Laboratory, NYpublic domain
HMMER ("biosequence analysis using profile hidden Markov models")HMMER development teampublic domain
HMMTOP ("Prediction of transmembrane helices and topology of proteins")HMMTOP team, Institute of Enzymology, Hungarypublic domain
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 Kongpublic domain
IGV - Integrative Genomics ViewerBroad Institutepublic domain
Illumina GenomeStudioIllumina Softwareproprietary
Infernal - INFERence of RNA ALignmentEddy group, HHMI Janelia Farm Research Campus, VApublic domain
Ingenuity Variant AnalysisQiagenproprietary
InterProEMBL-EBIpublic domain
jMOSAiCS - Joint Analysis of Multiple ChIP-seq DatasetsKeles Research Group, University of Wisconsinpublic domain
JPredBarton Group, University of Dundeepublic domain
KalignEMBL-EBIpublic domain
KELVINBattelle Center for Mathematical Medicine, Nationwide Children's Hospital, Ohiopublic domain
KelvizBattelle Center for Mathematical Medicine, Nationwide Children's Hospital, Ohiopublic domain
MACS - Model-based Analysis of ChIP-Seq dataHarvard Universitypublic domain
MAExplorer - Microarray ExplorerMAExplorer development teampublic domain
MAKER ("portable and [...] configurable genome annotation pipeline")Yandell Laboratory, University of Utahpublic domain
Maq - Mapping and Assembly with QualityMaq development teampublic domain
Maqview - graphical read alignment viewerMaqview development team (Ruan et al.)public domain
MascotMatrix Scienceproprietary
MATLAB Bioinformatics ToolboxThe Mathworks, Inc.proprietary
MATLAB Toolboxes (Optimization; Direct Search; Genetic Algorithms)The Mathworks, Inc.proprietary
MDscan - Motif Discovery scanStanford Medical Informatics, Stanford Universitypublic domain
MEGA - Molecular Evolutionary Genetics AnalysisMEGA teampublic domain
MEMSAT3 - MEMbrane protein Structure And TopologyMEMSAT team, University College London, UKproprietary
MetaQTLMetaQTL development teampublic domain
Methylator ("An SVM Based Method for DNA Methylation Prediction")Methylator Development Teampublic domain
MeV - MultiExperiment ViewerMeV development teampublic domain
Microarray Center cDNA Clone SearchNIEHSpublic domain
MIDAS - Multi Instance Data Acquisition SystemScience and Technology Facilities Council, UKpublic domain
MIRA - Whole Genome Shotgun and EST Sequence AssemblerBastien Chevreuxpublic domain
MISO - Mixture of Isoforms ("Probabilistic analysis and design of RNA-Seq experiments for identifying isoform regulation")Burge and Airoldi lab, MIT and Harvard Universitypublic domain
MOABS - MOdel based Analysis of Bisulfite Sequencing dataDeqiang Sun, Baylor College of Medicinepublic domain
MobyDickThe Rockefeller Universityproprietary
modMine ("data warehouse for the modENCODE project")University of Cambridge, Cambridge, UKpublic domain
Mold2USFDApublic domain
MOSAiCS - MOdel-based one and two Sample Analysis and Inference for ChIP-Seq DataKeles Research Group, University of Wisconsinpublic domain
MrBayesMrBayes development teampublic domain
mrsFAST (short-read mapper)mrsFAST development teampublic domain
MUSCLE - MUltiple Sequence Comparison by Log- ExpectationEMBL-EBIpublic domain
NCBI/ Primer-BLASTNational Center for Biotechnology Information, NLM, NIHpublic domain
NetRecodonNetRecodon development teampublic domain
Newbler ("software package for de novo DNA sequence assembly")454 Life Sciences, Roche Diagnostics Corporationproprietary
NovoalignNovocraft Technologiesproprietary
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 Wisconsinpublic domain
NuPoP - Nucleosome Positioning Prediction EngineNorthwestern University (J.-P. Wang)public domain
OptiRNAUniversity of Nebraskapublic domain
PaGE - Patterns from Gene ExpressionPaGE development team, University of Pennsylvaniapublic domain
PAM - Prediction Analysis for MicroarraysStanford Universitypublic domain
pepgrepUniversity of Essexpublic domain
Persephone ("Genome Visualization & Exploration Software")Ceres, Inc. proprietary
PFAAT - Protein Family Alignment Annotation ToolPFAAT development teampublic domain
PhyMLS. Guindon, et al., CNRSpublic domain
PhyreStructural Bioinformatics Group, Imperial College, Londonpublic domain
picard ("A set of Java command line tools for manipulating high-throughput sequencing data (HTS) data and formats")Broad Institute and picard development teampublic domain
PLINK ("Whole genome association analysis toolset")PLINK development team, CHGR - Massachusetts General Hospital, Boston, MApublic domain
PolyBayes ("automated analysis of single-nucleotide polymorphism (SNP) discovery in redundant DNA sequences")Washington University Genome Sequencing Centerpublic domain
Polyphred (single nucleotide substitution identification)University of Washington (Brent Ewing, Phil Green, David Gordon et al.)public domain
PRED-GPCRUniversity of Athens, Greecepublic domain
PredictProteinROSTLABpublic domain
Protein ProspectorUCSFpublic domain
PSI-BLAST - Protein Similarity Search BLASTEMBL-EBIpublic domain
QTDT (Linkage Disequilibrium Analyses for Quantitative and Discrete Traits)Abecasis Lab, University of Michiganpublic domain
QTXQTX development teampublic domain
QuEST - Quantitative Enrichment of Sequence TagsStanford Universitypublic domain
Ray (Assembly of reads obtained with sequencing technologies) S. Boisvert, F. Laviolette, J. Corbeilpublic domain
Reaxys system (Search substances, reactions, citations, patents, etc.)Reaxys development teampublic domain
REDUCEHarmen Bussemaker Laboratory, Columbia University
RMAP (next-generation sequencing read mapper)Cold Spring Harbor Laboratory, NY and USC, CApublic domain
RNA CoMPASS - RNA Comprehensive Multi-Processor Analysis System for SequencingGuorong Xu and RNA CoMPASS development teampublic domain
SAMBAShamir Laboratory, Tel Aviv Universitypublic domain
SAMtools - Sequence Alignment/MapLi et al., Wellcome Trust Sanger Institute, UK and Broad Institute of MIT and Harvard, USApublic domain
SANDYGerstein Laboratory, Yale Universitypublic domain
SCAMPI ("Prediction of membrane protein topology")Stockholm Bioinformatics Center, Stockholm Universitypublic domain
SCOP - Structural Classification of ProteinsMRC Laboratory of Molecular Biologypublic domain
SEQUESTYates Laboratory, University of Washingtonpublic domain
Shape SignaturesWelsh Laboratory, RWJMSproprietary
SICER ("clustering approach for identification of enriched domains from histone modification ChIP-Seq data")W. Peng lab, George Washington Universitypublic domain
SMART-BS-Seq - Specific Methylation Analysis and Report Tool for BS-Seq dataPython Software Foundationpublic domain
SNAP - Screening for Non-Acceptable PolymorphismsRost Lab, Columbia University, New Yorkpublic domain
SNAP - SNP Annotation and Proxy SearchSNAP Development Teampublic domain
SNP-o-matic (analysis of Solexa reads and comparison with reference)Sanger Institutepublic domain
SNPTrackUSFDApublic domain
SOAP - Short Oligonucleotide Analysis PackageBeijing Genomics Institutepublic domain
SOAPdenovo2 (Large-size genome de-novo assembler)Ruibang Luo, et al., Tai Po Industrial Estatepublic domain
SOPRA - Scaffolding algorithm for paired reads via statistical optimizationA. Sengupta lab, Rutgers Universitypublic domain
SOSUI ("predicts a part of the secondary structure of proteins from a given amino acid sequence")Tokyo Universitypublic domain
SSEARCH (sequence similarity search)SSEARCH teampublic domain
STRING - Search Tool for the Retrieval of Interacting Genes/ProteinsSTRING Teampublic domain
SUCcESS (Integration of quantitative information from ChIP-chip experiments into motif finding)Keles Research Group, University of Wisconsinpublic domain
SYBYL ("Molecular Modeling from Sequence through Lead Optimization")Certara, L.P. and Triposproprietary
T-CoffeeEMBL-EBIpublic domain
THREADER (Protein Structure Prediction tool)Bioinformatics Group, University College Londonpublic domain
TileHGMM (Mixture modeling for genome-wide localization of transcription factors)Keles Research Group, University of Wisconsinpublic domain
TMFinder ("Trans-Membrane protein prediction tool")TM-Finder development team and The Hospital for Sick Children (SickKids)public domain
TopHat (spliced read mapper for RNA-Seq)JHU Center for Computational Biologypublic domain
TopPred ("Topology prediction of membrane proteins")TopPred development teampublic domain
TopSpin (NMR data analysis and acquisition and processing of NMR spectra)Bruker Corporationproprietary
ToxmatchJoint Research Centre, IHCPpublic domain
Trinity RNA-Seq Assembly Broad Institute, Hebrew University of Jerusalem and Trinity Developers Grouppublic domain
Trinotate ("Transcriptome Functional Annotation and Analysis")Trinotate development teampublic domain
Tute ("web application [...] in the cloud and [...] analyze and annotate entire human genomes")Tute Genomicsproprietray
Twinscan/N-SCAN ("gene-structure prediction")Brent Lab, Washington University in St. Louispublic domain
VEGAS - Versatile Gene-based Association StudyVEGAS development team, Queensland Institute of Medical Research, Australiapublic domain
Velvet ("Sequence assembler for very short reads")EMBL-EBIpublic domain
X!TandemThe Global Proteome Machine Organizationpublic domain

Databases

ResourceDeveloperProprietary or Public Domain?
Alu Pairs DatabaseNIEHSpublic domain
ASAP - A Systematic Annotation Package For Community Analysis of GenomesUniversity of Wisconsin, Madisonpublic domain
Berkeley Drosophila Genome ProjectBerkeley Drosophila Genome Project Consortiumpublic domain
BioGPS ("gene annotation portal")BioGPS development teampublic domain
Blocks Database ("sequence analysis"; no longer updated)Fred Hutchinson Cancer Research Centerpublic domain
BOND - Biomolecular Object Network DatabankThomsonpublic domain
BRENDA - BRaunschweig ENzyme DAtabaseD. Schomburg, Technische Universität Braunschweig, Germanypublic domain
Cambridge Structural DatabaseCambridge Crystallographic Data Centrepublic domain
CATH ("Protein Structure Classification Database")University College, Londonpublic domain
CharProtDB - Characterized Protein DatabaseJ. Craig Venter Institutepublic domain
ChemBankBroad Institutepublic domain
ChromDB - The Chromatin DatabaseBIO5 Institutepublic domain
CluSTrEMBL-EBIpublic domain
CNV Project Data - Copy Number Variation Project DataWellcome Trust Sanger Institute, UKproprietary
COG - Clusters of Orthologous Groups of proteinsNational Center for Biotechnology Information, NLM, NIHpublic domain
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.)public domain
Database of Macromolecular MovementMark Gerstein, et al., Yale Universitypublic domain
DBCAT - DataBase of CpG islands and Analytical ToolResearch Center for Medical Excellence National Taiwan Universitypublic domain
dbGaP - Database of Genotypes and PhenotypesNational Center for Biotechnology Information, NLM, NIHpublic domain
dbSNPNational Center for Biotechnology Information, NLM, NIHpublic domain
DiseaseMeth - human disease methylation databaseCollege of Bioinformatics Sci. and Tech., Harbin Medical U., Chinapublic domain
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 Medicinepublic domain
ENA - European Nucleotide ArchiveEMBL-EBIpublic domain
ENCODE - Encyclopedia Of DNA ElementsNHGRI, NIHpublic domain
Ensembl Genome BrowserEMBL-EBI and Wellcome Trust Sanger Institute, UKpublic domain
GBrowse (Generic Genome Browser)GBrowse development teampublic domain
GenBankNational Center for Biotechnology Information, NLM, NIHpublic domain
Genetic Association DatabaseGAD development team and NIHpublic domain
Genomatix SuiteGenomatix Software GmbHproprietary
GLIDA - GPCR-Ligand DatabaseKyoto Universitypublic domain
GOLD - Genomes Online DatabaseGOLD Teampublic domain
GPCR NaVa database - G Protein-Coupled Receptors Natural Variants databaseLeiden/Amsterdam Center for Drug Research and Leiden Institute of Advanced Computer Sciencepublic domain
GPCR SARfari ("integrated chemogenomics research and discovery workbench for Class A G Protein Coupled Receptors")EMBL-EBIpublic domain
GPCRDB - G Protein-Coupled Receptor Data BaseGPCRDB development teampublic domain
GPCR-OKB - G Protein Coupled Receptor - Oligomer Knowledge BaseGPCR-OKB development teampublic domain
GPCR-PD ("database for G protein-coupled receptors")Incyte Genomicspublic domain
GVS - Genome Variation ServerUniversity of Washingtonpublic domain
HapMapInternational HapMap Projectpublic domain
HGMD - Human Gene Mutation Database (integrated with Ingenuity Variant Analysis) BIOBASEproprietary
Histone DatabaseNHGRI Division of Intramural Research, NIHpublic domain
HIV Sequence databaseLos Alamos National Laboratorypublic domain
HomoloGeneNational Center for Biotechnology Information, NLM, NIHpublic domain
Human DNA Polymerase Gamma Mutation DatabaseNIEHSpublic domain
Human Genome BrowserGenome Bioinformatics Group, UC Santa Cruz.public domain
HuRef Genome Browser (Individual Human Genome Browser)J. Craig Venter Institutepublic domain
IMGT - ImMunoGeneTics information systemMarie-Paule Lefrancpublic domain
IMGT/3Dstructure-DB - ImMunoGeneTicsMarie-Paule Lefrancpublic domain
Integr8EMBL-EBIpublic domain
InterProEMBL-EBIpublic domain
iProClassPIR - Protein Information Resourcepublic domain
IRD - Influenza Research DatabaseIRD Project Teampublic domain
JSNP - Japanese Single Nucleotide PolymorphismsUniversity of Tokyo and the Japan Science and Technology Agency (JST)public domain
KEGG GENES databaseKanehisa Laboratories, Japanpublic domain
LMPD - LIPID MAPS Proteome DatabaseUniversity of California, San Diegopublic domain
LMSD - LIPID MAPS Structure DatabaseUniversity of California, San Diegopublic domain
MethBase - a reference methylome databaseSmith lab, Molecular and Computational Biology, U. of Southern Californiapublic domain
MethylomeDB - Brain Methylome DatabaseHaghighi lab, Columbia Universitypublic domain
MGI - Mouse Genome InformaticsThe Jackson Laboratory, Maine and MGI teampublic domain
MINT - Molecular INTeraction databaseUniversity of Rome Tor Vergata, Italypublic domain
miRBase - microRNA databaseGriffiths-Jones lab, U. of Manchester and Wellcome Trust Sanger Institutepublic domain
miRBase ("the microRNA database")University of Manchester, UKpublic domain
MMDB - Molecular Modeling Database (NCBI Structure)National Center for Biotechnology Information, NLM, NIHpublic domain
modENCODE - Model Organism ENCyclopedia Of DNA ElementsmodENCODE Project Consortiumpublic domain
Mouse Genome Resequencing ProjectNIEHSpublic domain
NCBI GeneNational Center for Biotechnology Information, NLM, NIHpublic domain
NCBI Model Organisms GuideNational Center for Biotechnology Information, NLM, NIHpublic domain
NCBI Nucleotide Sequence DatabaseNational Center for Biotechnology Information, NLM, NIHpublic domain
NCI DIS 3D - National Cancer Institute Drug Information System 3D structure databaseNCI (National Cancer Institute), NIHpublic domain
NDB - Nucleic Acid Database ("A Portal for Three-dimensional Structural Information about Nucleic Acids")The Nucleic Acid Database Project, Rutgers Universitypublic domain
NGSmethDB - A database for next-generation sequencing single-cytosine-resolution DNA methylation databaseComputational Genomics and Bioinformatics Group, U. Granada, Spainpublic domain
NIEHS SNPs Exome Variant ServerNIEHS and University of Washingtonpublic domain
OChem - Online Chemical databaseeADMET GmbH, Germanypublic domain
ORDB - Olfactory Receptor DataBaseYale Universitypublic domain
Pan Asian SNP DatabasePan-Asian SNP Consortiumpublic domain
PDB - Protein Data BankRCSB PDB (Rutgers University, UCSD)public domain
Peptide AtlasPeptideAtlas team, Institute for Systems Biologypublic domain
Persephone ("Genome Visualization & Exploration Software")Ceres, Inc. proprietary
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, USpublic domain
RefSeq - NCBI Reference Sequence DatabaseNational Center for Biotechnology Information, NLM, NIHpublic domain
RGD - Rat Genome DatabaseMedical College of Wisconsinpublic domain
RNA World ("collection of links to RNA-related information")Leibniz Institute for Age Research, FLI, Germany and RNA World teampublic domain
SBKB - Structural Biology KnowledgebaseProtein Structure Initiative and Nature Publishing Grouppublic domain
SCAN ("SNP and CNV Annotation Database")The University of Chicagopublic domain
SEVENS database ("summarizes GPCR (G-protein coupled receptor) genes that are identified [...] from [...] eukaryote genomes")Computational Biology Research Center, AIST, Japanpublic domain
SGD - Saccharomyces Genome DatabaseStanford Universitypublic domain
SNP500CancerSAIC-Frederick, NCI-FCRDC, MDpublic domain
SNPinfo Web ServerNIEHSpublic domain
SpringerProtocolsSpringer-Verlagproprietary
Structural Biology Software DatabaseTheoretical and Computational Biophysics Group, University of Illinoispublic domain
TransFacGene Regulationpublic domain
UniSTS ("database of sequence tagged sites")National Center for Biotechnology Information, NLM, NIHpublic domain
VEGA - Vertebrate Genome AnnotationHAVANA group, Wellcome Trust Sanger Institute, UKpublic domain
ViPR - Virus Pathogen ResourceViPR Project teampublic domain
WormBaseWormBase development teampublic domain
wwPDB - Worldwide Protein Data BankRCSB PDB, USA, PDBe, Europe, PDBj, Japan and BMRB, USApublic domain
ZebrafishMineZFIN at University of Oregon and InterMine project at Cambridge Systems Biology Centre, UKpublic domain
Interactions/Biopathways/Bionetworks

Characterization of biomolecular interactions, pathways, and networks

Tools

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

Databases

ResourceDeveloperProprietary or Public Domain?
BBID - Biological Biochemical Image DatabaseNIA, Intramural Research Programpublic domain
BIND - Biomolecular Interaction Network DatabaseChristopher Hogue's Research Laboratorypublic domain
BioCartaBioCarta LLCproprietary
Biocatalysis/ Biodegradation DatabaseUniversity of Minnesotapublic domain
BioGRID - Biological General Repository for Interaction DatasetsBioGRID Teampublic domain
Cognoscente ("database and visualization tool for biomolecular interactions [...] in the literature")VanBuren laboratory, Texas A&M Health Science Centerpublic domain
eggNOG - evolutionary genealogy of genes: Non-supervised Orthologous GroupsEMBL, Germanypublic domain
FlyMine - "integrated database for Drosophila and Anopheles genomics"University of Cambridge, Cambridge, UKpublic domain
gpDB - "database of GPCRs, G-proteins, effectors and their interactions"University of Athens, Greecepublic domain
HumanCycSRI Internationalpublic domain
Human-gpDB ("database of human GPCRs, G-proteins, Effectors and their interactions")Human-gpDB teampublic domain
KEGG - Kyoto Encyclopedia of Genes and GenomesKanehisa Laboratories, Japanpublic domain
KEGG GENES databaseKanehisa Laboratories, Japanpublic domain
KUPKB - The Kidney and Urinary Pathway Knowledge BaseINSERM, France and University of Manchester, UKpublic domain
MetaCycSRI Internationalpublic domain
MetNetDB - MetNet DatabaseIowa State Universitypublic domain
MGI - Mouse Genome InformaticsThe Jackson Laboratory, Maine and MGI teampublic domain
MINT - Molecular INTeraction databaseUniversity of Rome Tor Vergata, Italypublic domain
MouseMine MGI at The Jackson Laboratory and InterMine project at Cambridge Systems Biology Centre, UKpublic domain
OrthoDBUniversity of Geneva Medical School, Switzerlandpublic domain
PANTHER - Protein ANalysis THrough Evolutionary RelationshipsPANTHER development team (Paul Thomas)public domain
PathArtJubilant Biosysproprietary
PathCase Pathways Database SystemCase Western Reserve Universitypublic domain
Pathway DatabaseProtein Loungepublic domain
PD map - Parkinson’s disease mapLCSB and Hiroaki Kitano team at SBI, Tokyopublic domain
PID - Pathway Interaction DatabaseNCI (National Cancer Institute), NIHpublic domain
RatMineUniversity of Cambridge, Cambridge, UKpublic domain
ReactomeReactome teampublic domain
RGD - Rat Genome DatabaseMedical College of Wisconsinpublic domain
SGD - Saccharomyces Genome DatabaseStanford Universitypublic domain
SPAD - Signaling Pathway DatabaseKyushu Universitypublic domain
SpringerProtocolsSpringer-Verlagproprietary
TransFacGene Regulationpublic domain
TransPathGene Regulationpublic domain
YeastMine ("Search and retrieve S. cerevisiae data")SGD and Intermine project at Cambridge Systems Biology Centre, UKpublic domain
YEASTNET ("A consensus reconstruction of yeast metabolism")Yeastnet development teampublic domain
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]

Tools

ResourceDeveloperProprietary or Public Domain?
ADME Workbench ("pharmacokinetic modeling by integrating [...] absorption, distribution, metabolism and excretion methods")The AEgis Technologies Groupproprietary
Affymetrix Expression ConsoleAffymetrixproprietary
Affymetrix Transcriptome Analysis ConsoleAffymetrixproprietary
ArrayTrack/ebTrackUSFDA and ebCTCpublic domain
Automated Particle Tracking and Analysis SoftwareUniversity of California, Irvinepublic domain
Bismark (tool to map bisulfite converted sequence reads and determine cytosine methylation states)Babraham Bioinformaticspublic domain
BMDExpress ("analyze microarray dose-response data")BMDExpress teampublic domain
BRB-ArrayToolsDr. Richard Simon and BRB-ArrayTools Development Teampublic domain
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 public domain
Cloe PredictCyprotexproprietary
CMARRT (A tool for the analysis of ChIP-chip data from tiling arrays by incorporating the correlation structure)Keles Research Group, University of Wisconsinpublic domain
CombiToolLeibniz Institute for Age Research - FLI, Germanyproprietary
CSEM - Multi-read Allocation for ChIP-seqKeles Research Group, University of Wisconsinpublic domain
Cufflinks - Transcript assembly, differential expression and regulation for RNA-Seq samplesUC Berkeley, JHU, and Caltechpublic domain
CVSimCVSim development teampublic domain
DBChIP - program to detect differentially bound sharp binding sites across multiple conditionsKeles Research Group, University of Wisconsinpublic domain
dChip - DNA-Chip AnalyzerHarvard University and Stanford Universitypublic domain
Decision ForestUSFDApublic domain
Disease/ Phenotype web-PAGE ("disease based gene set analysis of microarray gene expression")Gene Expression and Genomics Unit, NIA, NIHpublic domain
DORIAN - DOse-Response Information ANalysis systemComputational Chemodynamics Laboratoryproprietary
ELECANS - A Computational Cancer Systems Biology Simulation StudioDepartment of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Koreapublic domain
EMBERUniversity of Chicagopublic domain
EpiGRAPH - for advanced (epi-) genome analysis and predictionEpiGRAPH development teampublic domain
EpiSIM PlatformTIGA Center Heidelberg, Germanypublic domain
Galaxy - web-based platform for data intensive biomedical research ("Online bioinformatics analysis for everyone")Penn State and Emory U.public domain
GMC impute - Gaussian mixture clustering imputeComputational Chemodynamics Laboratoryproprietary
GSEA - Gene Set Enrichment AnalysisBroad Institutepublic domain
IGV - Integrative Genomics ViewerBroad Institutepublic domain
IPA - Ingenuity Pathway AnalysisQiagen N.V.proprietary
J/maanovaChurchill Group, Jackson Laboratorypublic domain
Java Treeview ("Viewer for Microarray Data in the PCL or CDT format")Stanford University School of Medicine (A. J. Saldanha) and Java Treeview development teampublic domain
jMOSAiCS - Joint Analysis of Multiple ChIP-seq DatasetsKeles Research Group, University of Wisconsinpublic domain
MAQC - MicroArray Quality ControlUSFDApublic domain
MATLAB Bioinformatics ToolboxThe Mathworks, Inc.proprietary
maxdViewManchester Bioinformaticspublic domain
MethToolsLeibniz Institute for Age Research - Fritz Lipmann Institute, Germanypublic domain
MOABS - MOdel based Analysis of Bisulfite Sequencing dataDeqiang Sun, Baylor College of Medicinepublic domain
Monocle - toolkit for analyzing single-cell gene expression experimentsCole Trapnellpublic domain
MOSAiCS - MOdel-based one and two Sample Analysis and Inference for ChIP-Seq DataKeles Research Group, University of Wisconsinpublic domain
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 Wisconsinpublic domain
OmicsOffice for MicroarraysIntegromicsproprietary
Pathway StudioPathway Studioproprietary
Persephone ("Genome Visualization & Exploration Software")Ceres, Inc. proprietary
ProteoIQ ("qualitative and quantitative suite for proteomics")Premier Biosoftproprietary
R/maanovaChurchill Group, Jackson Laboratorypublic domain
RealTimeDesign SoftwareBiosearch Technologiespublic domain
SBPOP Package ("Support for Model Based Drug Development – From Mechanistic Models to Complex Trial Simulation")SBPOP Package development team at Novartis Pharma AG Modeling & Simulationpublic domain
SimBiology app for MATLAB ("Model, simulate, and analyze biological systems")The MathWorks, Inc.proprietary
SMART-BS-Seq - Specific Methylation Analysis and Report Tool for BS-Seq dataPython Software Foundationpublic domain
SPELL - Serial Pattern of Expression Levels LocatorPrinceton Universitypublic domain
SPLS - Sparse partial least squaresKeles Research Group, University of Wisconsinpublic domain
SUCcESS (Integration of quantitative information from ChIP-chip experiments into motif finding)Keles Research Group, University of Wisconsinpublic domain
TileHGMM (Mixture modeling for genome-wide localization of transcription factors)Keles Research Group, University of Wisconsinpublic domain
ToxFXNIEHSpublic domain
WebArrayWebArray project teampublic domain

Databases

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

Data integration across biological scales

Tools

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

Databases

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