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  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