Bio-Ontologies
Computational Analysis Tools
Information Portals and Databases
Biomolecular Sequences/Structures
Characterizations and comparisons of biomolecular sequences and structures
Computational Analysis Tools
| Resource | Developer |
|---|---|
| 7TMRmine (“hierarchical mining tool for 7TMRs”) | University of Nebraska |
| ABySS – Assembly By Short Sequences | Michael Smith Genome Sciences Centre, Canada and BC Cancer Research Centre |
| ABySS-Explorer – Assembly By Short Sequences Explorer | Michael Smith Genome Sciences Centre, Canada and BC Cancer Research Centre |
| Affymetrix GeneChip Sequence Analysis Software | Affymetrix |
| Affymetrix Transcriptome Analysis Console | Affymetrix |
| ALLPATHS-LG (“genome assembly from low cost data”) | Broad Institute |
| Alscript (“program to format multiple sequence alignments in PostScript”) | University of Oxford |
| Antigenicity Plot | Luca 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 Toolbox | ETH, 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 Tool | Jim 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 Aligner | BWA development team |
| CD-HIT – Cluster Database at High Identity with Tolerance | Li 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 Viewer | CLC 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 Finder | Wellcome 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 cloud | University of MD |
| CSEM – Multi-read Allocation for ChIP-seq | Keles Research Group, University of Wisconsin |
| Cufflinks – Transcript assembly, differential expression and regulation for RNA-Seq samples | UC Berkeley, JHU, and Caltech |
| CummeRbund – To analyze Cufflinks RNA-Seq output | MIT and Harvard |
| DAVID – Database for Annotation, Visualization and Integrated Discovery | National Institute of Allergy and Infectious Diseases, NIH |
| DBChIP – program to detect differentially bound sharp binding sites across multiple conditions | Keles Research Group, University of Wisconsin |
| DISCOVAR – genome assembler and variant caller | Broad Institute |
| DISCOVAR de novo – Assembler for large genomes up to human size | Broad 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 Suite | EMBOSS development team (P. Rice and A. Bleasby et al.) |
| EpiGRAPH – for advanced (epi-) genome analysis and prediction | EpiGRAPH development team |
| FASTA – DNA and protein sequence alignment software package | EMBL-EBI |
| FastQC – Quality control tool for high throughput sequence data | Babraham Bioinformatics |
| FGENESH – “Program for predicting multiple genes in genomic DNA sequences” | Softberry, Inc. and The Sanger Centre, Cambridge, UK |
| FoundationOne | Foundation Medicine |
| Galaxy – web-based platform for data intensive biomedical research (“Online bioinformatics analysis for everyone”) | Penn State and Emory U. |
| GATK – Genome Analysis Toolkit | Broad Institute |
| GeneMANIA – “predict the function of […] genes and gene sets” | Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Canada |
| GeneSpring | Agilent Technologies |
| GeneTalk – “Analyze human sequence variants” | GeneTalk development team |
| GenMAPP – Gene Map Annotator and Pathway Profiler | Gladstone Institutes, UCSF |
| Genotyping Console | Affymetrix Inc |
| GENSCAN | Stanford University (C. Burge and S. Karlin) |
| Geospiza GeneSifter Analysis Edition | Perkin Elmer |
| geWorkBench – Genomics Workbench | NCI (National Cancer Institute), NIH |
| GlimmerHMM | Center for Bioinformatics and Computational Biology, University of Maryland |
| GMAP – Genomic Mapping and Alignment Program for mRNA and EST Sequences | Genentech, Inc., CA |
| GoMiner | NCI (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 tool | Bioinformatics Group, University College London |
| GRAM – Genetic RegulAtory Modules | Gifford Laboratory, MIT |
| GSNAP – Genomic Short-read Nucleotide Alignment Program | Genentech, 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 Depth | The Bioinformatics Research Group, University of Hong Kong |
| IGV – Integrative Genomics Viewer | Broad Institute |
| Illumina GenomeStudio | Illumina Software |
| Infernal – INFERence of RNA ALignment | Eddy group, HHMI Janelia Farm Research Campus, VA |
| Ingenuity Variant Analysis | Qiagen |
| InterPro | EMBL-EBI |
| jMOSAiCS – Joint Analysis of Multiple ChIP-seq Datasets | Keles Research Group, University of Wisconsin |
| JPred | Barton Group, University of Dundee |
| Kalign | EMBL-EBI |
| KELVIN | Battelle Center for Mathematical Medicine, Nationwide Children’s Hospital, Ohio |
| Kelviz | Battelle Center for Mathematical Medicine, Nationwide Children’s Hospital, Ohio |
| MACS – Model-based Analysis of ChIP-Seq data | Harvard University |
| MAExplorer – Microarray Explorer | MAExplorer development team |
| MAKER (“portable and […] configurable genome annotation pipeline”) | Yandell Laboratory, University of Utah |
| Maq – Mapping and Assembly with Quality | Maq development team |
| Maqview – graphical read alignment viewer | Maqview development team (Ruan et al.) |
| Mascot | Matrix Science |
| MATLAB Bioinformatics Toolbox | The Mathworks, Inc. |
| MATLAB Toolboxes (Optimization; Direct Search; Genetic Algorithms) | The Mathworks, Inc. |
| MDscan – Motif Discovery scan | Stanford Medical Informatics, Stanford University |
| MEGA – Molecular Evolutionary Genetics Analysis | MEGA team |
| MEMSAT3 – MEMbrane protein Structure And Topology | MEMSAT team, University College London, UK |
| MetaQTL | MetaQTL development team |
| Methylator (“An SVM Based Method for DNA Methylation Prediction”) | Methylator Development Team |
| MeV – MultiExperiment Viewer | MeV development team |
| Microarray Center cDNA Clone Search | NIEHS |
| MIDAS – Multi Instance Data Acquisition System | Science and Technology Facilities Council, UK |
| MIRA – Whole Genome Shotgun and EST Sequence Assembler | Bastien 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 data | Deqiang Sun, Baylor College of Medicine |
| MobyDick | The Rockefeller University |
| modMine (“data warehouse for the modENCODE project”) | University of Cambridge, Cambridge, UK |
| Mold2 | USFDA |
| MOSAiCS – MOdel-based one and two Sample Analysis and Inference for ChIP-Seq Data | Keles Research Group, University of Wisconsin |
| MrBayes | MrBayes development team |
| mrsFAST (short-read mapper) | mrsFAST development team |
| MUSCLE – MUltiple Sequence Comparison by Log- Expectation | EMBL-EBI |
| NCBI/ Primer-BLAST | National Center for Biotechnology Information, NLM, NIH |
| NetRecodon | NetRecodon development team |
| Newbler (“software package for de novo DNA sequence assembly”) | 454 Life Sciences, Roche Diagnostics Corporation |
| Novoalign | Novocraft Technologies |
| NucDe – A non-homogeneous hidden-state model on first order differences for automatic detection of nucleosome positions from MNase-chip and MNase-seq data | Keles Research Group, University of Wisconsin |
| NuPoP – Nucleosome Positioning Prediction Engine | Northwestern University (J.-P. Wang) |
| OptiRNA | University of Nebraska |
| PaGE – Patterns from Gene Expression | PaGE development team, University of Pennsylvania |
| PAM – Prediction Analysis for Microarrays | Stanford University |
| pepgrep | University of Essex |
| Persephone (“Genome Visualization & Exploration Software”) | Ceres, Inc. |
| PFAAT – Protein Family Alignment Annotation Tool | PFAAT development team |
| PhyML | S. Guindon, et al., CNRS |
| Phyre | Structural 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-GPCR | University of Athens, Greece |
| PredictProtein | ROSTLAB |
| Protein Prospector | UCSF |
| PSI-BLAST – Protein Similarity Search BLAST | EMBL-EBI |
| QTDT (Linkage Disequilibrium Analyses for Quantitative and Discrete Traits) | Abecasis Lab, University of Michigan |
| QTX | QTX development team |
| QuEST – Quantitative Enrichment of Sequence Tags | Stanford 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 |
| REDUCE | Harmen 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 Sequencing | Guorong Xu and RNA CoMPASS development team |
| SAMBA | Shamir Laboratory, Tel Aviv University |
| SAMtools – Sequence Alignment/Map | Li et al., Wellcome Trust Sanger Institute, UK and Broad Institute of MIT and Harvard, USA |
| SANDY | Gerstein Laboratory, Yale University |
| SCAMPI (“Prediction of membrane protein topology”) | Stockholm Bioinformatics Center, Stockholm University |
| SCOP – Structural Classification of Proteins | MRC Laboratory of Molecular Biology |
| SEQUEST | Yates Laboratory, University of Washington |
| Shape Signatures | Welsh 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 data | Python Software Foundation |
| SNAP – Screening for Non-Acceptable Polymorphisms | Rost Lab, Columbia University, New York |
| SNAP – SNP Annotation and Proxy Search | SNAP Development Team |
| SNP-o-matic (analysis of Solexa reads and comparison with reference) | Sanger Institute |
| SNPTrack | USFDA |
| SOAP – Short Oligonucleotide Analysis Package | Beijing 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 optimization | A. 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/Proteins | STRING 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-Coffee | EMBL-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 |
| Toxmatch | Joint 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 Study | VEGAS development team, Queensland Institute of Medical Research, Australia |
| Velvet (“Sequence assembler for very short reads”) | EMBL-EBI |
| X!Tandem | The Global Proteome Machine Organization |
Information Portals and Databases
| Resource | Developer |
|---|---|
| Alu Pairs Database | NIEHS |
| ASAP – A Systematic Annotation Package For Community Analysis of Genomes | University of Wisconsin, Madison |
| Berkeley Drosophila Genome Project | Berkeley 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 Databank | Thomson |
| BRENDA – BRaunschweig ENzyme DAtabase | D. Schomburg, Technische Universität Braunschweig, Germany |
| Cambridge Structural Database | Cambridge Crystallographic Data Centre |
| CATH (“Protein Structure Classification Database”) | University College, London |
| CharProtDB – Characterized Protein Database | J. Craig Venter Institute |
| ChemBank | Broad Institute |
| ChromDB – The Chromatin Database | BIO5 Institute |
| CluSTr | EMBL-EBI |
| CNV Project Data – Copy Number Variation Project Data | Wellcome Trust Sanger Institute, UK |
| COG – Clusters of Orthologous Groups of proteins | National 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 Movement | Mark Gerstein, et al., Yale University |
| DBCAT – DataBase of CpG islands and Analytical Tool | Research Center for Medical Excellence National Taiwan University |
| dbGaP – Database of Genotypes and Phenotypes | National Center for Biotechnology Information, NLM, NIH |
| dbSNP | National Center for Biotechnology Information, NLM, NIH |
| DiseaseMeth – human disease methylation database | College 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 Archive | EMBL-EBI |
| ENCODE – Encyclopedia Of DNA Elements | NHGRI, NIH |
| Ensembl Genome Browser | EMBL-EBI and Wellcome Trust Sanger Institute, UK |
| GBrowse (Generic Genome Browser) | GBrowse development team |
| GenBank | National Center for Biotechnology Information, NLM, NIH |
| Genetic Association Database | GAD development team and NIH |
| Genomatix Suite | Genomatix Software GmbH |
| GLIDA – GPCR-Ligand Database | Kyoto University |
| GOLD – Genomes Online Database | GOLD Team |
| GPCR NaVa database – G Protein-Coupled Receptors Natural Variants database | Leiden/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 Base | GPCRDB development team |
| GPCR-OKB – G Protein Coupled Receptor – Oligomer Knowledge Base | GPCR-OKB development team |
| GPCR-PD (“database for G protein-coupled receptors”) | Incyte Genomics |
| GVS – Genome Variation Server | University of Washington |
| HapMap | International HapMap Project |
| HGMD – Human Gene Mutation Database (integrated with Ingenuity Variant Analysis) | BIOBASE |
| Histone Database | NHGRI Division of Intramural Research, NIH |
| HIV Sequence database | Los Alamos National Laboratory |
| HomoloGene | National Center for Biotechnology Information, NLM, NIH |
| Human DNA Polymerase Gamma Mutation Database | NIEHS |
| Human Genome Browser | Genome Bioinformatics Group, UC Santa Cruz. |
| HuRef Genome Browser (Individual Human Genome Browser) | J. Craig Venter Institute |
| IMGT – ImMunoGeneTics information system | Marie-Paule Lefranc |
| IMGT/3Dstructure-DB – ImMunoGeneTics | Marie-Paule Lefranc |
| Integr8 | EMBL-EBI |
| InterPro | EMBL-EBI |
| iProClass | PIR – Protein Information Resource |
| IRD – Influenza Research Database | IRD Project Team |
| JSNP – Japanese Single Nucleotide Polymorphisms | University of Tokyo and the Japan Science and Technology Agency (JST) |
| KEGG GENES database | Kanehisa Laboratories, Japan |
| LMPD – LIPID MAPS Proteome Database | University of California, San Diego |
| LMSD – LIPID MAPS Structure Database | University of California, San Diego |
| MethBase – a reference methylome database | Smith lab, Molecular and Computational Biology, U. of Southern California |
| MethylomeDB – Brain Methylome Database | Haghighi lab, Columbia University |
| MGI – Mouse Genome Informatics | The Jackson Laboratory, Maine and MGI team |
| MINT – Molecular INTeraction database | University of Rome Tor Vergata, Italy |
| miRBase – microRNA database | Griffiths-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 Elements | modENCODE Project Consortium |
| Mouse Genome Resequencing Project | NIEHS |
| NCBI Gene | National Center for Biotechnology Information, NLM, NIH |
| NCBI Model Organisms Guide | National Center for Biotechnology Information, NLM, NIH |
| NCBI Nucleotide Sequence Database | National Center for Biotechnology Information, NLM, NIH |
| NCI DIS 3D – National Cancer Institute Drug Information System 3D structure database | NCI (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 database | Computational Genomics and Bioinformatics Group, U. Granada, Spain |
| NIEHS SNPs Exome Variant Server | NIEHS and University of Washington |
| OChem – Online Chemical database | eADMET GmbH, Germany |
| ORDB – Olfactory Receptor DataBase | Yale University |
| Pan Asian SNP Database | Pan-Asian SNP Consortium |
| PDB – Protein Data Bank | RCSB PDB (Rutgers University, UCSD) |
| Peptide Atlas | PeptideAtlas 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 Database | National Center for Biotechnology Information, NLM, NIH |
| RGD – Rat Genome Database | Medical 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 Knowledgebase | Protein 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 Database | Stanford University |
| SNP500Cancer | SAIC-Frederick, NCI-FCRDC, MD |
| SNPinfo Web Server | NIEHS |
| SpringerProtocols | Springer-Verlag |
| Structural Biology Software Database | Theoretical and Computational Biophysics Group, University of Illinois |
| TransFac | Gene Regulation |
| UniSTS (“database of sequence tagged sites”) | National Center for Biotechnology Information, NLM, NIH |
| VEGA – Vertebrate Genome Annotation | HAVANA group, Wellcome Trust Sanger Institute, UK |
| ViPR – Virus Pathogen Resource | ViPR Project team |
| WormBase | WormBase development team |
| wwPDB – Worldwide Protein Data Bank | RCSB PDB, USA, PDBe, Europe, PDBj, Japan and BMRB, USA |
| ZebrafishMine | ZFIN 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
| Resource | Developer |
|---|---|
| Accelerated Stochastic Simulation Algorithm for Reaction Networks | University 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 Exchange | BioPAX development team |
| Bio-PEPA Workbench | Bio-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.) |
| CellDesigner | Systems Biology Institute, Japan |
| CellNetAnalyzer / FluxAnalyzer | Max Planck Institute |
| CellNetOptimizer | CellNOpt 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 Maps | Hippron Physiomics Inc |
| Dynetica | Duke University |
| Ecolab (“software package […] looking at the dynamics of evolution”) | Ecolab development team |
| Edinburgh Pathway Editor | EPE development team |
| EMBOSS – European Molecular Biology Open Software Suite | EMBOSS 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 Tool | University of California, Irvine |
| Genes2FANs | SBCNY and Mount Sinai School of Medicine |
| GenMAPP – Gene Map Annotator and Pathway Profiler | Gladstone Institutes, UCSF |
| Gepasi (see COPASI) | Virginia Bioinformatics Institute, Virginia Tech |
| geWorkBench – Genomics Workbench | NCI (National Cancer Institute), NIH |
| GNA – Genetic Network Analyzer | Ibis |
| GRAM – Genetic RegulAtory Modules | Gifford Laboratory, MIT |
| IPA – Ingenuity Pathway Analysis | Qiagen N.V. |
| iPathwayGuide | Advaita Corporation |
| iPathways | The Systems Biology Institute, Japan |
| iTOL – Interactive Tree Of Life | EMBL, Germany |
| Maximally Informative Genes | Androulakis Laboratory, Rutgers University |
| MetaCore | Thomson Reuters |
| MetaMerge (reconcile differences in existing metabolic network models) | MetaMerge development team |
| Meteor | Lhasa Limited |
| MetNetGE | Iowa State University |
| Mgenome | Gu Laboratory, Iowa State University |
| MONGOOSE – MetabOlic Network GrOwth Optimization Solved Exactly | MONGOOSE development team, MIT |
| Moose – Multiscale Neuroscience and Systems Biology Simulator | Moose team |
| Network | Fluxus Technology Ltd. |
| NEURON (“for empirically-based simulations of neurons and networks of neurons”) | NEURON development team |
| NSL – Neural Simulation Language | NSL Development Team |
| Omix | Peter Droste |
| OpenFLUX (“MATLAB-based modelling software for 13C metabolic flux analysis”) | OpenFLUX development team |
| Osprey | Samuel Lunenfeld Research Institute, Canada |
| PathVisio (“a tool to edit and analyze biological pathways”) | PathVisio development team |
| Pathway Commons | Memorial Sloan-Kettering Cancer Center and University of Toronto |
| Pathway Map Creator | Thomson Reuters |
| Pathway Processor | Istituto Agrario di San Michele all’Adige, Italy |
| Pathway Studio | Pathway Studio |
| Pathway Tools | Pathway Tools development team |
| PathwayLab – in silico pathway analysis tool | Innetics |
| PHYLIP – PHYLogeny Inference Package | University of Washington |
| REDUCE | Harmen Bussemaker Laboratory, Columbia University |
| SAMBA | Shamir Laboratory, Tel Aviv University |
| SANDY | Gerstein 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 |
| Sets2Networks | SBCNY and Mount Sinai School of Medicine |
| SimBiology app for MATLAB (“Model, simulate, and analyze biological systems”) | The MathWorks, Inc. |
| SMBioNet | University of Nice, France |
| SNIP – S-Space Network Inference Procedure | Rabitz 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 Chemicals | STITCH development team |
| SubMAP – Subnetwork Mappings in Alignment of Pathways | Bioinformatics Lab, University of Florida |
| TargetP | Center for Biological Sequence Analysis, Technical University of Denmark |
| VANTED – Visualization and Analysis of Networks containing Experimental Data | Plant Bioinformatics Group, Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben, Germany |
| visANT | Boston University |
Information Portals and Databases
| Resource | Developer |
|---|---|
| BBID – Biological Biochemical Image Database | NIA, Intramural Research Program |
| BIND – Biomolecular Interaction Network Database | Christopher Hogue’s Research Laboratory |
| BioCarta | BioCarta LLC |
| Biocatalysis/ Biodegradation Database | University of Minnesota |
| BioGRID – Biological General Repository for Interaction Datasets | BioGRID 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 Groups | EMBL, 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 |
| HumanCyc | SRI International |
| Human-gpDB (“database of human GPCRs, G-proteins, Effectors and their interactions”) | Human-gpDB team |
| KEGG – Kyoto Encyclopedia of Genes and Genomes | Kanehisa Laboratories, Japan |
| KEGG GENES database | Kanehisa Laboratories, Japan |
| KUPKB – The Kidney and Urinary Pathway Knowledge Base | INSERM, France and University of Manchester, UK |
| MetaCyc | SRI International |
| MetNetDB – MetNet Database | Iowa State University |
| MGI – Mouse Genome Informatics | The Jackson Laboratory, Maine and MGI team |
| MINT – Molecular INTeraction database | University of Rome Tor Vergata, Italy |
| MouseMine | MGI at The Jackson Laboratory and InterMine project at Cambridge Systems Biology Centre, UK |
| OrthoDB | University of Geneva Medical School, Switzerland |
| PANTHER – Protein ANalysis THrough Evolutionary Relationships | PANTHER development team (Paul Thomas) |
| PathArt | Jubilant Biosys |
| PathCase Pathways Database System | Case Western Reserve University |
| Pathway Database | Protein Lounge |
| PD map – Parkinson’s disease map | LCSB and Hiroaki Kitano team at SBI, Tokyo |
| PID – Pathway Interaction Database | NCI (National Cancer Institute), NIH |
| RatMine | University of Cambridge, Cambridge, UK |
| Reactome | Reactome team |
| RGD – Rat Genome Database | Medical College of Wisconsin |
| SGD – Saccharomyces Genome Database | Stanford University |
| SPAD – Signaling Pathway Database | Kyushu University |
| SpringerProtocols | Springer-Verlag |
| TransFac | Gene Regulation |
| TransPath | Gene 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
| Resource | Developer |
|---|---|
| ADME Workbench (“pharmacokinetic modeling by integrating […] absorption, distribution, metabolism and excretion methods”) | The AEgis Technologies Group |
| Affymetrix Expression Console | Affymetrix |
| Affymetrix Transcriptome Analysis Console | Affymetrix |
| ArrayTrack/ebTrack | USFDA and ebCTC |
| Automated Particle Tracking and Analysis Software | University 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-ArrayTools | Dr. 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 Predict | Cyprotex |
| CMARRT (A tool for the analysis of ChIP-chip data from tiling arrays by incorporating the correlation structure) | Keles Research Group, University of Wisconsin |
| CombiTool | Leibniz Institute for Age Research – FLI, Germany |
| CSEM – Multi-read Allocation for ChIP-seq | Keles Research Group, University of Wisconsin |
| Cufflinks – Transcript assembly, differential expression and regulation for RNA-Seq samples | UC Berkeley, JHU, and Caltech |
| CVSim | CVSim development team |
| DBChIP – program to detect differentially bound sharp binding sites across multiple conditions | Keles Research Group, University of Wisconsin |
| dChip – DNA-Chip Analyzer | Harvard University and Stanford University |
| Decision Forest | USFDA |
| 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 system | Computational Chemodynamics Laboratory |
| ELECANS – A Computational Cancer Systems Biology Simulation Studio | Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Korea |
| EMBER | University of Chicago |
| EpiGRAPH – for advanced (epi-) genome analysis and prediction | EpiGRAPH development team |
| EpiSIM Platform | TIGA 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 impute | Computational Chemodynamics Laboratory |
| GSEA – Gene Set Enrichment Analysis | Broad Institute |
| IGV – Integrative Genomics Viewer | Broad Institute |
| IPA – Ingenuity Pathway Analysis | Qiagen N.V. |
| J/maanova | Churchill 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 Datasets | Keles Research Group, University of Wisconsin |
| MAQC – MicroArray Quality Control | USFDA |
| MATLAB Bioinformatics Toolbox | The Mathworks, Inc. |
| maxdView | Manchester Bioinformatics |
| MethTools | Leibniz Institute for Age Research – Fritz Lipmann Institute, Germany |
| MOABS – MOdel based Analysis of Bisulfite Sequencing data | Deqiang Sun, Baylor College of Medicine |
| Monocle – toolkit for analyzing single-cell gene expression experiments | Cole Trapnell |
| MOSAiCS – MOdel-based one and two Sample Analysis and Inference for ChIP-Seq Data | Keles 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 data | Keles Research Group, University of Wisconsin |
| OmicsOffice for Microarrays | Integromics |
| Pathway Studio | Pathway Studio |
| Persephone (“Genome Visualization & Exploration Software”) | Ceres, Inc. |
| ProteoIQ (“qualitative and quantitative suite for proteomics”) | Premier Biosoft |
| R/maanova | Churchill Group, Jackson Laboratory |
| RealTimeDesign Software | Biosearch 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 data | Python Software Foundation |
| SPELL – Serial Pattern of Expression Levels Locator | Princeton University |
| SPLS – Sparse partial least squares | Keles 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 |
| ToxFX | NIEHS |
| WebArray | WebArray project team |
Information Portals and Databases
| Resource | Developer |
|---|---|
| ACToR – Aggregated Computational Toxicology Resource | USEPA |
| AHEAD – Alliance for Human Epigenomics and Disease | AHEAD Task Force |
| AOPWiki – Adverse Outcome Pathway Wiki | AOPWiki team (includes European Commission JRC, USEPA ORD and OECD) |
| ArrayExpress | EMBL-EBI |
| Berkeley Drosophila Genome Project | Berkeley 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 Study | NIEHS |
| CEBS – Chemical Effects in Biological Systems | NIEHS |
| CGAP – Cancer Genome Anatomy Project | NCI (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 Database | Mount Desert Island Biological Laboratory |
| CREMOFAC – Chromatin Remodeling Factors | Chromatin Biology Lab, Jawaharlal Nehru Centre for Advanced Scientific Research, India |
| DrugMatrix | NIEHS |
| EADB – Estrogenic Activity Database | USFDA |
| EDKB – Endocrine Disruptor Knowledge Base | USFDA |
| EMAGE – e-Mouse Atlas of Gene Expression | EMAGE team |
| FDALabel – Full-Text Search of Drug Label Database | USFDA |
| FlyMine – “integrated database for Drosophila and Anopheles genomics” | University of Cambridge, Cambridge, UK |
| GAC – Genetic Alterations in Cancer | NIEHS |
| GeMDBJ – Genome Medicine Database of Japan | SGMGP (The Study Groups of Millennium Genome Project for Alzheimer’s disease, Cancer, Diabetes Mellitus, Hypertension, Asthma and Pharmacogenetics) |
| Gene Expression Atlas | EMBL-EBI |
| Gene Weaver | Jackson Laboratory, ME and collaborators |
| GeneTox | NLM |
| Genomatix Suite | Genomatix Software GmbH |
| GENSAT – Gene Expression Nervous System ATlas database | Rockefeller University |
| HEP – Human Epigenome Project | HEP Consortium |
| HEROIC – High-Throughput Epigenetic Regulatory Organization in Chromatin Project | HEROIC Project Consortium |
| HGMD – Human Gene Mutation Database (integrated with Ingenuity Variant Analysis) | BIOBASE |
| Human Epigenome Atlas | Bioinformatics Research Laboratory, Baylor College of Medicine |
| ICRP – International Commission on Radiological Protection – Database of Dose Coefficients | ICRP |
| IRIS – Integrated Risk Information System | USEPA |
| LIVERTOX™ | NIDDK and NLM |
| LTKB – Liver Toxicity Knowledge Base | USFDA |
| Mammalian Protein-Protein Interaction Database | Munich Information Center for Protein Sequences (MIPS), Institute of Bioinformatics and Systems Biology (IBIS), Germany |
| MeInfoText | National Taiwan University |
| MethDB – database for DNA methylation and environmental epigenetic effects | MethDB team |
| MethPrimerDB | Ghent University, Belgium |
| MethyCancer – Database for studying human DNA Methylation and Cancer | Chinese Academy of Sciences |
| MethyLogiX DNA methylation database | Epigenetics Group, Technical University of Munich, Germany (A. Schumacher) |
| MGI – Mouse Genome Informatics | The Jackson Laboratory, Maine and MGI team |
| microRNA.org | |
| MouseMine | MGI at The Jackson Laboratory and InterMine project at Cambridge Systems Biology Centre, UK |
| NCBI Epigenomics | National Center for Biotechnology Information, NLM, NIH |
| NCBI GEO – NCBI Gene Expression Omnibus database | National Center for Biotechnology Information, NLM, NIH |
| NIH Roadmap Epigenomics Project Data | National Center for Biotechnology Information, NLM, NIH |
| Oncomine | Life Technologies Corporation |
| Persephone (“Genome Visualization & Exploration Software”) | Ceres, Inc. |
| Personalized Medicine Research Project population-based bio-bank | Marshfield Clinic Research Foundation |
| PubMed | National Center for Biotechnology Information, NLM, NIH |
| PubMeth | BioBix, Laboratory for Bioinformatics and Computational Genomics, Ghent University, Belgium |
| PUMAdb – Princeton University MicroArray database (supersedes SMD) | Princeton University |
| RatMine | University of Cambridge, Cambridge, UK |
| REBASE – The Restriction Enzyme dataBASE | New England Biolabs, Inc. (Roberts, R.J., Macelis, D.) |
| RNAi database | NYU’s Center for Genomics & Systems Biology |
| Roadmap Epigenomics Project Data | NIEHS |
| RUCDR – Rutgers University Cell and DNA Repository | RUCDR Team |
| SGD – Saccharomyces Genome Database | Stanford University |
| SMD – Stanford Microarray Database (see PUMAdb) | Stanford University |
| SpringerProtocols | Springer-Verlag |
| StemBase (gene expression data obtained from stem cells) | Canadian Stem Cell Network |
| TissueDistributionDBs | German Cancer Research Center, DKFZ, Heidelberg |
| ToxCast – Toxicity Forecaster | USEPA |
| UCSC Genome Browser | Genome Bioinformatics Group, UC Santa Cruz |
| WashU Epigenome Browser | Washington 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
| Resource | Developer |
|---|---|
| ADZE – Allelic Diversity AnalyZEr | Stanford 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 Software | University of California, Irvine |
| Biopython (“tools for biological computation written in Python”) | Biopython development team |
| CellSys | Interdisciplinary 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 Discovery | National Institute of Allergy and Infectious Diseases, NIH |
| ELECANS – A Computational Cancer Systems Biology Simulation Studio | Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Korea |
| EpiSIM Platform | TIGA Center Heidelberg, Germany |
| FoundationOne | Foundation Medicine |
| Gene Network Inference Tool | University of California, Irvine |
| Gwyddion (“a modular program for SPM (scanning probe microscopy) data visualization and analysis”) | Gwyddion development team |
| KELVIN | Battelle Center for Mathematical Medicine, Nationwide Children’s Hospital, Ohio |
| Kelviz | Battelle Center for Mathematical Medicine, Nationwide Children’s Hospital, Ohio |
| Literature Lab | Acumenta 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.) |
| NewHybrids | NewHybrids development team |
| QTDT (Linkage Disequilibrium Analyses for Quantitative and Discrete Traits) | Abecasis Lab, University of Michigan |
| Taverna | myGrid, University of Manchester |
| Tute (“web application […] in the cloud and […] analyze and annotate entire human genomes”) | Tute Genomics |
| X-Tile | Yale University |
Information Portals and Databases
| Resource | Developer |
|---|---|
| Biocatalysis/ Biodegradation Database | University of Minnesota |
| BioGRID – Biological General Repository for Interaction Datasets | BioGRID Team |
| BioNumbers (“The Database of Useful Biological Numbers”) | Weizmann Institute, Israel |
| CEBS – Chemical Effects in Biological Systems | NIEHS |
| 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 Database | BIO5 Institute |
| COG – Clusters of Orthologous Groups of proteins | National Center for Biotechnology Information, NLM, NIH |
| CREMOFAC – Chromatin Remodeling Factors | Chromatin Biology Lab, Jawaharlal Nehru Centre for Advanced Scientific Research, India |
| dbGaP – Database of Genotypes and Phenotypes | National Center for Biotechnology Information, NLM, NIH |
| DiseaseMeth – human disease methylation database | College of Bioinformatics Sci. and Tech., Harbin Medical U., China |
| EMA – e-Mouse Atlas | EMA team |
| ESCAPE – Embryonic Stem Cells Atlas of Pluripotency Evidence | SBCNY 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 Catalog | NHGRI Division of Genomic Medicine, NIH |
| GWASdb | GWASdb team |
| Histone Database | NHGRI Division of Intramural Research, NIH |
| Human Epigenome Atlas | Bioinformatics 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 Database | IUPHAR-DB development team |
| KEGG – Kyoto Encyclopedia of Genes and Genomes | Kanehisa Laboratories, Japan |
| KUPKB – The Kidney and Urinary Pathway Knowledge Base | INSERM, France and University of Manchester, UK |
| LMPD – LIPID MAPS Proteome Database | University of California, San Diego |
| LMSD – LIPID MAPS Structure Database | University of California, San Diego |
| MeInfoText | National Taiwan University |
| MethDB – database for DNA methylation and environmental epigenetic effects | MethDB team |
| MethPrimerDB | Ghent University, Belgium |
| MGI – Mouse Genome Informatics | The Jackson Laboratory, Maine and MGI team |
| microBEnet – microbiology of the Built Environment network | Eisen Lab at University of California, Davis and Building Ecology Research Group |
| NCBI Epigenomics | National Center for Biotechnology Information, NLM, NIH |
| NIMH-RGR Data Explorer | NIMH Center for Collaborative Genomic Studies on Mental Disorders |
| OmicBrowse | Genome-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 Relationships | PANTHER development team (Paul Thomas) |
| PATRIC – Pathosystems Resource Integration Center | PATRIC Project Team |
| Personalized Medicine Research Project population-based bio-bank | Marshfield Clinic Research Foundation |
| PharmGKB – Pharmacogenomics Knowledgebase | US Dept of Health and Human Services |
| PubMeth | BioBix, Laboratory for Bioinformatics and Computational Genomics, Ghent University, Belgium |
| REBASE – The Restriction Enzyme dataBASE | New England Biolabs, Inc. (Roberts, R.J., Macelis, D.) |
| RGD – Rat Genome Database | Medical College of Wisconsin |
| RNAi database | NYU’s Center for Genomics & Systems Biology |
| Roadmap Epigenomics Project Data | NIEHS |
| RUCDR – Rutgers University Cell and DNA Repository | RUCDR Team |
| SBKB – Structural Biology Knowledgebase | Protein Structure Initiative and Nature Publishing Group |
| SKY/M-FISH and CGH Database | National Center for Biotechnology Information, NLM, NIH and National Cancer Institute, NIH |
| SpringerProtocols | Springer-Verlag |
| VectorBase (“Bioinformatics Resource for Invertebrate Vectors of Human Pathogens”) | VectorBase Project team |
| ViPR – Virus Pathogen Resource | ViPR Project team |
| WashU Epigenome Browser | Washington University |
| Yeast GFP Fusion Localization Database | University of California, San Francisco and SGD |