Bioinformatics

Bio-Ontologies

Computational Analysis Tools

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

Information Portals and Databases

Resource	Developer
CharProtDB - Characterized Protein Database	J. Craig Venter Institute
ChEBI - Chemical Entities of Biological Interest	EMBL-EBI
FlyMine - "integrated database for Drosophila and Anopheles genomics"	University of Cambridge, Cambridge, UK
Gene Weaver	Jackson Laboratory, ME and collaborators
GFBio - German Federation for the curation of Biological data	GFBio
GO Database - Gene Ontology Database	Gene Ontology Consortium
MouseMine	MGI at The Jackson Laboratory and InterMine project at Cambridge Systems Biology Centre, UK
RatMine	University of Cambridge, Cambridge, UK
YeastMine ("Search and retrieve S. cerevisiae data")	SGD and Intermine project at Cambridge Systems Biology Centre, UK
ZebrafishMine	ZFIN at University of Oregon and InterMine project at Cambridge Systems Biology Centre, UK

Biomolecular Sequences/Structures

Characterizations and comparisons of biomolecular sequences and structures

Computational Analysis Tools

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