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Use the direct search box below to find tools, databases and resources by name or developer. The search results will appear in a table below the search box.

ResourceDeveloperCategory
@RISK - At Risk ("risk analysis using Monte Carlo simulation")Palisade CorporationData/Simulation Pattern Analysis - Sensitivity/Uncertainty Analysis
1000Minds ("decision-making software")1000Minds Ltd. and University of Otago (P. Hansen, F. Ombler)Data/Simulation Pattern Analysis - Data Mining/Pattern Recognition
2MOD ("estimate the relative likelihoods of a model of immigration-drift equilibrium versus drift since a certain time")2MOD team (M. Beaumont)Exposure/Risk Analysis - Ecological Risks
3DFEMWATER/ 3DLEWASTE - Three-Dimensional Finite Element Model of Water Flow/ Three-Dimensional Lagrangian-Eulerian Finite Element Model of Waste TransportUSEPAEnviroinformatics - Environmental Fate and Transport
7TMRmine ("hierarchical mining tool for 7TMRs")University of NebraskaBioinformatics - Biomolecular Sequences/Structures
ABySS - Assembly By Short SequencesMichael Smith Genome Sciences Centre, Canada and BC Cancer Research CentreBioinformatics - Biomolecular Sequences/Structures
ABySS-Explorer - Assembly By Short Sequences ExplorerMichael Smith Genome Sciences Centre, Canada and BC Cancer Research CentreBioinformatics - Biomolecular Sequences/Structures
Accelerated Stochastic Simulation Algorithm for Reaction NetworksUniversity of California, IrvineBioinformatics - Interactions/Biopathways/Bionetworks
Accelrys Discovery Studio ("predictive science application for the Life Sciences")AccelrysCheminformatics - Property/Activity Prediction
ACD/NMR DatabasesACD/LabsCheminformatics - Structure Elucidation
ACD/NMR ExpertACD/LabsCheminformatics - Structure Elucidation
ACD/NMR PredictorsACD/LabsCheminformatics - Structure Elucidation
ACD/NMR Processor Academic Edition (processing of 1D and 2D NMR data)ACD/LabsCheminformatics - Structure Elucidation
ACD/Tox SuiteACD/LabsCheminformatics - Property/Activity Prediction
ACE - Acute-to-Chronic Estimation with Time-Concentration-Effect ModelsUSEPAExposure/Risk Analysis - Ecological Risks
ACRES - Assessment, Cleanup and Redevelopment Exchange SystemUSEPAEnviroinformatics - Release Mapping/Modeling
acslX ("modeling and simulation of dynamic systems and processes")AEgis TechnologiesGeneral Development Tools - Development and Programming
ACToR - Aggregated Computational Toxicology ResourceUSEPABioinformatics - Biological Dose-Response; Computational Toxicology - Toxicoinformatics
Acts/ Risk - Analytical Contaminant Transport Analysis System/ Health Risk Analysis SoftwareM. M. Aral et al., Georgia Institute of Technology, GAEnviroinformatics - Environmental Fate and Transport
ADAPT ("computational modeling platform [...] for pharmacokinetic and pharmacodynamic applications")Biomedical Simulations Resource, USCComputational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
ADB - Assessment Database ("database application for tracking water quality assessment data")USEPAEnviroinformatics - Spatiotemporal Mapping/Analysis; Enviroinformatics - Environmental Fate and Transport
ADME Workbench ("pharmacokinetic modeling by integrating [...] absorption, distribution, metabolism and excretion methods")The AEgis Technologies GroupBioinformatics - Biological Dose-Response; Computational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
ADMET Predictor - Absorption, Distribution, Metabolism, Elimination, Toxicity PredictorSimulations Plus, Inc.Cheminformatics - Property/Activity Prediction; Computational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
ADZE - Allelic Diversity AnalyZErStanford UniversityBioinformatics - Data Integration
AEGL - Acute Exposure Guideline LevelsUSEPACheminformatics - Property/Activity Prediction
AERMOD - AMS/EPA Regulatory ModelUSEPAEnviroinformatics - Environmental Fate and Transport
AERONET - AErosol RObotic NETwork dataAERONETEnviroinformatics - Spatiotemporal Mapping/Analysis
Affymetrix Expression ConsoleAffymetrixBioinformatics - Biological Dose-Response; Exposure/Risk Analysis - Biomarkers
Affymetrix GeneChip Sequence Analysis SoftwareAffymetrixBioinformatics - Biomolecular Sequences/Structures; Exposure/Risk Analysis - Biomarkers
Affymetrix Transcriptome Analysis ConsoleAffymetrixBioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Biological Dose-Response; Exposure/Risk Analysis - Biomarkers
AFLP-SURV ("estimates genetic diversity and population genetic structure from population samples analysed with AFLP or RAPD methods")Xavier VekemansBioinformatics - Data Integration
AGDISP - AGricultural DISPersalUSDA Forest ServiceEnviroinformatics - Environmental Fate and Transport; Exposure/Risk Analysis - Ecological Risks
AgDRIFTUSEPA, USDA Forest Service and Spray Drift Task ForceEnviroinformatics - Environmental Fate and Transport; Exposure/Risk Analysis - Ecological Risks
Agent Analyst ("Agent Based Modeling Extension for ArcGIS")University of Redlands, Argonne National LaboratoryEnviroinformatics - Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis - Socioeconomic/LSB Modeling
Agricultural Chemical Use DatabaseNational Agricultural Statistics ServiceEnviroinformatics - Release Mapping/Modeling
AGWA - Automated Geospatial Watershed AssessmentUSEPA, USDA and University of ArizonaEnviroinformatics - Environmental Fate and Transport
AHEAD - Alliance for Human Epigenomics and DiseaseAHEAD Task ForceBioinformatics - Biological Dose-Response; Exposure/Risk Analysis - Biomarkers
AHS - American Housing SurveyUS Census BureauEnviroinformatics - Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis - Microenvironmental/LCA Modeling; Exposure/Risk Analysis - Socioeconomic/LSB Modeling
Air Liquide Gas EncyclopediaAir LiquideCheminformatics - Property/Activity Prediction
AirBase ("European air quality database")European Environment Agency and European Topic Centre on Air Pollution and Climate Change and Mitigation (ETC/ACM)Enviroinformatics - Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis - Cumulative/Aggregate Exposures
AirDataUSEPAEnviroinformatics - Release Mapping/Modeling
AIRMEX (European Indoor Air Monitoring and Exposure Assessment Project database)European Commission, JRC, IHCPEnviroinformatics - Spatiotemporal Mapping/Analysis; Enviroinformatics - Release Mapping/Modeling
AIRS/AFS - Air Facility SystemUSEPAEnviroinformatics - Release Mapping/Modeling
AllergomeAllergome platform development teamExposure/Risk Analysis - Microenvironmental/LCA Modeling
ALLPATHS-LG ("genome assembly from low cost data")Broad InstituteBioinformatics - Biomolecular Sequences/Structures
ALOGPS ("provides interactive on-line prediction of logP, water solubility and pKa(s) of compounds")Virtual Computational Chemistry LaboratoryCheminformatics - Property/Activity Prediction
ALOHA - Areal Locations of Hazardous AtmospheresNOAAEnviroinformatics - Release Mapping/Modeling; Enviroinformatics - Environmental Fate and Transport; Exposure/Risk Analysis - Human Health Risks
ALOHA (Areal Locations of Hazardous Atmospheres) ArcMap Import ToolsUS NOAA Office of Response and RestorationEnviroinformatics - Release Mapping/Modeling; Enviroinformatics - Environmental Fate and Transport; Exposure/Risk Analysis - Human Health Risks
Alscript ("program to format multiple sequence alignments in PostScript")University of OxfordBioinformatics - Biomolecular Sequences/Structures
Alu Pairs DatabaseNIEHSBioinformatics - Biomolecular Sequences/Structures
AMDIS - Automated MS Deconvolution and Identification SystemNISTCheminformatics - Structure Elucidation
AMEM - ADL Migration Estimation ModelUSEPAExposure/Risk Analysis - Microenvironmental/LCA Modeling
American Cleaning Institute Cleaning Product Ingredient InventoryAmerican Cleaning InstituteExposure/Risk Analysis - Microenvironmental/LCA Modeling
American Communities ProjectAmerican Communities Project, American University, Washington, DCEnviroinformatics - Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis - Socioeconomic/LSB Modeling
AmiGO (Gene Ontology database search)AmiGO development teamBioinformatics - Bio-Ontologies; Computational Toxicology - Virtual Cells, Tissues, Organs
AMP - Agent Modeling PlatformEclipse FoundationExposure/Risk Analysis - Socioeconomic/LSB Modeling; General Development Tools - Development and Programming
AnalyticaLumina Decision SystemsGeneral Development Tools - Development and Programming
ANSYS CFD (Computational Fluid Dynamics)ANSYSGeneral Development Tools - Development and Programming
ANSYS Fluent ("Flow Modeling Simulation Software")ANSYSGeneral Development Tools - Development and Programming
ANTHROPAC ("program for cultural domain analysis")Analytic TechnologiesEnviroinformatics - Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis - Socioeconomic/LSB Modeling
Antigenicity PlotLuca ToldoBioinformatics - Biomolecular Sequences/Structures
AnyLogic ("simulation tool that supports Discrete Event, Agent Based, and System Dynamics Simulation")AnyLogic CompanyExposure/Risk Analysis - Socioeconomic/LSB Modeling; General Development Tools - Development and Programming
AOPWiki - Adverse Outcome Pathway WikiAOPWiki team (includes European Commission JRC, USEPA ORD and OECD)Bioinformatics - Biological Dose-Response; Computational Toxicology - Toxicoinformatics; Computational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
AqQAAqQA, LLCGeneral Development Tools - Data Visualization
AQS - Air Quality SystemUSEPAEnviroinformatics - Spatiotemporal Mapping/Analysis; Enviroinformatics - Release Mapping/Modeling
AQTESOLV - AQuifer TEst SOLVerHydroSOLVE, Inc.Enviroinformatics - Environmental Fate and Transport
AQUATOX ("simulation model for aquatic systems")USEPA and R. Park, EcomodelingEnviroinformatics - Environmental Fate and Transport; Exposure/Risk Analysis - Ecological Risks
AquiferWin32ESI Ltd.Enviroinformatics - Environmental Fate and Transport; Exposure/Risk Analysis - Ecological Risks
ARAGORN (tRNA and tmRNA detection)ARAGORN development teamBioinformatics - Biomolecular Sequences/Structures
Arc Hydro (ArcGIS add-in to support geospatial and temporal data analyses)EsriEnviroinformatics - Spatiotemporal Mapping/Analysis
ArcGIS (geographical information system mapping and visualization)EsriEnviroinformatics - Spatiotemporal Mapping/Analysis; General Development Tools - Data Visualization
ARCON96 ("model for calculating concentrations in the vicinity of buildings")US Nuclear Regulatory Commission/ Pacific Northwest National Laboratory
ArcPadEsriEnviroinformatics - Spatiotemporal Mapping/Analysis; General Development Tools - Data Visualization
Arcv2CADGuthrie CAD/GIS Software Pty Ltd.General Development Tools - Data Visualization
ARES Commander EditionGraebert GmbHGeneral Development Tools - Development and Programming; General Development Tools - Data Visualization
ArrayExpressEMBL-EBIBioinformatics - Biological Dose-Response; Computational Toxicology - Toxicoinformatics; Exposure/Risk Analysis - Biomarkers
ArrayTrack/ebTrackUSFDA and ebCTCBioinformatics - Biological Dose-Response; Computational Toxicology - Toxicoinformatics
ARS Water databaseUSDA-ARS Hydrology LaboratoryEnviroinformatics - Environmental Fate and Transport
Artboard ("vector-based drawing software" for Mac OS X)Mapdiva, LLCGeneral Development Tools - Data Visualization
ASAP - A Systematic Annotation Package For Community Analysis of GenomesUniversity of Wisconsin, MadisonBioinformatics - Biomolecular Sequences/Structures
Ascape ("developing and exploring general-purpose agent-based models")Ascape development teamExposure/Risk Analysis - Socioeconomic/LSB Modeling; General Development Tools - Development and Programming
ASOS/AWOS - Automated Surface and Weather Observing SystemsFAAEnviroinformatics - Environmental Fate and Transport
ASPEN - Assessment System for Population Exposure NationwideUSEPAEnviroinformatics - Environmental Fate and Transport
ASTER - Assessment Tools for the Evaluation of RiskUSEPAExposure/Risk Analysis - Ecological Risks
atBioNet ("an Integrated Network Analysis Tool […] in Genomics and Proteomics")USFDABioinformatics - Interactions/Biopathways/Bionetworks; Bioinformatics - Data Integration
Atlas of United States MortalityCDCEnviroinformatics - Spatiotemporal Mapping/Analysis
ATTAINS - Assessment, TMDL Tracking and ImplementatioN SystemUSEPAEnviroinformatics - Release Mapping/Modeling
ATTILA - Analytical Tools Interface for Landscape AssessmentsUSEPAExposure/Risk Analysis - Ecological Risks
ATUS - American Time Use SurveyU.S. Bureau of Labor StatisticsExposure/Risk Analysis - Microenvironmental/LCA Modeling; Exposure/Risk Analysis - Socioeconomic/LSB Modeling; Exposure/Risk Analysis - Cumulative/Aggregate Exposures
AUGUSTUS ("predicts genes in eukaryotic genomic sequences")University of Göttingen and University of Greifswald, GermanyBioinformatics - Biomolecular Sequences/Structures
AutoDock (docking tools suite)The Scripps Research InstituteCheminformatics - Property/Activity Prediction; Bioinformatics - Biomolecular Sequences/Structures
Automated Particle Tracking and Analysis SoftwareUniversity of California, IrvineBioinformatics - Biological Dose-Response; Bioinformatics - Data Integration; Data/Simulation Pattern Analysis - Machine Learning Algorithms
AuvTool ("statistical analysis of variability and uncertainty associated with fitting parametric probability distributions to data sets")North Carolina State University and USEPAData/Simulation Pattern Analysis - Data Mining/Pattern Recognition; Data/Simulation Pattern Analysis - Sensitivity/Uncertainty Analysis
BANJO: Bayesian Network Inference with Java ObjectsDuke UniversityData/Simulation Pattern Analysis - Data Mining/Pattern Recognition
BASE - BioArray Software EnvironmentBASE development team
BASINS - Better Assessment Science Integrating point & Non-point SourcesUSEPAEnviroinformatics - Environmental Fate and Transport
BASS - Bioaccumulation and Aquatic System SimulatorUSEPAExposure/Risk Analysis - Ecological Risks
BBID - Biological Biochemical Image DatabaseNIA, Intramural Research ProgramBioinformatics - Interactions/Biopathways/Bionetworks
BCF database - Bio-concentration Factors Gold standard databaseCefic LRI and EURASExposure/Risk Analysis - Human Health Risks; Exposure/Risk Analysis - Ecological Risks
BEACON - Beach Advisory and Closing On-line NotificationUSEPAEnviroinformatics - Release Mapping/Modeling; Exposure/Risk Analysis - Ecological Risks
bear ("data analysis tool for average bioequivalence (ABE) and bioavailability (BA) for useR")bear development teamComputational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
behaviorsearch ("Adaptive search and exploration of agent-based model parameters")behaviorsearch development teamGeneral Development Tools - Development and Programming
Behaviour Composer Modelling4All project and University of OxfordGeneral Development Tools - Development and Programming
BEIS - Biogenic Emission Inventory SystemUSEPAEnviroinformatics - Release Mapping/Modeling
BELD - Biogenic Emissions Landuse DatabaseUSEPAEnviroinformatics - Release Mapping/Modeling
BenMAP ("estimate the health impacts and economic benefits [...] when populations experience changes in air quality")USEPAExposure/Risk Analysis - Microenvironmental/LCA Modeling; Exposure/Risk Analysis - Human Health Risks
BENSOLVE ("MATLAB implementation of Benson's algorithm")M.L.-U. Halle-Wittenberg, Germany (Andreas Lohne)General Development Tools - Development and Programming
Berkeley Drosophila Genome ProjectBerkeley Drosophila Genome Project ConsortiumBioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Biological Dose-Response; Computational Toxicology - Virtual Model Organisms
Berkeley Madonna ("modeling and analysis of dynamic systems")UC BerkeleyGeneral Development Tools - Development and Programming
BEs - Biomonitoring EquivalentsSummit Toxicology, LLPComputational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics; Exposure/Risk Analysis - Biomarkers
BetaBuster ("Bayesian Epidemiologic Screening" technique for "obtaining specific Beta prior distributions")BetaBuster teamData/Simulation Pattern Analysis - Sensitivity/Uncertainty Analysis
BicAT - Biclustering Analysis ToolboxETH, ZurichBioinformatics - Biomolecular Sequences/Structures; Data/Simulation Pattern Analysis - Classification/Clustering
BIND - Biomolecular Interaction Network DatabaseChristopher Hogue's Research LaboratoryBioinformatics - Interactions/Biopathways/Bionetworks
BioCartaBioCarta LLCBioinformatics - Interactions/Biopathways/Bionetworks; Computational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics; Exposure/Risk Analysis - Biomarkers
Biocatalysis/ Biodegradation DatabaseUniversity of MinnesotaBioinformatics - Interactions/Biopathways/Bionetworks; Bioinformatics - Data Integration
Biocellion ("Computer Simulation of Living Cell Systems")biocellion development teamComputational Toxicology - Virtual Cells, Tissues, Organs
Bioclipse ("workbench for the life sciences" based on Eclipse Rich Client Platform)Bioclipse development teamCheminformatics - Structure Elucidation; Cheminformatics - Property/Activity Prediction; Bioinformatics - Biomolecular Sequences/Structures
Bioconductor ("provides tools for the analysis and comprehension of high-throughput genomic data" using R)Bioconductor development teamBioinformatics - Bio-Ontologies; Bioinformatics - Biomolecular Sequences/Structures
BioDMET ("physiologically-based pharmacokinetic (PBPK) modeling and simulation tool")GE and DTRAComputational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
Bioeffects ProgramCenter for Coastal Monitoring and Assessment, National Ocean ServiceExposure/Risk Analysis - Ecological Risks
BioGPS ("gene annotation portal")BioGPS development teamBioinformatics - Biomolecular Sequences/Structures
BioGRID - Biological General Repository for Interaction DatasetsBioGRID TeamBioinformatics - Interactions/Biopathways/Bionetworks; Bioinformatics - Data Integration; Exposure/Risk Analysis - Biomarkers
Biokmod ("Mathematica toolbox […] with application for modeling Linear and Nonlinear Biokinetic Systems")Guillermo SanchezComputational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
BiokmodWebGuillermo SanchezComputational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
BioLayout Express3D ("visualization and analysis of network graphs")BioLayout Express3D TeamBioinformatics - Interactions/Biopathways/Bionetworks; General Development Tools - Data Visualization
Biomarkers Database (last updated in August 2004)USEPABioinformatics - Biological Dose-Response; Computational Toxicology - Toxicoinformatics; Computational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics; Exposure/Risk Analysis - Biomarkers
BioModels ("repository of computational models of biological processes")EMBL-EBIComputational Toxicology - Virtual Cells, Tissues, Organs
BioNumbers ("The Database of Useful Biological Numbers")Weizmann Institute, IsraelBioinformatics - Biological Dose-Response; Bioinformatics - Data Integration; Computational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
BioPAX - Biological Pathway ExchangeBioPAX development teamBioinformatics - Interactions/Biopathways/Bionetworks
Bio-PEPA WorkbenchBio-PEPA development teamBioinformatics - Interactions/Biopathways/Bionetworks; General Development Tools - Development and Programming
BIOPLUME III ("simulating the natural attenuation of organic contaminants in groundwater")US Air Force (Groundwater Services, Inc.) and the USEPAExposure/Risk Analysis - Ecological Risks
Biopython ("tools for biological computation written in Python")Biopython development teamBioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Data Integration; Data/Simulation Pattern Analysis - Classification/Clustering
BioTapestry ("tool for building, visualizing, and simulating [...] networks")Institute for Systems Biology, Davidson Laboratory at CaltechBioinformatics - Interactions/Biopathways/Bionetworks
BiQ Analyzer ("software tool for DNA methylation analysis")Max Planck Institute for Informatics, GermanyBioinformatics - Biomolecular Sequences/Structures; Exposure/Risk Analysis - Biomarkers
Bismark (tool to map bisulfite converted sequence reads and determine cytosine methylation states)Babraham BioinformaticsBioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Biological Dose-Response; Exposure/Risk Analysis - Biomarkers
BLAST - Basic Local Alignment Search Tool (see also PSI-BLAST for Protein Similarity Search)National Center for Biotechnology Information, NLM, NIHBioinformatics - Biomolecular Sequences/Structures
BLAT - BLAST-like Alignment ToolJim KentBioinformatics - Biomolecular Sequences/Structures
BLM - Biotic Ligand ModelHydroQualExposure/Risk Analysis - Ecological Risks
Blocks Database ("sequence analysis"; no longer updated)Fred Hutchinson Cancer Research CenterBioinformatics - Biomolecular Sequences/Structures
BMDExpress ("analyze microarray dose-response data")BMDExpress teamBioinformatics - Biological Dose-Response; Computational Toxicology - Toxicoinformatics
BMDS - Benchmark Dose SoftwareUSEPAComputational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics; Exposure/Risk Analysis - Human Health Risks
BMElib ("MATLAB toolbox of modern spatiotemporal geostatistics implementing the Bayesian Maximum Entropy theory")Marc Serre, University of North CarolinaEnviroinformatics - Spatiotemporal Mapping/Analysis
BMRB - Biological Magnetic Resonance Data BankBMRB project team, University of WisconsinCheminformatics - Structure Elucidation
BOND - Biomolecular Object Network DatabankThomsonBioinformatics - Biomolecular Sequences/Structures
Boomer ("Non-Linear Regression Program")D.W.A. BourneComputational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
BOSS - Biomarkers of Oxidative Stress StudyNIEHSBioinformatics - Biological Dose-Response; Computational Toxicology - Toxicoinformatics; Computational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics; Exposure/Risk Analysis - Biomarkers
Bowtie (DNA sequence alignment tool)Bowtie development teamBioinformatics - Biomolecular Sequences/Structures
Bowtie 2 (sequencing reads to long reference sequences aligner)Bowtie 2 development teamBioinformatics - Biomolecular Sequences/Structures
Boxshade ("program for creating good looking printouts from multiple-aligned [...] sequences")Boxshade Development TeamGeneral Development Tools - Data Visualization
BRB-ArrayToolsDr. Richard Simon and BRB-ArrayTools Development TeamBioinformatics - Biological Dose-Response; Computational Toxicology - Toxicoinformatics
BRENDA - BRaunschweig ENzyme DAtabaseD. Schomburg, Technische Universität Braunschweig, GermanyBioinformatics - Biomolecular Sequences/Structures
Breve ("build 3D simulations of multi-agent systems and artificial life")Jon KleinExposure/Risk Analysis - Socioeconomic/LSB Modeling; General Development Tools - Development and Programming
BRFSS - Behavioral Risk Factor Surveillance SystemCDCExposure/Risk Analysis - Microenvironmental/LCA Modeling
bsim-bccs ("Models the stochastic interactions of bacteria and particles in a fluid based environment")bsim-bccs development teamBioinformatics - Interactions/Biopathways/Bionetworks; Exposure/Risk Analysis - Ecological Risks
BUGS - Bayesian inference Using Gibbs Sampling (OpenBUGS/ WinBUGS)BUGS project teamData/Simulation Pattern Analysis - Sensitivity/Uncertainty Analysis
BugsXLA - A GUI for WinBugsPhil WoodwardData/Simulation Pattern Analysis - Sensitivity/Uncertainty Analysis
BWA - Burrows-Wheeler AlignerBWA development teamBioinformatics - Biomolecular Sequences/Structures
C++C++ development teamGeneral Development Tools - Development and Programming
CAD ViewerTailor Made SoftwareGeneral Development Tools - Data Visualization
CAD2ShapeGuthrie CAD/GIS Software Pty Ltd.General Development Tools - Data Visualization
CAESAR - Computer Assisted Evaluation of industrial chemical Substances According to RegulationsVEGACheminformatics - Property/Activity Prediction
Cain ("Stochastic Simulations for Chemical Kinetics")Cain development team (Sean Mauch et al.)Bioinformatics - Interactions/Biopathways/Bionetworks
CalcuSynBiosoftComputational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
California Safe Cosmetics Program Product DatabaseCalifornia Safe Cosmetics Program, California Department of Public HealthExposure/Risk Analysis - Microenvironmental/LCA Modeling; Exposure/Risk Analysis - Cumulative/Aggregate Exposures
CALPro (CALPUFF, CALMET)Atmospheric Studies Group at TRCEnviroinformatics - Environmental Fate and Transport
CalTOXCalifornia DTSCEnviroinformatics - Environmental Fate and Transport; Exposure/Risk Analysis - Microenvironmental/LCA Modeling; Exposure/Risk Analysis - Ecological Risks
Cambridge Structural DatabaseCambridge Crystallographic Data CentreCheminformatics - Property/Activity Prediction; Bioinformatics - Biomolecular Sequences/Structures
CAMEO MARPLOT (Mapping applications for response, planning, and local operational tasks)USEPA and NOAAEnviroinformatics - Spatiotemporal Mapping/Analysis; Enviroinformatics - Release Mapping/Modeling
CAMx - Comprehensive Air Quality Model with ExtensionsEnvironEnviroinformatics - Environmental Fate and Transport
caNanoLab - cancer Nanotechnology LaboratoryNCI (National Cancer Institute), NIHExposure/Risk Analysis - Microenvironmental/LCA Modeling
Cancer Mortality MapsNCI (National Cancer Institute), NIHEnviroinformatics - Spatiotemporal Mapping/Analysis
CARBDOSEUSEPAExposure/Risk Analysis - Human Health Risks
CARES - Cumulative and Aggregate Risk Evaluation SystemCropLife America, ILSI Research FoundationExposure/Risk Analysis - Cumulative/Aggregate Exposures
CartoDBVizzuality teamEnviroinformatics - Spatiotemporal Mapping/Analysis; General Development Tools - Data Visualization
CartographicaClueTrustEnviroinformatics - Spatiotemporal Mapping/Analysis; General Development Tools - Data Visualization
CartoMobileClueTrustEnviroinformatics - Spatiotemporal Mapping/Analysis; General Development Tools - Data Visualization
CASCADEAlterra and Plant Research InternationalExposure/Risk Analysis - Ecological Risks
CASEUltraMultiCase Inc.Cheminformatics - Property/Activity Prediction
Cassandra database ("open source distributed database management system")Apache Cassandra development team and The Apache Software FoundationGeneral Development Tools - Development and Programming
CATH ("Protein Structure Classification Database")University College, LondonBioinformatics - Biomolecular Sequences/Structures
CATS - Contaminants in Aquatic and Terrestrial ecoSystemsRIVMEnviroinformatics - Environmental Fate and Transport
CBECS - Commercial Buildings Energy Consumption SurveyU.S. Energy Information AdministrationExposure/Risk Analysis - Microenvironmental/LCA Modeling; Exposure/Risk Analysis - Socioeconomic/LSB Modeling
CCRIS - Chemical Carcinogenesis Research Information SystemNLMCheminformatics - Property/Activity Prediction
CDC WONDER - Wide-ranging Online Data for Epidemiologic ResearchCDCEnviroinformatics - Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis - Microenvironmental/LCA Modeling
CD-HIT - Cluster Database at High Identity with ToleranceLi group, University of California, San Diego (developed at Burnham Institute)Bioinformatics - Biomolecular Sequences/Structures
CEBS - Chemical Effects in Biological SystemsNIEHSBioinformatics - Biological Dose-Response; Bioinformatics - Data Integration; Computational Toxicology - Toxicoinformatics; Computational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
CEE-TV - Contaminant Exposure and Effects-Terrestrial VertebratesUS Geological SurveyExposure/Risk Analysis - Ecological Risks
Cefic LRI Toolbox - Long-range Research Initiative ToolboxCeficExposure/Risk Analysis - Human Health Risks
Cell ExplorerCell Explorer teamComputational Toxicology - Virtual Cells, Tissues, Organs
CellDesignerSystems Biology Institute, JapanBioinformatics - Interactions/Biopathways/Bionetworks; Computational Toxicology - Virtual Cells, Tissues, Organs
CellMLAuckland Bioengineering Institute, University of Auckland, NZComputational Toxicology - Virtual Cells, Tissues, Organs
CellNetAnalyzer / FluxAnalyzerMax Planck InstituteBioinformatics - Interactions/Biopathways/Bionetworks
CellNetOptimizerCellNOpt development teamBioinformatics - Interactions/Biopathways/Bionetworks
CellSysInterdisciplinary Centre for Bioinformatics, University of Leipzig, GermanyBioinformatics - Data Integration; Computational Toxicology - Virtual Cells, Tissues, Organs
Census of AgricultureUSDA NASSEnviroinformatics - Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis - Microenvironmental/LCA Modeling
CEP - Cumulative Exposure ProjectUSEPAEnviroinformatics - Spatiotemporal Mapping/Analysis
CEPST - Chemical Exposure Priority Setting ToolThe LifeLine GroupExposure/Risk Analysis - Human Health Risks
CE-QUAL-ICMU.S. Army Corps of EngineersExposure/Risk Analysis - Ecological Risks
CE-QUAL-W2U.S. Army Corps of Engineers and Portland State UniversityEnviroinformatics - Environmental Fate and Transport; Exposure/Risk Analysis - Ecological Risks
CERCLIS - Comprehensive Environmental Response, Compensation, and Liability Information SystemUSEPAEnviroinformatics - Release Mapping/Modeling
C-FERST - Community-Focused Exposure and Risk Screening ToolUSEPAExposure/Risk Analysis - Cumulative/Aggregate Exposures; Exposure/Risk Analysis - Human Health Risks
CGAP - Cancer Genome Anatomy ProjectNCI (National Cancer Institute), NIHBioinformatics - Biological Dose-Response; Exposure/Risk Analysis - Biomarkers
CGD - Customized Geographic DatabaseBiota of North America Program (BONAP)Enviroinformatics - Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis - Socioeconomic/LSB Modeling
CHAD - Consolidated Human Activity DatabaseUSEPAExposure/Risk Analysis - Microenvironmental/LCA Modeling; Exposure/Risk Analysis - Socioeconomic/LSB Modeling; Exposure/Risk Analysis - Cumulative/Aggregate Exposures
CHARM - Complex Hazardous Air Release ModelDr. Mark Eltgroth
CharProtDB - Characterized Protein DatabaseJ. Craig Venter InstituteBioinformatics - Bio-Ontologies; Bioinformatics - Biomolecular Sequences/Structures
Chaste ("general purpose simulation package [...] in biology and physiology")Computational Biology Group, Dept. of Computer Science, University of OxfordBioinformatics - Data Integration
ChEBI - Chemical Entities of Biological InterestEMBL-EBIBioinformatics - Bio-Ontologies
ChemBankBroad InstituteCheminformatics - Property/Activity Prediction; Bioinformatics - Biomolecular Sequences/Structures
ChemBioNavigator (visualization of chemical and biological space of molecular groups)University of Hamburg and BioSolveITCheminformatics - Property/Activity Prediction
ChemGate (chemical structure search)John Wiley & Sons, Inc. and eMolecules, Inc.Cheminformatics - Structure Elucidation
Chemical Data ReportingUSEPAEnviroinformatics - Release Mapping/Modeling
Chemicalize (search chemical structures)ChemAxonCheminformatics - Property/Activity Prediction
ChemIDplus AdvancedNLMCheminformatics - Property/Activity Prediction
ChemPoint ("Environmental Data Management System")Starpoint Software Inc.General Development Tools - Data Visualization
ChemSpiderRoyal Society of Chemistry, CambridgeCheminformatics - Structure Elucidation; Cheminformatics - Property/Activity Prediction
ChemStat ("statistical analysis of ground water monitoring data at RCRA facilities")Starpoint Software Inc.Enviroinformatics - Environmental Fate and Transport; Exposure/Risk Analysis - Ecological Risks
ChemSTEER - Chemical Screening Tool For Exposures & Environmental ReleasesUSEPAExposure/Risk Analysis - Cumulative/Aggregate Exposures
ChemViewUSEPAExposure/Risk Analysis - Microenvironmental/LCA Modeling
CheS-Mapper ("Chemical Space Mapping and Visualization in 3D")Albert-Ludwigs-Universität Freiburg, Germany (M. Gutlein et al.)Cheminformatics - Structure Elucidation; Cheminformatics - Property/Activity Prediction; Computational Toxicology - Toxicoinformatics
Child-Specific Exposure Factors HandbookUSEPAExposure/Risk Analysis - Microenvironmental/LCA Modeling; Exposure/Risk Analysis - Cumulative/Aggregate Exposures
ChIPBase ("decoding transcription factor binding maps [...] and transcriptional regulation [...] from ChIP-Seq data")Qu lab at Sun Yat-sen University (J. Yang)Bioinformatics - Biological Dose-Response; Bioinformatics - Data Integration; Exposure/Risk Analysis - Biomarkers
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 Bioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Biological Dose-Response
CHMMBOX - Coupled Hidden Markov Modelling ToolboxUniversity of OxfordData/Simulation Pattern Analysis - Sensitivity/Uncertainty Analysis
ChromDB - The Chromatin DatabaseBIO5 InstituteBioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Data Integration
CHSI - Community Health Status IndicatorsCDCEnviroinformatics - Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis - Socioeconomic/LSB Modeling
CICAD - Concise International Chemical Assessment DocumentsIPCS INCHEMCheminformatics - Property/Activity Prediction
CLC Sequence ViewerCLC bioBioinformatics - Biomolecular Sequences/Structures
CLCbio Genomics Workbench (analysis, comparison and visualization of next generation sequencing data)CLCbioBioinformatics - Biomolecular Sequences/Structures
CLIP - Closed-Loop Identification ProtocolRabitz Laboratory, Princeton UniversityCheminformatics - Interaction/Reaction Modeling
Cloe PKCyprotex PLCComputational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
Cloe PredictCyprotexBioinformatics - Biological Dose-Response; Computational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
Clustal Omega (Multiple DNA, RNA and protein sequence alignment program)Conway Institute, UCD DublinBioinformatics - Biomolecular Sequences/Structures
ClustalW2 (see Clustal Omega)EMBL-EBIBioinformatics - Biomolecular Sequences/Structures
CluSTrEMBL-EBIBioinformatics - Biomolecular Sequences/Structures
CMAQ - Community Multi-scale Air Quality modeling systemCMAS Center, UNC-Chapel HillEnviroinformatics - Environmental Fate and Transport
CMARRT (A tool for the analysis of ChIP-chip data from tiling arrays by incorporating the correlation structure)Keles Research Group, University of WisconsinBioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Biological Dose-Response; Exposure/Risk Analysis - Biomarkers
Cmgui - Continuum Mechanics, Image Analysis, Signal Processing and System Identification Graphical User InterfaceAuckland Bioengineering Institute, University of Auckland, NZComputational Toxicology - Virtual Cells, Tissues, Organs
CNV Project Data - Copy Number Variation Project DataWellcome Trust Sanger Institute, UKBioinformatics - Biomolecular Sequences/Structures; Exposure/Risk Analysis - Biomarkers
CNVFinder - Copy Number Variant FinderWellcome Trust Sanger Institute, UKBioinformatics - Biomolecular Sequences/Structures; Exposure/Risk Analysis - Biomarkers
COG - Clusters of Orthologous Groups of proteinsNational Center for Biotechnology Information, NLM, NIHBioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Data Integration
Cognoscente ("database and visualization tool for biomolecular interactions [...] in the literature")VanBuren laboratory, Texas A&M Health Science CenterBioinformatics - Interactions/Biopathways/Bionetworks
CombiToolLeibniz Institute for Age Research - FLI, GermanyBioinformatics - Biological Dose-Response
COMBO - COral Mortality and Bleaching OutputCOMBO TeamExposure/Risk Analysis - Ecological Risks
COMMUTERUSEPAEnviroinformatics - Environmental Fate and Transport
Comparative Toxicogenomics DatabaseMount Desert Island Biological LaboratoryBioinformatics - Biological Dose-Response; Computational Toxicology - Toxicoinformatics; Computational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
CompassBruker DaltonicsExposure/Risk Analysis - Biomarkers
Compass OpenAccessBruker DaltonicsExposure/Risk Analysis - Biomarkers
CompMoby ("detect over-represented motifs in the upstream or 3' UTR sequences of co-expressed genes")QB3 and UCSFBioinformatics - Biomolecular Sequences/Structures
Comprehensive Cancer InformationNCI (National Cancer Institute), NIHComputational Toxicology - Toxicoinformatics; Exposure/Risk Analysis - Human Health Risks
CompuCell 3DIndiana University and Biocomplexity InstituteComputational Toxicology - Virtual Cells, Tissues, Organs
COMSOL MultiPhysicsCOMSOLGeneral Development Tools - Development and Programming
ConsExpo (a set of models "that enables the estimation and assessment of exposure to substances from consumer products that are used indoor and their uptake by humans")RIVMExposure/Risk Analysis - Microenvironmental/LCA Modeling
Consumer Expenditure SurveyU.S. Bureau of Labor StatisticsExposure/Risk Analysis - Microenvironmental/LCA Modeling; Exposure/Risk Analysis - Socioeconomic/LSB Modeling
Consumer Products Inventory ("inventory of nanotechnology-based consumer products introduced on the market")The Project on Emerging NanotechnologiesExposure/Risk Analysis - Microenvironmental/LCA Modeling
CONTAMNISTExposure/Risk Analysis - Microenvironmental/LCA Modeling
Contrail - To assemble large genomes in the cloudUniversity of MDBioinformatics - Biomolecular Sequences/Structures
COPASI - Complex Pathway Simulator ("successor of Gepasi")Virginia Bioinformatics Institute, Virginia TechCheminformatics - Interaction/Reaction Modeling; Bioinformatics - Interactions/Biopathways/Bionetworks
CORINA ("3D structure generator for small and medium sized, [...] molecules")Molecular Networks GmbHCheminformatics - Property/Activity Prediction
CormasCormas development team, CiradExposure/Risk Analysis - Ecological Risks
COS.SIM ("Agent Based Traffic MicroSimulation")COS.SIM development teamExposure/Risk Analysis - Microenvironmental/LCA Modeling
Cosmeticsinfo.orgPersonal Care Products CouncilExposure/Risk Analysis - Cumulative/Aggregate Exposures
COSMIC - Catalogue Of Somatic Mutations In CancerWellcome Trust Sanger Institute, UKExposure/Risk Analysis - Biomarkers
CPCat - Chemical and Product CategoriesUSEPAComputational Toxicology - Toxicoinformatics; Exposure/Risk Analysis - Microenvironmental/LCA Modeling
CPDB - Carcinogenic Potency DatabaseCPDB development teamComputational Toxicology - Toxicoinformatics; Exposure/Risk Analysis - Human Health Risks
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.)Bioinformatics - Biomolecular Sequences/Structures
CPID - Consumer Product Information DatabaseCDC and DeLima Associates, Virginia, USAExposure/Risk Analysis - Microenvironmental/LCA Modeling; Exposure/Risk Analysis - Cumulative/Aggregate Exposures
CPS - Current Population SurveyUS Census BureauEnviroinformatics - Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis - Socioeconomic/LSB Modeling
CRC Handbook of Chemistry and PhysicsCRC PressCheminformatics - Property/Activity Prediction
CRC Handbook of Data on Organic CompoundsCRC PressCheminformatics - Property/Activity Prediction
Creme - RIFM Aggregate Exposure Model for Fragrance MaterialsCreme Global and RIFMExposure/Risk Analysis - Microenvironmental/LCA Modeling
CREMOFAC - Chromatin Remodeling FactorsChromatin Biology Lab, Jawaharlal Nehru Centre for Advanced Scientific Research, IndiaBioinformatics - Biological Dose-Response; Bioinformatics - Data Integration
CropScape ("crop-specific land cover data layer created annually for the continental United States")USDA National Agricultural Statistics ServiceEnviroinformatics - Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis - Cumulative/Aggregate Exposures
Crystal BallDecisioneering Inc./ OracleData/Simulation Pattern Analysis - Sensitivity/Uncertainty Analysis
CSD - Cambridge Structural DatabaseCambridge Crystallographic Data CentreCheminformatics - Structure Elucidation
CSD Linker DatabaseChemical Computing GroupCheminformatics - Structure Elucidation
CSDS - Cambridge Structural Database SystemCambridge Crystallographic Data CentreCheminformatics - Structure Elucidation
CSEM - Multi-read Allocation for ChIP-seqKeles Research Group, University of WisconsinBioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Biological Dose-Response; Exposure/Risk Analysis - Biomarkers
CSFII - Continuing Survey of Food Intakes by IndividualsUSDAExposure/Risk Analysis - Microenvironmental/LCA Modeling; Exposure/Risk Analysis - Socioeconomic/LSB Modeling
CTEPP - Children's Total Exposure to Persistent Pesticides and Other Persistent Organic PollutantsUSEPAEnviroinformatics - Release Mapping/Modeling
Cufflinks - Transcript assembly, differential expression and regulation for RNA-Seq samplesUC Berkeley, JHU, and CaltechBioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Biological Dose-Response; Exposure/Risk Analysis - Biomarkers
CummeRbund - To analyze Cufflinks RNA-Seq outputMIT and HarvardBioinformatics - Biomolecular Sequences/Structures; Exposure/Risk Analysis - Biomarkers
CureTogether (a blog where "patients [...] share quantitative information on over 500 medical conditions")CureTogether teamExposure/Risk Analysis - Biomarkers
CVSimCVSim development teamBioinformatics - Biological Dose-Response; Computational Toxicology - Virtual Cells, Tissues, Organs
Cyber PatientMichael B. Bolger, USCComputational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
CySBGN ("SBGN diagrams in Cytoscape")CySBGN development team, Saez-Rodriguez Group, EMBL-EBIBioinformatics - Interactions/Biopathways/Bionetworks
CytoscapeCytoscape Consortium and Institut PasteurGeneral Development Tools - Data Visualization
DALY Calculator - Disability-Adjusted Life Year CalculatorDALY Calculator development teamExposure/Risk Analysis - Human Health Risks
DART - Developmental and Reproductive Toxicology DatabaseNLM, NIHCheminformatics - Property/Activity Prediction; Computational Toxicology - Toxicoinformatics
Database of Macromolecular MovementMark Gerstein, et al., Yale UniversityCheminformatics - Structure Elucidation; Bioinformatics - Biomolecular Sequences/Structures
DAVID - Database for Annotation, Visualization and Integrated DiscoveryNational Institute of Allergy and Infectious Diseases, NIHBioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Data Integration
DBCAT - DataBase of CpG islands and Analytical ToolResearch Center for Medical Excellence National Taiwan UniversityBioinformatics - Biomolecular Sequences/Structures
DBChIP - program to detect differentially bound sharp binding sites across multiple conditionsKeles Research Group, University of WisconsinBioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Biological Dose-Response; Exposure/Risk Analysis - Biomarkers
dbGaP - Database of Genotypes and PhenotypesNational Center for Biotechnology Information, NLM, NIHBioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Data Integration; Exposure/Risk Analysis - Biomarkers
dbSNPNational Center for Biotechnology Information, NLM, NIHBioinformatics - Biomolecular Sequences/Structures; Exposure/Risk Analysis - Biomarkers
dbZachZacharewski Laboratory, Michigan State University
DCAL - Dose and Risk Calculation SoftwareOak Ridge National Laboratory and USEPAComputational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
dChip - DNA-Chip AnalyzerHarvard University and Stanford UniversityBioinformatics - Biological Dose-Response
DDI PredictAureus SciencesComputational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
DEBToxUniversity of AmsterdamExposure/Risk Analysis - Ecological Risks
Decision ForestUSFDABioinformatics - Biological Dose-Response; Computational Toxicology - Toxicoinformatics
DEEM-FCID/ Calendex - Dietary Exposure Evaluation Model-Food Commodity Intake Database/ CalendexUSEPAExposure/Risk Analysis - Microenvironmental/LCA Modeling; Exposure/Risk Analysis - Cumulative/Aggregate Exposures
Defra Risk AssessmentDefra team and Department for Environment, Food & Rural AffairsExposure/Risk Analysis - Ecological Risks
DeltaGraph ("combines [...] statistical tools with [...] data visualization capabilities")Red Rock Software, Inc.General Development Tools - Data Visualization
DEPM - Dietary Exposure Potential ModelUSEPAExposure/Risk Analysis - Cumulative/Aggregate Exposures
Derek NexusLhasa LimitedCheminformatics - Property/Activity Prediction
DEVS-SuiteDEVS-Suite development teamGeneral Development Tools - Development and Programming
DFCI Gene IndexGene Index Project, Harvard University
DFLOWUSEPAEnviroinformatics - Environmental Fate and Transport; Exposure/Risk Analysis - Ecological Risks
Diabetes Public Health ResourceCDC
Didger ("geoprocessing and data conversion tool")Golden Software Inc.Enviroinformatics - Spatiotemporal Mapping/Analysis; General Development Tools - Data Visualization
Digital Elevation DataUSDA NRCSEnviroinformatics - Spatiotemporal Mapping/Analysis
DIP - Database of Interacting ProteinsDavid Eisenberg, UCLA
DIPPR 801 DatabaseDIPPR, AIChECheminformatics - Property/Activity Prediction
DISCOVAR - genome assembler and variant callerBroad InstituteBioinformatics - Biomolecular Sequences/Structures
DISCOVAR de novo - Assembler for large genomes up to human sizeBroad InstituteBioinformatics - Biomolecular Sequences/Structures
Discrete Dynamics Lab ("Tools for researching Cellular Automata, Random Boolean Networks, multi-value Discrete Dynamical Networks, and beyond")DDLab development teamBioinformatics - Interactions/Biopathways/Bionetworks; General Development Tools - Development and Programming
Disease Maps 2012US Geological SurveyEnviroinformatics - Spatiotemporal Mapping/Analysis
Disease/ Phenotype web-PAGE ("disease based gene set analysis of microarray gene expression")Gene Expression and Genomics Unit, NIA, NIHBioinformatics - Biological Dose-Response; Exposure/Risk Analysis - Biomarkers; Exposure/Risk Analysis - Human Health Risks
DiseaseMeth - human disease methylation databaseCollege of Bioinformatics Sci. and Tech., Harbin Medical U., ChinaBioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Data Integration
DisEBML ("Intrinsic Protein Disorder Prediction")DisEBML development team, EMBLBioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Interactions/Biopathways/Bionetworks
DIVA-GIS ("mapping and geographic data analysis")DIVA-GIS development teamEnviroinformatics - Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis - Socioeconomic/LSB Modeling; General Development Tools - Data Visualization
DIVA-GIS (GIS data by country)DIVA-GIS development teamEnviroinformatics - Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis - Socioeconomic/LSB Modeling
DMR Pollutant Loading Tool - Discharge Monitoring Report Pollutant Loading ToolUSEPAEnviroinformatics - Release Mapping/Modeling; Enviroinformatics - Environmental Fate and Transport; Exposure/Risk Analysis - Microenvironmental/LCA Modeling; Exposure/Risk Analysis - Cumulative/Aggregate Exposures; Exposure/Risk Analysis - Ecological Risks
DORIAN - DOse-Response Information ANalysis systemComputational Chemodynamics LaboratoryBioinformatics - Biological Dose-Response; Computational Toxicology - Toxicoinformatics; Computational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
DoseSimSCB Research Group, Colorado State UniversityComputational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
Downhole Explorer ("drillhole presentation and plotting program")Downhole Explorer development teamGeneral Development Tools - Data Visualization
DRINK - Drinking Water Research Information NetworkUSEPA
DROPLETAlterra and Wageningen UR, The NetherlandsExposure/Risk Analysis - Ecological Risks
Drug Information PortalNLM, NIHComputational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
DrugMatrixNIEHSBioinformatics - Biological Dose-Response; Computational Toxicology - Toxicoinformatics; Computational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
DSID - Dietary Supplement Ingredient DatabaseUSDA Nutrient Data Laboratory and Office of Dietary Supplements, NIHExposure/Risk Analysis - Microenvironmental/LCA Modeling
DSSTox - Distributed Structure-Searchable ToxicityUSEPACheminformatics - Property/Activity Prediction
DUST ("model to calculate the dermal uptake of pesticides by birds and mammals")USEPAExposure/Risk Analysis - Ecological Risks
DWS - Drinking Water StandardsUSEPAExposure/Risk Analysis - Microenvironmental/LCA Modeling
Dynamic Signaling MapsHippron Physiomics IncCheminformatics - Interaction/Reaction Modeling; Bioinformatics - Interactions/Biopathways/Bionetworks
DyneticaDuke UniversityBioinformatics - Interactions/Biopathways/Bionetworks
EADB - Estrogenic Activity DatabaseUSFDABioinformatics - Biological Dose-Response; Computational Toxicology - Toxicoinformatics; Exposure/Risk Analysis - Biomarkers
EAFUS - Everything Added to Food in the United StatesUSFDAExposure/Risk Analysis - Microenvironmental/LCA Modeling
E-CellE-Cell Project TeamComputational Toxicology - Virtual Cells, Tissues, Organs
ECETOC Science Areas - European Centre for Ecotoxicology and Toxicology of Chemicals Science AreasECETOCExposure/Risk Analysis - Microenvironmental/LCA Modeling; Exposure/Risk Analysis - Human Health Risks; Exposure/Risk Analysis - Ecological Risks
ECHO - Enforcement and Compliance History OnlineUSEPAEnviroinformatics - Release Mapping/Modeling
Ecolab ("software package [...] looking at the dynamics of evolution")Ecolab development teamBioinformatics - Interactions/Biopathways/Bionetworks
EcolegoSwedish Radiation Safety Authority, Sweden and Norwegian Radiation Protection AuthorityGeneral Development Tools - Development and Programming
ECOSAR - Ecological Structure Activity RelationshipsSyracuse Research Corporation and USEPAExposure/Risk Analysis - Ecological Risks
ECOTOX - ECOTOXicologyUSEPACheminformatics - Property/Activity Prediction; Exposure/Risk Analysis - Ecological Risks
Edinburgh Pathway EditorEPE development teamBioinformatics - Interactions/Biopathways/Bionetworks
EDKB - Endocrine Disruptor Knowledge BaseUSFDABioinformatics - Biological Dose-Response; Computational Toxicology - Toxicoinformatics; Exposure/Risk Analysis - Biomarkers
E-FAST - Exposure and Fate Assessment Screening ToolUSEPAExposure/Risk Analysis - Cumulative/Aggregate Exposures; Exposure/Risk Analysis - Ecological Risks
EFDB - Environmental Fate Data BaseSRC IncEnviroinformatics - Environmental Fate and Transport; Cheminformatics - Property/Activity Prediction
EFDC - Environmental Fluid Dynamics CodeVirginia Institute of Marine Science, The College of William and Mary (J. M. Hamrick) and USEPAEnviroinformatics - Environmental Fate and Transport
eggNOG - evolutionary genealogy of genes: Non-supervised Orthologous GroupsEMBL, GermanyBioinformatics - Interactions/Biopathways/Bionetworks
EIGENSOFT ("combines functionality from our population genetics methods [...] and our EIGENSTRAT stratification correction method")EIGENSOFT development team, Harvard School of Public HealthBioinformatics - Biomolecular Sequences/Structures; Exposure/Risk Analysis - Biomarkers
EIO-LCA - Economic Input-Output Life Cycle AssessmentGreen Design Institute, Carnegie Mellon University, PAExposure/Risk Analysis - Socioeconomic/LSB Modeling
EJView ("mapping tool [...] to create maps and generate detailed reports based on the geographic areas and data sets")USEPAEnviroinformatics - Spatiotemporal Mapping/Analysis
ELECANS - A Computational Cancer Systems Biology Simulation StudioDepartment of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, KoreaBioinformatics - Biological Dose-Response; Bioinformatics - Data Integration
EMA - e-Mouse AtlasEMA teamBioinformatics - Data Integration; Computational Toxicology - Virtual Model Organisms
EMAGE - e-Mouse Atlas of Gene ExpressionEMAGE teamBioinformatics - Biological Dose-Response; Computational Toxicology - Toxicoinformatics
EMAP - Environmental Monitoring and Assessment ProgramUSEPAEnviroinformatics - Spatiotemporal Mapping/Analysis; Enviroinformatics - Release Mapping/Modeling
EMBERUniversity of ChicagoBioinformatics - Biological Dose-Response
EMBOSS - European Molecular Biology Open Software SuiteEMBOSS development team (P. Rice and A. Bleasby et al.)Cheminformatics - Structure Elucidation; Cheminformatics - Interaction/Reaction Modeling; Bioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Interactions/Biopathways/Bionetworks
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 MedicineBioinformatics - Biomolecular Sequences/Structures
EMI - Exposure Model for IndividualsUSEPAExposure/Risk Analysis - Microenvironmental/LCA Modeling; Exposure/Risk Analysis - Cumulative/Aggregate Exposures
EMS-HAP - Emissions Modeling System for Hazardous PollutantsUSEPAEnviroinformatics - Release Mapping/Modeling
EMSOFT - Exposure Model for Soil-Organic Fate and TransportRTPEnviroinformatics - Environmental Fate and Transport; Exposure/Risk Analysis - Ecological Risks
ENA - European Nucleotide ArchiveEMBL-EBIBioinformatics - Biomolecular Sequences/Structures
ENCODE - Encyclopedia Of DNA ElementsNHGRI, NIHBioinformatics - Biomolecular Sequences/Structures; Exposure/Risk Analysis - Biomarkers
Encom Discover ("desktop Geographical Information System")Encom and Pitney BowesEnviroinformatics - Spatiotemporal Mapping/Analysis; General Development Tools - Data Visualization
Encom Discover PA - Encom Discover Profile Analyst Encom and Pitney BowesEnviroinformatics - Spatiotemporal Mapping/Analysis
Encom QuickMag ("magnetic modeling package")Encom and Pitney BowesEnviroinformatics - Spatiotemporal Mapping/Analysis
E-Net ("software for analyzing ego network data")Analytic TechnologiesExposure/Risk Analysis - Socioeconomic/LSB Modeling; General Development Tools - Data Visualization
Ensembl Genome BrowserEMBL-EBI and Wellcome Trust Sanger Institute, UKBioinformatics - Biomolecular Sequences/Structures
EntoramaBranimir CaceGeneral Development Tools - Development and Programming
Envirofacts (provides environmental information at a local area of interest)USEPAEnviroinformatics - Release Mapping/Modeling
Enviromapper for Envirofacts ("provides […] information about environmental activities that may affect air, water, and land anywhere in the US")USEPAEnviroinformatics - Release Mapping/Modeling
Environmental Genome Project/ SNPs ProgramNIEHS and University of WashingtonComputational Toxicology - Toxicoinformatics
Envision ("A spatially explicit, distributed, multiagent-based framework for policy assessment and alternative futuring")Envision development team, Oregon State UniversityEnviroinformatics - Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis - Socioeconomic/LSB Modeling
EnvStats - Package for Environmental Statistics, including US EPA GuidanceS.P. MillardEnviroinformatics - Spatiotemporal Mapping/Analysis; Enviroinformatics - Release Mapping/Modeling; Enviroinformatics - Environmental Fate and Transport
ENZYME ("Enzyme nomenclature database")Swiss-Prot group, Swiss Institute of Bioinformatics
Enzyme Structures DatabaseEMBL-EBI
EP_GOS_ClustFloudas Research Group, Princeton UniversityData/Simulation Pattern Analysis - Classification/Clustering
EPA-Expo-Box - EPA’s EXPOsure toolBOX ("A Toolbox for Exposure Assessors")USEPAComputational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics; Exposure/Risk Analysis - Microenvironmental/LCA Modeling; Exposure/Risk Analysis - Cumulative/Aggregate Exposures; Exposure/Risk Analysis - Biomarkers; Exposure/Risk Analysis - Human Health Risks
EPANET ("Models the Hydraulic and Water Quality Behavior of Water Distribution Piping Systems")USEPAEnviroinformatics - Environmental Fate and Transport; Exposure/Risk Analysis - Microenvironmental/LCA Modeling
EPI - Estimation Program Interface Suite - suite of physical/chemical property and environmental fate estimation programsUSEPAEnviroinformatics - Environmental Fate and Transport; Cheminformatics - Property/Activity Prediction
EpiGRAPH - for advanced (epi-) genome analysis and predictionEpiGRAPH development teamBioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Biological Dose-Response; Exposure/Risk Analysis - Biomarkers
EpiSIM PlatformTIGA Center Heidelberg, GermanyBioinformatics - Biological Dose-Response; Bioinformatics - Data Integration; Computational Toxicology - Virtual Cells, Tissues, Organs
EPPIC - Evolutionary Protein-Protein Interface Classifier (interface classification in protein crystal lattice to determine biological relevance)Paul Scherrer Institut & SyBIT, Zurich (G. Capitani)Bioinformatics - Interactions/Biopathways/Bionetworks
EPR - Environmental Polymorphisms RegistryNIEHSComputational Toxicology - Toxicoinformatics; Exposure/Risk Analysis - Biomarkers
EQuIS ("Environmental data management")EarthSoft Inc.Enviroinformatics - Spatiotemporal Mapping/Analysis; Enviroinformatics - Release Mapping/Modeling; Enviroinformatics - Environmental Fate and Transport
ERDAS Imagine ("geospatial data authoring system, supplies tools for [...] Remote Sensing, Photogrammetry and GIS needs")Hexagon GeospatialEnviroinformatics - Spatiotemporal Mapping/Analysis
ERDEM - Exposure Related Dose Estimating ModelUSEPAComputational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
ERPG - Emergency Response Planning GuidelinesAIHACheminformatics - Property/Activity Prediction
ESCAPE - Embryonic Stem Cells Atlas of Pluripotency EvidenceSBCNY and Mount Sinai School of MedicineBioinformatics - Data Integration
Esri Business AnalystEsriEnviroinformatics - Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis - Microenvironmental/LCA Modeling; Exposure/Risk Analysis - Socioeconomic/LSB Modeling
EuPathDB - Eukaryotic Pathogen Database ResourcesEuPathDB Project TeamExposure/Risk Analysis - Biomarkers; Exposure/Risk Analysis - Human Health Risks
European AirBase reporting stationsEuropean Environment AgencyEnviroinformatics - Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis - Microenvironmental/LCA Modeling; Exposure/Risk Analysis - Cumulative/Aggregate Exposures
EUSES - European Union System for the Evaluation of SubstancesEuropean Commission, JRC, IHCPExposure/Risk Analysis - Microenvironmental/LCA Modeling
EVS Pro - Environmental Visualization System Pro - 3D MappingC TechEnviroinformatics - Spatiotemporal Mapping/Analysis; General Development Tools - Data Visualization
EwE - Ecopath with EcosimInternational Center for Living Aquatic Resources Management, PhilippinesExposure/Risk Analysis - Ecological Risks
EXAMS - Exposure Analysis Modeling SystemUSEPAEnviroinformatics - Environmental Fate and Transport; Exposure/Risk Analysis - Ecological Risks
exaptiveExaptive, Inc.General Development Tools - Development and Programming
ExPASy ("SIB Bioinformatics Resource Portal")SIB - Swiss Institute of Bioinformatics
ExpoCastDB - Exposure Forecaster DatabaseUSEPAExposure/Risk Analysis - Microenvironmental/LCA Modeling; Exposure/Risk Analysis - Cumulative/Aggregate Exposures; Exposure/Risk Analysis - Biomarkers
ExpoFacts - European Exposure Factors SourcebookEuropean Commission, JRC, IHCPExposure/Risk Analysis - Human Health Risks
EXPOLIS DatabaseMatti Jantunen, KTL Air Hygiene Laboratory, FinlandExposure/Risk Analysis - Cumulative/Aggregate Exposures
Exposure Factors HandbookUSEPAExposure/Risk Analysis - Cumulative/Aggregate Exposures; Exposure/Risk Analysis - Human Health Risks
EXTOXNET - EXTension TOXicology NETworkUniversity of California, Davis, Oregon State University, Michigan State University, Cornell University, and University of IdahoComputational Toxicology - Toxicoinformatics
FACET - Flavourings, Additives and food Contact materials Exposure TaskCreme Global and collaboratorsExposure/Risk Analysis - Microenvironmental/LCA Modeling
FACT - Flow And Contaminant TransportSavannah River Technology Center and US DOEEnviroinformatics - Environmental Fate and Transport
Factual ("Global Products with Ingredients and Nutrition")Factual Inc.Exposure/Risk Analysis - Microenvironmental/LCA Modeling; Exposure/Risk Analysis - Cumulative/Aggregate Exposures
FARE MicrobialExponent, Inc. and USFDAExposure/Risk Analysis - Human Health Risks
FASCAT - Food and Agriculture Sector Criticality Assessment ToolNational Center for Food Protection and Defense
Fast Numerical Algorithms for Stiff Reaction-Diffusion EquationsUniversity of California, IrvineGeneral Development Tools - Development and Programming
FASTA - DNA and protein sequence alignment software packageEMBL-EBIBioinformatics - Biomolecular Sequences/Structures
FastQC - Quality control tool for high throughput sequence dataBabraham BioinformaticsBioinformatics - Biomolecular Sequences/Structures
FDA-iRISKUSFDAExposure/Risk Analysis - Human Health Risks
FDALabel - Full-Text Search of Drug Label DatabaseUSFDABioinformatics - Biological Dose-Response
FGENESH - "Program for predicting multiple genes in genomic DNA sequences"Softberry, Inc. and The Sanger Centre, Cambridge, UKBioinformatics - Biomolecular Sequences/Structures
FGETS - Food and Gill Exchange of Toxic SubstancesUSEPAExposure/Risk Analysis - Ecological Risks
FieldMLAuckland Bioengineering Institute, University of Auckland, NZComputational Toxicology - Virtual Cells, Tissues, Organs
FileMakerFilemaker, IncGeneral Development Tools - Development and Programming
FIRST - FQPA Index Reservoir Screening ToolUSEPAEnviroinformatics - Environmental Fate and Transport; Exposure/Risk Analysis - Ecological Risks
FLAME - Flexible Large-scale Agent-based Modeling EnvironmentSoftware Engineering Group, CSED, STFCExposure/Risk Analysis - Socioeconomic/LSB Modeling; General Development Tools - Development and Programming
flexImagingBruker DaltonicsExposure/Risk Analysis - Biomarkers
FlexXBioSolveITCheminformatics - Property/Activity Prediction
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, GermanyBioinformatics - Interactions/Biopathways/Bionetworks
FlyBase - "A Database of Drosophila Genes & Genomes"FlyBase development teamComputational Toxicology - Virtual Model Organisms
FlyMine - "integrated database for Drosophila and Anopheles genomics"University of Cambridge, Cambridge, UKBioinformatics - Bio-Ontologies; Bioinformatics - Interactions/Biopathways/Bionetworks; Bioinformatics - Biological Dose-Response; Computational Toxicology - Virtual Model Organisms
FOCUS - FOrum for Co-ordination of pesticide fate models and their USeFOCUS team, EU CommissionEnviroinformatics - Environmental Fate and Transport; Exposure/Risk Analysis - Ecological Risks
Food Environment AtlasUSDAExposure/Risk Analysis - Socioeconomic/LSB Modeling
FortranFree Software Foundation, IncGeneral Development Tools - Development and Programming
FoundationOneFoundation MedicineBioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Data Integration
FRAMES-3MRA - Multimedia, Multi-pathway, Multi-receptor Exposure and Risk AssessmentUSEPAEnviroinformatics - Environmental Fate and Transport; Exposure/Risk Analysis - Cumulative/Aggregate Exposures; Exposure/Risk Analysis - Ecological Risks
freshwaterecology.infoInstitute of Hydrobiology & Aquatic Ecosystem Management, ViennaExposure/Risk Analysis - Ecological Risks
FRS - Facility Registry SystemUSEPAEnviroinformatics - Release Mapping/Modeling
FunDO ("Exploring Genes Using Functional Disease Ontology Annotations")Northwestern University Biomedical Informatics CenterBioinformatics - Bio-Ontologies; Exposure/Risk Analysis - Biomarkers
GAC - Genetic Alterations in CancerNIEHSBioinformatics - Biological Dose-Response; Computational Toxicology - Toxicoinformatics; Computational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics; Exposure/Risk Analysis - Biomarkers; Exposure/Risk Analysis - Human Health Risks
GADM database of Global Administrative AreasGADM development teamEnviroinformatics - Spatiotemporal Mapping/Analysis
Galaxy - web-based platform for data intensive biomedical research ("Online bioinformatics analysis for everyone")Penn State and Emory U.Bioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Biological Dose-Response
GAMAIRD/UPMC International Research Unit, UMMISCOGeneral Development Tools - Development and Programming
GARR - Gross Alpha Radium RegulationUSEPAEnviroinformatics - Environmental Fate and Transport; Exposure/Risk Analysis - Ecological Risks
GasSim ("simulates the fate of landfill gas arising from managed or unmanaged landfill sites")Golder Associates and Environment Agency of England and WalesEnviroinformatics - Environmental Fate and Transport; Data/Simulation Pattern Analysis - Sensitivity/Uncertainty Analysis
GastroPlusSimulations Plus IncComputational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
GATK - Genome Analysis ToolkitBroad InstituteBioinformatics - Biomolecular Sequences/Structures
GBPCALC - Gross Beta Photon CalculatorUSEPAEnviroinformatics - Environmental Fate and Transport; Exposure/Risk Analysis - Ecological Risks
GBrowse (Generic Genome Browser)GBrowse development teamBioinformatics - Biomolecular Sequences/Structures
GeMDBJ - Genome Medicine Database of JapanSGMGP (The Study Groups of Millennium Genome Project for Alzheimer's disease, Cancer, Diabetes Mellitus, Hypertension, Asthma and Pharmacogenetics)Bioinformatics - Biological Dose-Response; Exposure/Risk Analysis - Biomarkers; Exposure/Risk Analysis - Human Health Risks
GenAge DatabaseHAGR - Human Ageing Genomic ResourcesComputational Toxicology - Virtual Model Organisms; Exposure/Risk Analysis - Biomarkers
GenBankNational Center for Biotechnology Information, NLM, NIHBioinformatics - Biomolecular Sequences/Structures; Exposure/Risk Analysis - Biomarkers
Gene Expression AtlasEMBL-EBIBioinformatics - Biological Dose-Response; Exposure/Risk Analysis - Biomarkers
Gene FinderNCI (National Cancer Institute), NIHExposure/Risk Analysis - Biomarkers
Gene Network Inference ToolUniversity of California, IrvineBioinformatics - Interactions/Biopathways/Bionetworks; Bioinformatics - Data Integration
Gene WeaverJackson Laboratory, ME and collaboratorsBioinformatics - Bio-Ontologies; Bioinformatics - Biological Dose-Response
GENEEC2 - Generic Estimated Environmental ConcentrationUSEPAEnviroinformatics - Environmental Fate and Transport; Exposure/Risk Analysis - Ecological Risks
GeneLocWeizmann Institute of ScienceExposure/Risk Analysis - Biomarkers
GeneMANIA - "predict the function of [...] genes and gene sets"Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, CanadaBioinformatics - Biomolecular Sequences/Structures; Exposure/Risk Analysis - Biomarkers
Genes2FANsSBCNY and Mount Sinai School of MedicineBioinformatics - Interactions/Biopathways/Bionetworks
GeneSpringAgilent TechnologiesBioinformatics - Biomolecular Sequences/Structures; Exposure/Risk Analysis - Biomarkers
GeneTalk - "Analyze human sequence variants"GeneTalk development teamBioinformatics - Biomolecular Sequences/Structures
Genetic Association DatabaseGAD development team and NIHBioinformatics - Biomolecular Sequences/Structures
GeneToxNLMCheminformatics - Property/Activity Prediction; Bioinformatics - Biological Dose-Response; Computational Toxicology - Toxicoinformatics; Exposure/Risk Analysis - Biomarkers
GenMAPP - Gene Map Annotator and Pathway ProfilerGladstone Institutes, UCSFBioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Interactions/Biopathways/Bionetworks
Genomatix SuiteGenomatix Software GmbHBioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Biological Dose-Response; Exposure/Risk Analysis - Biomarkers
Genotyping ConsoleAffymetrix IncBioinformatics - Biomolecular Sequences/Structures; Exposure/Risk Analysis - Biomarkers
GENSAT - Gene Expression Nervous System ATlas databaseRockefeller UniversityBioinformatics - Biological Dose-Response; Exposure/Risk Analysis - Biomarkers
GENSCANStanford University (C. Burge and S. Karlin)Bioinformatics - Biomolecular Sequences/Structures
GeoLytics Demographics Estimates/ ProjectionsGeoLytics, Inc.Enviroinformatics - Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis - Socioeconomic/LSB Modeling
GEON Integrated Data ViewerUNAVCOGeneral Development Tools - Data Visualization
Geospiza GeneSifter Analysis EditionPerkin ElmerBioinformatics - Biomolecular Sequences/Structures
Gepasi (see COPASI)Virginia Bioinformatics Institute, Virginia TechCheminformatics - Interaction/Reaction Modeling; Bioinformatics - Interactions/Biopathways/Bionetworks
geppetto ("a web-based [...] simulation platform [...] to support the simulation of complex biological systems and their surrounding environment")geppetto development teamGeneral Development Tools - Development and Programming
GerES - German Environmental SurveyThe Federal Environment Agency, GermanyComputational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics; Exposure/Risk Analysis - Cumulative/Aggregate Exposures
GESTIS - International limit values for chemical agentsIFA - Institut fur ArbeitsschutzCheminformatics - Property/Activity Prediction
geWorkBench - Genomics WorkbenchNCI (National Cancer Institute), NIHBioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Interactions/Biopathways/Bionetworks; Data/Simulation Pattern Analysis - Classification/Clustering
GFBio - German Federation for the curation of Biological dataGFBioBioinformatics - Bio-Ontologies
GLEAMviz - Global Epidemic and Mobility modelNortheastern University, ISI Foundation and Indiana UniversityExposure/Risk Analysis - Microenvironmental/LCA Modeling
GLIDA - GPCR-Ligand DatabaseKyoto UniversityBioinformatics - Biomolecular Sequences/Structures
GlimmerHMMCenter for Bioinformatics and Computational Biology, University of MarylandBioinformatics - Biomolecular Sequences/Structures
Globally Optimal BiclusteringAndroulakis Laboratory, Rutgers UniversityData/Simulation Pattern Analysis - Classification/Clustering
GMAP - Genomic Mapping and Alignment Program for mRNA and EST SequencesGenentech, Inc., CABioinformatics - Biomolecular Sequences/Structures
GMC impute - Gaussian mixture clustering imputeComputational Chemodynamics LaboratoryBioinformatics - Biological Dose-Response; Data/Simulation Pattern Analysis - Classification/Clustering; Data/Simulation Pattern Analysis - Machine Learning Algorithms
GME - Geospatial Modelling EnvironmentSpatial Ecology LLCEnviroinformatics - Spatiotemporal Mapping/Analysis
GMS - Groundwater Modeling SystemAquaveoEnviroinformatics - Environmental Fate and Transport
GNA - Genetic Network AnalyzerIbisBioinformatics - Interactions/Biopathways/Bionetworks
GNPD - Mintel Global New Products DatabaseMintel Group Ltd.Exposure/Risk Analysis - Microenvironmental/LCA Modeling
GO Database - Gene Ontology DatabaseGene Ontology ConsortiumBioinformatics - Bio-Ontologies
GOFFA - Gene Ontology for Functional AnalysisUSFDABioinformatics - Bio-Ontologies; Computational Toxicology - Virtual Cells, Tissues, Organs
GOLD - Genomes Online DatabaseGOLD TeamBioinformatics - Biomolecular Sequences/Structures
GoMinerNCI (National Cancer Institute), NIHBioinformatics - Biomolecular Sequences/Structures
GoodGuide ("source of information on health, environmental, and social impacts of consumer products")GoodGuide teamExposure/Risk Analysis - Microenvironmental/LCA Modeling
Google Earth Pro ("3D interactive globe that can be used to aid planning, analysis and decision making")GoogleEnviroinformatics - Spatiotemporal Mapping/Analysis; General Development Tools - Data Visualization
Google Map Maker ("allows [...] to add and update geographic information for [...] users to see in Google Maps and Google Earth")GoogleEnviroinformatics - Spatiotemporal Mapping/Analysis; General Development Tools - Data Visualization
GPCR NaVa database - G Protein-Coupled Receptors Natural Variants databaseLeiden/Amsterdam Center for Drug Research and Leiden Institute of Advanced Computer ScienceBioinformatics - Biomolecular Sequences/Structures
GPCR SARfari ("integrated chemogenomics research and discovery workbench for Class A G Protein Coupled Receptors")EMBL-EBIBioinformatics - Biomolecular Sequences/Structures
GPCRDB - G Protein-Coupled Receptor Data BaseGPCRDB development teamCheminformatics - Structure Elucidation; Bioinformatics - Biomolecular Sequences/Structures
GPCRHMM - "GPCR detection method"Stockholm Bioinformatics CentreBioinformatics - Biomolecular Sequences/Structures
GPCR-OKB - G Protein Coupled Receptor - Oligomer Knowledge BaseGPCR-OKB development teamBioinformatics - Biomolecular Sequences/Structures
GPCR-PD ("database for G protein-coupled receptors")Incyte GenomicsBioinformatics - Biomolecular Sequences/Structures
GPCRTree - "hierarchical classification of GPCR function"University of Oxford, UKBioinformatics - Biomolecular Sequences/Structures
gpDB - "database of GPCRs, G-proteins, effectors and their interactions"University of Athens, GreeceBioinformatics - Interactions/Biopathways/Bionetworks; Bioinformatics - Data Integration
GPU Codes for 3D Model of Epidermal DevelopmentUniversity of California, IrvineComputational Toxicology - Virtual Cells, Tissues, Organs
GPUFRAGFOLD - Protein Structure Prediction toolBioinformatics Group, University College LondonCheminformatics - Structure Elucidation; Bioinformatics - Biomolecular Sequences/Structures
GRAM - Genetic RegulAtory ModulesGifford Laboratory, MITBioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Interactions/Biopathways/Bionetworks
Grapher - "Graphing software"Golden Software Inc.General Development Tools - Data Visualization
GraphPad PrismGraphPad Software, Inc.General Development Tools - Data Visualization
Graphviz ("Graph Visualization Software")Graphviz Development TeamGeneral Development Tools - Data Visualization
GRASS GIS - Geographic Resources Analysis Support System Geographic information systemOpen Source Geospatial FoundationEnviroinformatics - Spatiotemporal Mapping/Analysis
GRNN_ImputeComputational Chemodynamics LaboratoryData/Simulation Pattern Analysis - Classification/Clustering
Groundwater Vistas ("3D groundwater flow and contaminant transport modeling, calibration and optimization using the MODFLOW suite of codes")Groundwater Vistas development teamEnviroinformatics - Environmental Fate and Transport; Exposure/Risk Analysis - Ecological Risks
GS+ ("Geostatistics for the Environmental Sciences")Gamma Design SoftwareEnviroinformatics - Spatiotemporal Mapping/Analysis
GSEA - Gene Set Enrichment AnalysisBroad InstituteBioinformatics - Biological Dose-Response
GSLIB - Geostatistical Software LibraryStanford UniversityEnviroinformatics - Spatiotemporal Mapping/Analysis
GSNAP - Genomic Short-read Nucleotide Alignment ProgramGenentech, Inc., CABioinformatics - Biomolecular Sequences/Structures
GUTS - General Unified Threshold model for SurvivalGUTS teamExposure/Risk Analysis - Ecological Risks
GVS - Genome Variation ServerUniversity of WashingtonBioinformatics - Biomolecular Sequences/Structures; Exposure/Risk Analysis - Biomarkers
GWA - Ground Water AtlasUS Geological SurveyEnviroinformatics - Release Mapping/Modeling
GWAS Catalog - Genome-Wide Association Studies CatalogNHGRI Division of Genomic Medicine, NIHBioinformatics - Data Integration; Exposure/Risk Analysis - Biomarkers
GWASdbGWASdb teamBioinformatics - Data Integration; Exposure/Risk Analysis - Biomarkers
Gwyddion ("a modular program for SPM (scanning probe microscopy) data visualization and analysis")Gwyddion development teamBioinformatics - Data Integration; General Development Tools - Data Visualization
HADCM3 - Hadley Centre Coupled ModelThe Hadley Centre for Climate Prediction and Research and USEPAEnviroinformatics - Spatiotemporal Mapping/Analysis
Hadoop ("open-source software for [...] scalable, distributed computing")The Apache Software FoundationGeneral Development Tools - Development and Programming
HAIR - HArmonized environmental Indicators for pesticide RiskAlterra and Wageningen UR, The NetherlandsExposure/Risk Analysis - Ecological Risks
HAPEM - Hazardous Air Pollutant Exposure ModelUSEPAExposure/Risk Analysis - Cumulative/Aggregate Exposures
HapMapInternational HapMap ProjectBioinformatics - Biomolecular Sequences/Structures; Exposure/Risk Analysis - Biomarkers
HazardExpert ProCompuDrugCheminformatics - Property/Activity Prediction
HCA - Hydrophobic Cluster AnalysisMobyleNet
HDMFinder ("Methylation prediction software")Zhang Lab, Cold Spring Harbor Laboratory, NYBioinformatics - Biomolecular Sequences/Structures; Exposure/Risk Analysis - Biomarkers
Health Indicators WarehouseNational Center for Health StatisticsEnviroinformatics - Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis - Socioeconomic/LSB Modeling
HealthMapBoston Children's HospitalEnviroinformatics - Spatiotemporal Mapping/Analysis
HEDS - Human Exposure Database SystemUSEPAExposure/Risk Analysis - Microenvironmental/LCA Modeling; Exposure/Risk Analysis - Cumulative/Aggregate Exposures; Exposure/Risk Analysis - Human Health Risks
HEP - Human Epigenome ProjectHEP ConsortiumBioinformatics - Biological Dose-Response; Exposure/Risk Analysis - Biomarkers
HERO - Health and Environmental Research Online databaseUSEPAExposure/Risk Analysis - Human Health Risks; Exposure/Risk Analysis - Ecological Risks
HEROIC - High-Throughput Epigenetic Regulatory Organization in Chromatin ProjectHEROIC Project ConsortiumBioinformatics - Biological Dose-Response; Exposure/Risk Analysis - Biomarkers
HexSim (previously PATCH)USEPAExposure/Risk Analysis - Ecological Risks
HGMD - Human Gene Mutation Database (integrated with Ingenuity Variant Analysis) BIOBASEBioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Biological Dose-Response; Computational Toxicology - Toxicoinformatics; Computational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics; Exposure/Risk Analysis - Biomarkers
Histone DatabaseNHGRI Division of Intramural Research, NIHBioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Data Integration
HIV Molecular Immunology DatabaseLos Alamos National LaboratoryExposure/Risk Analysis - Biomarkers
HIV Sequence databaseLos Alamos National LaboratoryBioinformatics - Biomolecular Sequences/Structures; Exposure/Risk Analysis - Biomarkers
Hive ("data warehouse software")Apache Hive development team and The Apache Software FoundationGeneral Development Tools - Development and Programming
HLM - Hierarchical Linear and Nonlinear ModelingScientific Software International, Inc.Exposure/Risk Analysis - Socioeconomic/LSB Modeling; General Development Tools - Development and Programming
HMMER ("biosequence analysis using profile hidden Markov models")HMMER development teamBioinformatics - Biomolecular Sequences/Structures
HMMTOP ("Prediction of transmembrane helices and topology of proteins")HMMTOP team, Institute of Enzymology, HungaryBioinformatics - Biomolecular Sequences/Structures
HMPDACC Data Browser (Human Microbiome Project DACC Data Portal)NIH Human Microbiome Project DACCExposure/Risk Analysis - Biomarkers
HomoloGeneNational Center for Biotechnology Information, NLM, NIHBioinformatics - Biomolecular Sequences/Structures
Howard's Handbook of Environmental Fate and Exposure Data for Organic ChemicalsPhilip Hall HowardCheminformatics - Property/Activity Prediction
HPAC - Hazard Prediction and Assessment CapabilityDTRA - Defense Threat Reduction AgencyEnviroinformatics - Environmental Fate and Transport
HPD - Household Products DatabaseNational Library of MedicineEnviroinformatics - Release Mapping/Modeling; Exposure/Risk Analysis - Microenvironmental/LCA Modeling
HPVIS - High Production Volume Information SystemUSEPAExposure/Risk Analysis - Microenvironmental/LCA Modeling
HSDB - Hazardous Substances Data BankNational Library of MedicineCheminformatics - Property/Activity Prediction; Computational Toxicology - Toxicoinformatics
HSPF - Hydrological Simulation Program - FORTRANUSEPAEnviroinformatics - Environmental Fate and Transport
Human Anatomy OnlineHowToMedia Inc
Human DNA Polymerase Gamma Mutation DatabaseNIEHSBioinformatics - Biomolecular Sequences/Structures; Exposure/Risk Analysis - Biomarkers
Human Epigenome AtlasBioinformatics Research Laboratory, Baylor College of MedicineBioinformatics - Biological Dose-Response; Bioinformatics - Data Integration
Human Genome BrowserGenome Bioinformatics Group, UC Santa Cruz.Bioinformatics - Biomolecular Sequences/Structures
HumanCycSRI InternationalBioinformatics - Interactions/Biopathways/Bionetworks
Human-gpDB ("database of human GPCRs, G-proteins, Effectors and their interactions")Human-gpDB teamBioinformatics - Interactions/Biopathways/Bionetworks; Bioinformatics - Data Integration
HuRef Genome Browser (Individual Human Genome Browser)J. Craig Venter InstituteBioinformatics - Biomolecular Sequences/Structures
HYPACT - Hybrid Particle And Concentration Transport ModelATMETEnviroinformatics - Environmental Fate and Transport
Hypertable ("open source database system")Hypertable Inc.General Development Tools - Development and Programming
HYSPLIT - Hybrid Single Particle Lagrangian Integrated Trajectory ModelNOAA Air Resources LaboratoryEnviroinformatics - Environmental Fate and Transport
IAQX - Simulation Tool Kit for Indoor Air Quality and Inhalation ExposureUSEPAEnviroinformatics - Environmental Fate and Transport
IARC Monographs- ClassificationsIARC, WHOComputational Toxicology - Toxicoinformatics; Exposure/Risk Analysis - Human Health Risks
IARC TP53 DatabaseIARC, WHOComputational Toxicology - Toxicoinformatics; Exposure/Risk Analysis - Biomarkers
IBM SPSS ModelerSPSS Inc. and IBMData/Simulation Pattern Analysis - Data Mining/Pattern Recognition
IBM SPSS StatisticsSPSS Inc. and IBMGeneral Development Tools - Development and Programming
ICIS - Integrated Compliance Information SystemUSEPAEnviroinformatics - Release Mapping/Modeling
ICRP - International Commission on Radiological Protection - Database of Dose CoefficientsICRPBioinformatics - Biological Dose-Response; Computational Toxicology - Toxicoinformatics; Computational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics; Exposure/Risk Analysis - Human Health Risks
ICSC - International Chemical Safety CardsInternational Labour OrganizationCheminformatics - Property/Activity Prediction
icsiboosticsiboost project teamData/Simulation Pattern Analysis - Data Mining/Pattern Recognition; Data/Simulation Pattern Analysis - Classification/Clustering; Data/Simulation Pattern Analysis - Machine Learning Algorithms
IDBA-UD - iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing DepthThe Bioinformatics Research Group, University of Hong KongBioinformatics - Biomolecular Sequences/Structures
IDEA - Infusing satellite Data into Environmental air quality ApplicationsNASA- EPA-NOAA partnershipEnviroinformatics - Spatiotemporal Mapping/Analysis; Enviroinformatics - Release Mapping/Modeling
iemHUB ("online community resource for those involved in the development, evaluation, and application of environmental models")iemHUB teamEnviroinformatics - Environmental Fate and Transport; Exposure/Risk Analysis - Microenvironmental/LCA Modeling; Exposure/Risk Analysis - Cumulative/Aggregate Exposures
IGSM - Integrated Global System ModelMIT Joint Program on the Science and Policy of Global Change and USEPAEnviroinformatics - Environmental Fate and Transport
IGV - Integrative Genomics ViewerBroad InstituteBioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Biological Dose-Response
IIPP - Inert Ingredients in Pesticide ProductsUSEPACheminformatics - Property/Activity Prediction
Illumina GenomeStudioIllumina SoftwareBioinformatics - Biomolecular Sequences/Structures
ImageJImageJ development teamGeneral Development Tools - Data Visualization
IMGT - ImMunoGeneTics information systemMarie-Paule LefrancBioinformatics - Biomolecular Sequences/Structures
IMGT/3Dstructure-DB - ImMunoGeneTicsMarie-Paule LefrancBioinformatics - Biomolecular Sequences/Structures
Index Mundi - MapsIndexMundi development teamEnviroinformatics - Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis - Socioeconomic/LSB Modeling
InDose ("Internal Dosimetry Code Using Biokinetics Models")Soreq - Nuclear Research Center, Israel (I. Silverman)Computational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
Infernal - INFERence of RNA ALignmentEddy group, HHMI Janelia Farm Research Campus, VABioinformatics - Biomolecular Sequences/Structures
Information Collection Rule Drinking Water Microbial And Disinfection Byproduct InformationUSEPAEnviroinformatics - Release Mapping/Modeling; Exposure/Risk Analysis - Microenvironmental/LCA Modeling
Ingenuity Variant AnalysisQiagenBioinformatics - Biomolecular Sequences/Structures; Computational Toxicology - Toxicoinformatics; Exposure/Risk Analysis - Biomarkers
Integr8EMBL-EBIBioinformatics - Biomolecular Sequences/Structures
Interactive Lyme Disease MapCDCEnviroinformatics - Spatiotemporal Mapping/Analysis
InterNanoNational Nanomanufacturing NetworkExposure/Risk Analysis - Microenvironmental/LCA Modeling; Exposure/Risk Analysis - Cumulative/Aggregate Exposures
InterProEMBL-EBIBioinformatics - Biomolecular Sequences/Structures
IONEX - Ion ExchangeUSEPAExposure/Risk Analysis - Ecological Risks
IPA - Ingenuity Pathway AnalysisQiagen N.V.Bioinformatics - Interactions/Biopathways/Bionetworks; Bioinformatics - Biological Dose-Response; Computational Toxicology - Toxicoinformatics; Exposure/Risk Analysis - Biomarkers
iPathwayGuideAdvaita CorporationBioinformatics - Interactions/Biopathways/Bionetworks
iPathwaysThe Systems Biology Institute, JapanBioinformatics - Interactions/Biopathways/Bionetworks
iProClassPIR - Protein Information ResourceBioinformatics - Biomolecular Sequences/Structures
IPython - Shell interface for interactive computing in multiple programming languagesIPython development teamGeneral Development Tools - Data Visualization
IRD - Influenza Research DatabaseIRD Project TeamBioinformatics - Biomolecular Sequences/Structures; Exposure/Risk Analysis - Biomarkers
IRIS - Integrated Risk Information SystemUSEPABioinformatics - Biological Dose-Response; Computational Toxicology - Toxicoinformatics; Computational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics; Exposure/Risk Analysis - Human Health Risks
ISDD - In vitro Sedimentation, Diffusion and Dosimetry modelPNNLComputational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
isee NetSim (Web-based Simulation Sharing for STELLA and iThink models)isee Systems, Inc.General Development Tools - Development and Programming
IsoConcUSEPAEnviroinformatics - Environmental Fate and Transport; Exposure/Risk Analysis - Ecological Risks
IsoErrorUSEPAExposure/Risk Analysis - Ecological Risks
IsoSourceUSEPAEnviroinformatics - Environmental Fate and Transport; Exposure/Risk Analysis - Ecological Risks
iSTREEMAmerican Cleaning InstituteExposure/Risk Analysis - Microenvironmental/LCA Modeling; Exposure/Risk Analysis - Ecological Risks
i-SVOC ("application for dynamic modeling of the emissions, transport, sorption, and distribution of semi-volatile organic compounds (SVOCs) in the indoor environment")USEPAEnviroinformatics - Release Mapping/Modeling; Enviroinformatics - Environmental Fate and Transport; Exposure/Risk Analysis - Microenvironmental/LCA Modeling
Italian demographics dataISTATEnviroinformatics - Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis - Socioeconomic/LSB Modeling
ITER - International Toxicity Estimates for RiskNational Library of MedicineCheminformatics - Property/Activity Prediction
iTOL - Interactive Tree Of LifeEMBL, GermanyBioinformatics - Interactions/Biopathways/Bionetworks
IUPHAR-DB - International Union of Basic and Clinical Pharmacology DatabaseIUPHAR-DB development teamBioinformatics - Data Integration; Computational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics; Exposure/Risk Analysis - Biomarkers
IUR data - Inventory Update Reporting dataUSEPAEnviroinformatics - Release Mapping/Modeling
J/maanovaChurchill Group, Jackson LaboratoryBioinformatics - Biological Dose-Response
Jaguar ("ab initio electronic structure package")Schrödinger, LLCCheminformatics - Structure Elucidation; Cheminformatics - Property/Activity Prediction; Cheminformatics - Interaction/Reaction Modeling
JasonJason development teamGeneral Development Tools - Development and Programming
JavaOracleGeneral Development Tools - Development and Programming
Java Treeview ("Viewer for Microarray Data in the PCL or CDT format")Stanford University School of Medicine (A. J. Saldanha) and Java Treeview development teamBioinformatics - Biological Dose-Response; General Development Tools - Data Visualization
JigCellVirgina TechComputational Toxicology - Virtual Cells, Tissues, Organs
JILDT - Jason Induction of Logical Decison TreesJILDT development teamGeneral Development Tools - Development and Programming
J-MADeM - Multi-modal Agent Decision Making (library integrated into Jason)MADeM development teamExposure/Risk Analysis - Socioeconomic/LSB Modeling; General Development Tools - Development and Programming
jMOSAiCS - Joint Analysis of Multiple ChIP-seq DatasetsKeles Research Group, University of WisconsinBioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Biological Dose-Response; Exposure/Risk Analysis - Biomarkers
JPredBarton Group, University of DundeeBioinformatics - Biomolecular Sequences/Structures
JsimPhysiome Project, University of WashingtonGeneral Development Tools - Development and Programming
JSNP - Japanese Single Nucleotide PolymorphismsUniversity of Tokyo and the Japan Science and Technology Agency (JST)Bioinformatics - Biomolecular Sequences/Structures; Exposure/Risk Analysis - Biomarkers
JSoarSoar Technology, Inc. and Dave RayGeneral Development Tools - Development and Programming
KABAM - Kow (based) Aquatic BioAccumulation ModelUSEPAEnviroinformatics - Environmental Fate and Transport; Exposure/Risk Analysis - Ecological Risks
KalignEMBL-EBIBioinformatics - Biomolecular Sequences/Structures
KEGG - Kyoto Encyclopedia of Genes and GenomesKanehisa Laboratories, JapanBioinformatics - Interactions/Biopathways/Bionetworks; Bioinformatics - Data Integration; Exposure/Risk Analysis - Biomarkers
KEGG DRUGKanehisa Laboratories, JapanExposure/Risk Analysis - Biomarkers
KEGG GENES databaseKanehisa Laboratories, JapanBioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Interactions/Biopathways/Bionetworks
KEGG LIGAND databaseKanehisa Laboratories, JapanCheminformatics - Interaction/Reaction Modeling
KEGG MEDICUSKanehisa Laboratories, JapanComputational Toxicology - Toxicoinformatics; Computational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
KELVINBattelle Center for Mathematical Medicine, Nationwide Children's Hospital, OhioBioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Data Integration
KelvizBattelle Center for Mathematical Medicine, Nationwide Children's Hospital, OhioBioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Data Integration
Keyplayer ("Finding sets of key players in a network")Analytic TechnologiesExposure/Risk Analysis - Socioeconomic/LSB Modeling
Kirk-Othmer Encyclopedia of Chemical TechnologyWiley Online LibraryCheminformatics - Property/Activity Prediction
KNB - Knowledge Network for BiocomplexityKNB teamExposure/Risk Analysis - Ecological Risks
KNIME - Konstanz Information MinerKNIME development teamGeneral Development Tools - Development and Programming
KNN_ImputeComputational Chemodynamics LaboratoryData/Simulation Pattern Analysis - Classification/Clustering
Krackplot ("Network visualization")Analytic TechnologiesExposure/Risk Analysis - Socioeconomic/LSB Modeling; General Development Tools - Data Visualization
KUPKB - The Kidney and Urinary Pathway Knowledge BaseINSERM, France and University of Manchester, UKBioinformatics - Interactions/Biopathways/Bionetworks; Bioinformatics - Data Integration; Computational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics; Exposure/Risk Analysis - Biomarkers
LandGEM - Landfill Gas Emissions ModelUSEPAEnviroinformatics - Release Mapping/Modeling
LandScan USAOak Ridge National LaboratoryEnviroinformatics - Spatiotemporal Mapping/Analysis
LandViewUS Census BureauEnviroinformatics - Spatiotemporal Mapping/Analysis
Lange's Handbook of ChemistryMcGraw-HillCheminformatics - Property/Activity Prediction
Lazar - chemical toxicity predictionIn Silico Toxicology GmBHCheminformatics - Property/Activity Prediction
LibSBML/ JSBML - Programming library for C++, Java, Python and othersSBML TeamComputational Toxicology - Virtual Cells, Tissues, Organs
LifelineLifeLine GroupExposure/Risk Analysis - Cumulative/Aggregate Exposures
LISREL ("for structural equation modeling")Scientific Software International, Inc.Exposure/Risk Analysis - Socioeconomic/LSB Modeling; General Development Tools - Development and Programming
Literature LabAcumenta BiotechBioinformatics - Data Integration
LIVERTOX™NIDDK and NLMBioinformatics - Biological Dose-Response; Computational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
LMPD - LIPID MAPS Proteome DatabaseUniversity of California, San DiegoBioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Data Integration
LMSD - LIPID MAPS Structure DatabaseUniversity of California, San DiegoBioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Data Integration
LOGKOW databaseSangster Research Laboratories, CanadaCheminformatics - Property/Activity Prediction
LONI AtlasesLaboratory of Neuro Imaging, UCLA
LSD ("platform for the development, use and distribution of simulations")Laboratory for Simulation DevelopmentGeneral Development Tools - Development and Programming
LSPC - Loading Simulation Program in C++USEPAEnviroinformatics - Environmental Fate and Transport
LTKB - Liver Toxicity Knowledge BaseUSFDABioinformatics - Biological Dose-Response; Computational Toxicology - Toxicoinformatics
Lucene ("text search engine library")Apache Software FoundationGeneral Development Tools - Development and Programming
LUDEP - Lung Dose Evaluation ProgramNational Radiological Protection Board, UKComputational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
LULC - Land Use and Land CoverUS Geological SurveyEnviroinformatics - Spatiotemporal Mapping/Analysis
Mackay's Handbook of Physical-Chemical Properties and Environmental Fate for Organic ChemicalsCRC PressCheminformatics - Property/Activity Prediction
Macromodel ("program for molecular modeling")Schrödinger, LLCCheminformatics - Interaction/Reaction Modeling
MACS - Model-based Analysis of ChIP-Seq dataHarvard UniversityBioinformatics - Biomolecular Sequences/Structures
MADARA - Multi-Agent Distributed Adaptive Resource Allocationmadara development teamGeneral Development Tools - Development and Programming
MADr-BMD - Model Averaging for Dichotomous Response Benchmark DoseWheeler and BailerComputational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
MAExplorer - Microarray ExplorerMAExplorer development teamBioinformatics - Biomolecular Sequences/Structures
MAGICC/SCENGEN - Model for the Assessment of Greenhouse Gas Induced Climate Change/Scenario GeneratorNational Center for Atmospheric ResearchEnviroinformatics - Environmental Fate and Transport
MAKER ("portable and [...] configurable genome annotation pipeline")Yandell Laboratory, University of UtahBioinformatics - Biomolecular Sequences/Structures
Mammalian Protein-Protein Interaction DatabaseMunich Information Center for Protein Sequences (MIPS), Institute of Bioinformatics and Systems Biology (IBIS), GermanyBioinformatics - Biological Dose-Response
MapBoxMapBox teamEnviroinformatics - Spatiotemporal Mapping/Analysis; General Development Tools - Data Visualization
MapInfo Professional ("desktop mapping application")MapInfo and Pitney BowesEnviroinformatics - Spatiotemporal Mapping/Analysis; General Development Tools - Data Visualization
MapInfo Vertical Mapper ("tool for geospatial data analysis")MapInfo and Pitney BowesEnviroinformatics - Spatiotemporal Mapping/Analysis; General Development Tools - Data Visualization
MapleMapleSoftGeneral Development Tools - Development and Programming
MapTalesMapTales teamGeneral Development Tools - Data Visualization
MapUSA - Human mapping projectJohn LoganEnviroinformatics - Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis - Socioeconomic/LSB Modeling
Maq - Mapping and Assembly with QualityMaq development teamBioinformatics - Biomolecular Sequences/Structures
MAQC - MicroArray Quality ControlUSFDABioinformatics - Biological Dose-Response
Maqview - graphical read alignment viewerMaqview development team (Ruan et al.)Bioinformatics - Biomolecular Sequences/Structures
MarathonUniversity of California, IrvineData/Simulation Pattern Analysis - Data Mining/Pattern Recognition
MariaDBMariaDB FoundationGeneral Development Tools - Development and Programming
Marker MapsNCI (National Cancer Institute), NIH
MarkerViewAB SciexExposure/Risk Analysis - Biomarkers
MascotMatrix ScienceBioinformatics - Biomolecular Sequences/Structures; Exposure/Risk Analysis - Biomarkers
MASON - Multi-Agent Simulator Of NeighborhoodsGMU Evolutionary Computation Laboratory and GMU Center for Social ComplexityExposure/Risk Analysis - Socioeconomic/LSB Modeling; General Development Tools - Development and Programming
MASS - Multi-Agent Simulation SuiteAITIA International IncExposure/Risk Analysis - Socioeconomic/LSB Modeling; General Development Tools - Development and Programming
MASTEP - Metapopulation model for Assessing Spatial and Temporal Effects of PesticidesAlterra and Wageningen UR, The NetherlandsExposure/Risk Analysis - Ecological Risks
MASyV - Multi-Agent System VisualizationMASyV development teamExposure/Risk Analysis - Socioeconomic/LSB Modeling; General Development Tools - Development and Programming
MathcadPTCGeneral Development Tools - Development and Programming
MathematicaWolfram ResearchGeneral Development Tools - Development and Programming
MATLABThe Mathworks, Inc.General Development Tools - Development and Programming
MATLAB Bioinformatics ToolboxThe Mathworks, Inc.Bioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Biological Dose-Response; Computational Toxicology - Toxicoinformatics
MATLAB Toolboxes (Optimization; Direct Search; Genetic Algorithms)The Mathworks, Inc.Bioinformatics - Biomolecular Sequences/Structures
MATSim - Multi-Agent Transport SimulationI.L.S.T.S., Technische Universität Berlin; I.T.P.S., Swiss Federal Institute of Technology, Zurich and SenozonEnviroinformatics - Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis - Socioeconomic/LSB Modeling
maxdViewManchester BioinformaticsBioinformatics - Biological Dose-Response; Computational Toxicology - Toxicoinformatics
Maximally Informative GenesAndroulakis Laboratory, Rutgers UniversityBioinformatics - Interactions/Biopathways/Bionetworks
MCCEM - Multi-Chamber Concentration and Exposure ModelVersar Inc. and USEPAExposure/Risk Analysis - Microenvironmental/LCA Modeling
MCell - Monte Carlo cellPittsburgh Supercomputing Center and Computational Neurobiology Laboratory, Salk InstituteComputational Toxicology - Virtual Cells, Tissues, Organs
MCIP - Meteorology-Chemistry Interface ProcessorUSEPAEnviroinformatics - Release Mapping/Modeling
MCSimFree Software Foundation, IncData/Simulation Pattern Analysis - Sensitivity/Uncertainty Analysis
MDscan - Motif Discovery scanStanford Medical Informatics, Stanford UniversityBioinformatics - Biomolecular Sequences/Structures
MEANSIM - Mean Similarity AnalysisUSEPAData/Simulation Pattern Analysis - Data Mining/Pattern Recognition
MEASURE - Mobile Emissions Assessment System for Urban and Regional EvaluationGeorgia Institute of Technology and USEPAEnviroinformatics - Environmental Fate and Transport
MEGA - Molecular Evolutionary Genetics AnalysisMEGA teamBioinformatics - Biomolecular Sequences/Structures
MEGAN - Model of Emissions of Gases and Aerosols from NatureNCAR Earth System LaboratoryEnviroinformatics - Release Mapping/Modeling
MeInfoTextNational Taiwan UniversityBioinformatics - Biological Dose-Response; Bioinformatics - Data Integration; Exposure/Risk Analysis - Biomarkers
MEMSAT3 - MEMbrane protein Structure And TopologyMEMSAT team, University College London, UKBioinformatics - Biomolecular Sequences/Structures
MENTOR - Modeling ENvironment for TOtal Risk studiesComputational Chemodynamics LaboratoryExposure/Risk Analysis - Biomarkers
MENTOR-1A - Modeling ENvironment for TOtal Risk studies in a One Atmosphere settingComputational Chemodynamics LaboratoryEnviroinformatics - Environmental Fate and Transport
MENTOR-2E - Modeling ENvironment for TOtal Risk studies for Emergency Event applicationsComputational Chemodynamics LaboratoryExposure/Risk Analysis - Cumulative/Aggregate Exposures
MENTOR-3P - Modeling ENvironment for TOtal Risk studies using Physiologically-based Pharmacokinetic modeling tools for Population assessmentsComputational Chemodynamics LaboratoryComputational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
MENTOR-4M - Modeling ENvironment for TOtal Risk studies for Multiple co-occurring contaminants and Multimedia, Multipathway, Multiroute exposuresComputational Chemodynamics LaboratoryEnviroinformatics - Environmental Fate and Transport; Exposure/Risk Analysis - Cumulative/Aggregate Exposures
MENTOR-DOT - Modeling ENvironment for TOtal Risk studies Diagnostic and Optimization ToolsComputational Chemodynamics LaboratoryData/Simulation Pattern Analysis - Data Mining/Pattern Recognition; Data/Simulation Pattern Analysis - Sensitivity/Uncertainty Analysis
MEPAS - Multimedia Environmental Pollutant Assessment SystemPacific Northwest National LaboratoryEnviroinformatics - Environmental Fate and Transport; Exposure/Risk Analysis - Cumulative/Aggregate Exposures
Merck IndexMerck & Co IncCheminformatics - Property/Activity Prediction
Mercury MapsUSEPAExposure/Risk Analysis - Ecological Risks
MESOPUFF - Mesoscale Puff ModelUSEPAEnviroinformatics - Environmental Fate and Transport
MesoWest (Current and archived weather observations and summaries from across the United States)Dept. of Atmos. Sci., University of UtahEnviroinformatics - Spatiotemporal Mapping/Analysis; Enviroinformatics - Environmental Fate and Transport
MetaboliteToolsBruker DaltonicsExposure/Risk Analysis - Biomarkers
MetaCoreThomson ReutersBioinformatics - Interactions/Biopathways/Bionetworks
MetaCycSRI InternationalBioinformatics - Interactions/Biopathways/Bionetworks
MetaMerge (reconcile differences in existing metabolic network models)MetaMerge development teamBioinformatics - Interactions/Biopathways/Bionetworks
METAPCMulticase IncCheminformatics - Interaction/Reaction Modeling
MetaQTLMetaQTL development teamBioinformatics - Biomolecular Sequences/Structures
MetaSD ("A system dynamics model archive")MetaSD development teamGeneral Development Tools - Development and Programming
MetaSiteMolecular DiscoveryCheminformatics - Interaction/Reaction Modeling
MeteorLhasa LimitedCheminformatics - Interaction/Reaction Modeling; Bioinformatics - Interactions/Biopathways/Bionetworks
MethBase - a reference methylome databaseSmith lab, Molecular and Computational Biology, U. of Southern CaliforniaBioinformatics - Biomolecular Sequences/Structures
MethDB - database for DNA methylation and environmental epigenetic effectsMethDB teamBioinformatics - Biological Dose-Response; Bioinformatics - Data Integration
MethPrimerDBGhent University, BelgiumBioinformatics - Biological Dose-Response; Bioinformatics - Data Integration
MethToolsLeibniz Institute for Age Research - Fritz Lipmann Institute, GermanyBioinformatics - Biological Dose-Response
MethyCancer - Database for studying human DNA Methylation and CancerChinese Academy of SciencesBioinformatics - Biological Dose-Response; Exposure/Risk Analysis - Biomarkers
Methylator ("An SVM Based Method for DNA Methylation Prediction")Methylator Development TeamBioinformatics - Biomolecular Sequences/Structures; Exposure/Risk Analysis - Biomarkers
MethyLogiX DNA methylation databaseEpigenetics Group, Technical University of Munich, Germany (A. Schumacher)Bioinformatics - Biological Dose-Response
MethylomeDB - Brain Methylome DatabaseHaghighi lab, Columbia UniversityBioinformatics - Biomolecular Sequences/Structures
MetNetDB - MetNet DatabaseIowa State UniversityBioinformatics - Interactions/Biopathways/Bionetworks
MetNetGEIowa State UniversityBioinformatics - Interactions/Biopathways/Bionetworks
MetworksThermo ScientificCheminformatics - Structure Elucidation
MeV - MultiExperiment ViewerMeV development teamBioinformatics - Biomolecular Sequences/Structures
MEXAlertCompuDrugCheminformatics - Interaction/Reaction Modeling
MFFRST - Metal Finishing Facility Risk Screening ToolUSEPAExposure/Risk Analysis - Human Health Risks
MgenomeGu Laboratory, Iowa State UniversityBioinformatics - Interactions/Biopathways/Bionetworks
MGI - Mouse Genome InformaticsThe Jackson Laboratory, Maine and MGI teamBioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Interactions/Biopathways/Bionetworks; Bioinformatics - Biological Dose-Response; Bioinformatics - Data Integration; Computational Toxicology - Toxicoinformatics; Computational Toxicology - Virtual Model Organisms
MIAMExpress (no longer maintained)EMBL-EBI
Microarray Center cDNA Clone SearchNIEHSBioinformatics - Biomolecular Sequences/Structures
microBEnet - microbiology of the Built Environment networkEisen Lab at University of California, Davis and Building Ecology Research GroupBioinformatics - Data Integration; Exposure/Risk Analysis - Ecological Risks
microRNA.orgBioinformatics - Biological Dose-Response; Exposure/Risk Analysis - Biomarkers
MIDAS - Multi Instance Data Acquisition SystemScience and Technology Facilities Council, UKBioinformatics - Biomolecular Sequences/Structures; Exposure/Risk Analysis - Biomarkers
MIEP - Modeling Immunity to Enteric PathogensCenter for Modeling Immunity to Enteric Pathogens, Virginia TechComputational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
Mimosa ("modeling and simulation platform")Mimosa development team and CiradGeneral Development Tools - Development and Programming
MinitabMinitab Inc.General Development Tools - Development and Programming
MINT - Molecular INTeraction databaseUniversity of Rome Tor Vergata, ItalyBioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Interactions/Biopathways/Bionetworks
MINTEQA2USEPA and Jerry Allison, Computer Sciences Corp.Enviroinformatics - Environmental Fate and Transport
MIRA - Whole Genome Shotgun and EST Sequence AssemblerBastien ChevreuxBioinformatics - Biomolecular Sequences/Structures
miRBase - microRNA databaseGriffiths-Jones lab, U. of Manchester and Wellcome Trust Sanger InstituteBioinformatics - Biomolecular Sequences/Structures
miRBase ("the microRNA database")University of Manchester, UKBioinformatics - Biomolecular Sequences/Structures
MISO - Mixture of Isoforms ("Probabilistic analysis and design of RNA-Seq experiments for identifying isoform regulation")Burge and Airoldi lab, MIT and Harvard UniversityBioinformatics - Biomolecular Sequences/Structures
Mitelman Database of Chromosome Aberrations and Gene Fusions in CancerUniversity Hospital, Lund, SwedenExposure/Risk Analysis - Biomarkers
MLC++Silicon Graphics International Corp., CAData/Simulation Pattern Analysis - Machine Learning Algorithms
MM5 or PSU/NCAR mesoscale modelPennsylvania State University National Center for Atmospheric ResearchEnviroinformatics - Environmental Fate and Transport
MMDB - Molecular Modeling Database (NCBI Structure)National Center for Biotechnology Information, NLM, NIHCheminformatics - Structure Elucidation; Bioinformatics - Biomolecular Sequences/Structures
MMG - Medical Management GuidelinesATSDR, CDCCheminformatics - Property/Activity Prediction
MOABS - MOdel based Analysis of Bisulfite Sequencing dataDeqiang Sun, Baylor College of MedicineBioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Biological Dose-Response; Exposure/Risk Analysis - Biomarkers
Mobidyc - MOdelling Based on Individuals for the DYnamics of CommunitiesMobidyc development teamExposure/Risk Analysis - Socioeconomic/LSB Modeling; General Development Tools - Development and Programming
MOBILEUSEPAEnviroinformatics - Release Mapping/Modeling
MobyDickThe Rockefeller UniversityBioinformatics - Biomolecular Sequences/Structures
Model BuilderFlavio CoelhoGeneral Development Tools - Development and Programming
ModelAssist (for @RISK and Crystal Ball)Vose Software, BelgiumData/Simulation Pattern Analysis - Sensitivity/Uncertainty Analysis
ModelMakerThe University of Nottingham and FamilyGenetixGeneral Development Tools - Development and Programming
ModelMaker ToolsModelMaker ToolsGeneral Development Tools - Development and Programming
ModelRiskVose Software, BelgiumData/Simulation Pattern Analysis - Sensitivity/Uncertainty Analysis
Models-3 Technical Support ForumCMAS CenterEnviroinformatics - Environmental Fate and Transport
modENCODE - Model Organism ENCyclopedia Of DNA ElementsmodENCODE Project ConsortiumBioinformatics - Biomolecular Sequences/Structures; Computational Toxicology - Virtual Model Organisms
ModflowUS Geological SurveyEnviroinformatics - Environmental Fate and Transport
Modgen - Model generatorStatistics CanadaGeneral Development Tools - Development and Programming
MODIS Satellite Land, Ocean, Atmosphere ProductsNASAEnviroinformatics - Spatiotemporal Mapping/Analysis
modMine ("data warehouse for the modENCODE project")University of Cambridge, Cambridge, UKBioinformatics - Biomolecular Sequences/Structures; Computational Toxicology - Virtual Model Organisms
MOE - Molecular Operating EnvironmentChemical Computing GroupCheminformatics - Property/Activity Prediction
MoKaMolecular Discovery LtdCheminformatics - Property/Activity Prediction
Mold2USFDABioinformatics - Biomolecular Sequences/Structures
MonetDB ("open source column-oriented database management system")MonetDB development teamGeneral Development Tools - Development and Programming
MongoDB ("open-source document database, and [...] NoSQL database")MongoDB, Inc.General Development Tools - Development and Programming
MONGOOSE - MetabOlic Network GrOwth Optimization Solved ExactlyMONGOOSE development team, MITBioinformatics - Interactions/Biopathways/Bionetworks
Monocle - toolkit for analyzing single-cell gene expression experimentsCole TrapnellBioinformatics - Biological Dose-Response; Exposure/Risk Analysis - Biomarkers
Moose - Multiscale Neuroscience and Systems Biology SimulatorMoose teamBioinformatics - Interactions/Biopathways/Bionetworks
Morpheus ("modeling and simulation environment for the study of multiscale and multicellular systems")Center for Information Services and High Performance Computing, Technische Universität Dresden, GermanyBioinformatics - Data Integration; Computational Toxicology - Virtual Cells, Tissues, Organs
MOSAiCS - MOdel-based one and two Sample Analysis and Inference for ChIP-Seq DataKeles Research Group, University of WisconsinBioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Biological Dose-Response; Exposure/Risk Analysis - Biomarkers
Mouse Genome Resequencing ProjectNIEHSBioinformatics - Biomolecular Sequences/Structures; Computational Toxicology - Virtual Model Organisms
MouseMine MGI at The Jackson Laboratory and InterMine project at Cambridge Systems Biology Centre, UKBioinformatics - Bio-Ontologies; Bioinformatics - Interactions/Biopathways/Bionetworks; Bioinformatics - Biological Dose-Response; Computational Toxicology - Virtual Model Organisms
MOVES - Motor Vehicle Emission SimulatorUSEPAEnviroinformatics - Release Mapping/Modeling
MPPD - Multiple-Path Particle Dosimetry ModelApplied Research AssociatesComputational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
MrBayesMrBayes development teamBioinformatics - Biomolecular Sequences/Structures
mrsFAST (short-read mapper)mrsFAST development teamBioinformatics - Biomolecular Sequences/Structures
MSDS - Material Safety Data Sheets3E CompanyCheminformatics - Property/Activity Prediction
MT3DMS - Modular 3-D Multi-Species Transport model (previously MT3D)S.S. Papadopulos & Associates, Inc. and USEPAEnviroinformatics - Environmental Fate and Transport
MUSCLE - MUltiple Sequence Comparison by Log- ExpectationEMBL-EBIBioinformatics - Biomolecular Sequences/Structures
Mussel Watch ProgramCenter for Coastal Monitoring and Assessment, National Ocean ServiceExposure/Risk Analysis - Ecological Risks
MySQLOracleGeneral Development Tools - Development and Programming
mzMINEMZmine team (open-source)Exposure/Risk Analysis - Biomarkers
NACJD - National Archive of Criminal Justice DataICPSR, University of MichiganEnviroinformatics - Spatiotemporal Mapping/Analysis
NADP - National Atmospheric Deposition ProgramNational Atmospheric Deposition ProgramEnviroinformatics - Spatiotemporal Mapping/Analysis
Nanomaterial RegistryRTI InternationalExposure/Risk Analysis - Microenvironmental/LCA Modeling
Nanowerk Nanotechnology Products and ApplicationsNanowerkExposure/Risk Analysis - Microenvironmental/LCA Modeling
NAPA - North American Plant AtlasBiota of North America Program (BONAP)Enviroinformatics - Spatiotemporal Mapping/Analysis
NASQAN - National Stream Quality Accounting NetworkUS Geological SurveyEnviroinformatics - Release Mapping/Modeling
NATA - National Air Toxics AssessmentsUSEPAEnviroinformatics - Spatiotemporal Mapping/Analysis; Enviroinformatics - Release Mapping/Modeling; Exposure/Risk Analysis - Human Health Risks
National Atlas (service will be removed on September 30, 2014)United States Department of the InteriorEnviroinformatics - Spatiotemporal Mapping/Analysis
National Geochemical SurveyUS Geological SurveyEnviroinformatics - Spatiotemporal Mapping/Analysis; Enviroinformatics - Release Mapping/Modeling
National Lake Fish Tissue StudyUSEPAExposure/Risk Analysis - Ecological Risks
National Listing of Fish Advisories DatabaseUSEPAExposure/Risk Analysis - Ecological Risks
National Nutrient Database for Standard ReferenceUSDAExposure/Risk Analysis - Microenvironmental/LCA Modeling
National Status & Trends in Coastal ZonesCenter for Coastal Monitoring and Assessment, National Ocean ServiceExposure/Risk Analysis - Ecological Risks
National Toxicology Program Technical ReportsNIEHSComputational Toxicology - Toxicoinformatics; Exposure/Risk Analysis - Human Health Risks
NAWQA - National Water-Quality Assessment ProgramUS Geological SurveyEnviroinformatics - Spatiotemporal Mapping/Analysis; Enviroinformatics - Release Mapping/Modeling
NCAR GraphicsUniversity Corporation for Atmospheric ResearchGeneral Development Tools - Data Visualization
NCBI EpigenomicsNational Center for Biotechnology Information, NLM, NIHBioinformatics - Biological Dose-Response; Bioinformatics - Data Integration
NCBI GeneNational Center for Biotechnology Information, NLM, NIHBioinformatics - Biomolecular Sequences/Structures
NCBI GEO - NCBI Gene Expression Omnibus databaseNational Center for Biotechnology Information, NLM, NIHBioinformatics - Biological Dose-Response; Exposure/Risk Analysis - Biomarkers
NCBI Model Organisms GuideNational Center for Biotechnology Information, NLM, NIHBioinformatics - Biomolecular Sequences/Structures; Computational Toxicology - Virtual Model Organisms
NCBI Nucleotide Sequence DatabaseNational Center for Biotechnology Information, NLM, NIHBioinformatics - Biomolecular Sequences/Structures
NCBI/ Primer-BLASTNational Center for Biotechnology Information, NLM, NIHBioinformatics - Biomolecular Sequences/Structures
NCDC - NOAA National Climatic Data CenterNOAAEnviroinformatics - Environmental Fate and Transport
NCFAP Pesticide Use DatabaseNational Center for Food and Agricultural Policy (NCFAP)Enviroinformatics - Release Mapping/Modeling
NCHS - National Center for Health Statistics DataCDCEnviroinformatics - Spatiotemporal Mapping/Analysis
NCI DIS 3D - National Cancer Institute Drug Information System 3D structure databaseNCI (National Cancer Institute), NIHCheminformatics - Structure Elucidation; Bioinformatics - Biomolecular Sequences/Structures
NCI State Cancer ProfilesNCI (National Cancer Institute), NIHEnviroinformatics - Spatiotemporal Mapping/Analysis
NCOD - National Contaminant Occurrence DatabaseUSEPAExposure/Risk Analysis - Microenvironmental/LCA Modeling
NCTRlcdb - NCTR Liver Cancer DatabaseUSFDAComputational Toxicology - Toxicoinformatics; Computational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics; Exposure/Risk Analysis - Human Health Risks
NDB - Nucleic Acid Database ("A Portal for Three-dimensional Structural Information about Nucleic Acids")The Nucleic Acid Database Project, Rutgers UniversityBioinformatics - Biomolecular Sequences/Structures
NED - National Elevation DatasetUS Geological SurveyEnviroinformatics - Spatiotemporal Mapping/Analysis
NEI - National Emissions InventoryUSEPAEnviroinformatics - Release Mapping/Modeling
Nemo - "forward-time, individual-based, genetically explicit, and stochastic simulation program"Nemo development team (F. Guillaume et al.)Bioinformatics - Data Integration
NetDraw ("program for visualizing social network data")Analytic TechnologiesExposure/Risk Analysis - Socioeconomic/LSB Modeling; General Development Tools - Data Visualization
NetLogoUri Wilensky, Center for Connected LearningExposure/Risk Analysis - Socioeconomic/LSB Modeling; General Development Tools - Development and Programming
NetRecodonNetRecodon development teamBioinformatics - Biomolecular Sequences/Structures
NetworkFluxus Technology Ltd.Bioinformatics - Interactions/Biopathways/Bionetworks; General Development Tools - Development and Programming
NeurodatabaseWeill Medical College, Cornell University
NEURON ("for empirically-based simulations of neurons and networks of neurons")NEURON development teamBioinformatics - Interactions/Biopathways/Bionetworks; Computational Toxicology - Virtual Cells, Tissues, Organs
Newbler ("software package for de novo DNA sequence assembly")454 Life Sciences, Roche Diagnostics CorporationBioinformatics - Biomolecular Sequences/Structures
NewHybridsNewHybrids development teamBioinformatics - Data Integration
NGA - National Geochemical AtlasUSGSEnviroinformatics - Spatiotemporal Mapping/Analysis
NGSmethDB - A database for next-generation sequencing single-cytosine-resolution DNA methylation databaseComputational Genomics and Bioinformatics Group, U. Granada, SpainBioinformatics - Biomolecular Sequences/Structures
NHANES - National Health and Nutrition Examination SurveyCDCComputational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics; Exposure/Risk Analysis - Microenvironmental/LCA Modeling; Exposure/Risk Analysis - Cumulative/Aggregate Exposures; Exposure/Risk Analysis - Biomarkers
NHAPS - The National Human Activity Pattern SurveyUSEPAEnviroinformatics - Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis - Socioeconomic/LSB Modeling
NHATS - National Human Adipose Tissue SurveyUSEPAComputational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics; Exposure/Risk Analysis - Biomarkers
NHEXAS - National Human Exposure Assessment Survey (project completed)USEPAExposure/Risk Analysis - Microenvironmental/LCA Modeling; Exposure/Risk Analysis - Cumulative/Aggregate Exposures; Exposure/Risk Analysis - Biomarkers
NHPN - National Highway Planning NetworkUS Department of TransportationEnviroinformatics - Spatiotemporal Mapping/Analysis
NIEHS SNPs Exome Variant ServerNIEHS and University of WashingtonBioinformatics - Biomolecular Sequences/Structures; Exposure/Risk Analysis - Biomarkers
NIH Human Microbiome Project (HMP) Roadmap ProjectNational Center for Biotechnology Information, NLM, NIHExposure/Risk Analysis - Biomarkers
NIH Model Organisms for Biomedical ResearchNIHComputational Toxicology - Virtual Model Organisms
NIH Roadmap Epigenomics Project DataNational Center for Biotechnology Information, NLM, NIHBioinformatics - Biological Dose-Response
NIMH-RGR Data ExplorerNIMH Center for Collaborative Genomic Studies on Mental DisordersBioinformatics - Data Integration; Exposure/Risk Analysis - Biomarkers
NIST Chemistry WebBookNISTCheminformatics - Structure Elucidation; Cheminformatics - Property/Activity Prediction
NJ-HSFS - Right to Know Hazardous Substance Fact SheetsNJ Department of HealthCheminformatics - Property/Activity Prediction
NJ-RTKHSL - Right to Know Hazardous Substance ListNJ Department of HealthCheminformatics - Property/Activity Prediction
NLCD - National Land Cover DatasetUS Geological SurveyEnviroinformatics - Spatiotemporal Mapping/Analysis
NLM ChemIDplus AdvancedNational Library of MedicineCheminformatics - Property/Activity Prediction
NMFS - National Marine Fisheries ServiceNOAAEnviroinformatics - Spatiotemporal Mapping/Analysis
NMPDR - National Microbial Pathogen Data Resource (no longer maintained; see PATRIC)NMPDR Project TeamExposure/Risk Analysis - Biomarkers
NMRShiftDBnmrshiftdb2 development teamCheminformatics - Structure Elucidation
NOES - National Occupational Exposure SurveyCDC - NIOSHExposure/Risk Analysis - Microenvironmental/LCA Modeling
Nonhuman Primate HIV/SIV Vaccine Trials DatabaseLos Alamos National LaboratoryExposure/Risk Analysis - Biomarkers
NONMEMICON Development Solutions and Regents of the University of CaliforniaComputational Toxicology - Toxicoinformatics; Computational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
NovoalignNovocraft TechnologiesBioinformatics - Biomolecular Sequences/Structures
NPDWR - National Primary Drinking Water RegulationsUSEPAExposure/Risk Analysis - Microenvironmental/LCA Modeling
NPG - NIOSH Pocket Guide to Chemical HazardsCDC - NIOSHCheminformatics - Property/Activity Prediction
NPIRS - National Pesticide Information Retrieval SystemPurdue UniversityEnviroinformatics - Release Mapping/Modeling
NRWQC - National Recommended Water Quality CriteriaUSEPAEnviroinformatics - Release Mapping/Modeling
NSL - Neural Simulation LanguageNSL Development TeamBioinformatics - Interactions/Biopathways/Bionetworks
NSQS - National Sediment Quality SurveyUSEPAEnviroinformatics - Release Mapping/Modeling
NucDe - A non-homogeneous hidden-state model on first order differences for automatic detection of nucleosome positions from MNase-chip and MNase-seq dataKeles Research Group, University of WisconsinBioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Biological Dose-Response; Exposure/Risk Analysis - Biomarkers
NuPoP - Nucleosome Positioning Prediction EngineNorthwestern University (J.-P. Wang)Bioinformatics - Biomolecular Sequences/Structures
NWIS - National Water Information SystemUS Geological SurveyEnviroinformatics - Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis - Microenvironmental/LCA Modeling
NWPCAM - Nation Water Pollution Control Assessment ModelUSEPAEnviroinformatics - Environmental Fate and Transport; Exposure/Risk Analysis - Ecological Risks
NWS - National Weather ServiceNOAAEnviroinformatics - Environmental Fate and Transport
Objective CAppleGeneral Development Tools - Development and Programming
OChD - OSHA Occupational Chemical DatabaseOSHACheminformatics - Property/Activity Prediction
OChem - Online Chemical databaseeADMET GmbH, GermanyCheminformatics - Property/Activity Prediction; Bioinformatics - Biomolecular Sequences/Structures
OctaveJohn W. EatonGeneral Development Tools - Development and Programming
OECD Existing Chemicals DatabaseOECD SecretariatEnviroinformatics - Release Mapping/Modeling
OmicBrowseGenome-Phenome Superbrain ProjectBioinformatics - Data Integration
OmicsOffice for MicroarraysIntegromicsBioinformatics - Biological Dose-Response; Exposure/Risk Analysis - Biomarkers
OMIM - Online Mendelian Inheritance in Man ("Online Catalog of Human Genes and Genetic Disorders")Johns Hopkins University and NCBI, NLM, NIHBioinformatics - Data Integration; Exposure/Risk Analysis - Biomarkers
OmixPeter DrosteCheminformatics - Interaction/Reaction Modeling; Bioinformatics - Interactions/Biopathways/Bionetworks
OncoLogic - Evaluate the carcinogenic potential of chemicalsUSEPACheminformatics - Property/Activity Prediction
OncomineLife Technologies CorporationBioinformatics - Biological Dose-Response; Computational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics; Exposure/Risk Analysis - Biomarkers
Online SMILES Translator and Structure File GeneratorCADD Group, Chemical Biology Laboratory, NCICheminformatics - Structure Elucidation
OpenCell (for CellML models)Auckland Bioengineering Institute, University of Auckland, NZComputational Toxicology - Virtual Cells, Tissues, Organs
OpenCMISS/CM - Open Continuum Mechanics, Imaging, Signal processing and System identificationAuckland Bioengineering Institute, University of Auckland, NZComputational Toxicology - Virtual Cells, Tissues, Organs
OpenFLUX ("MATLAB-based modelling software for 13C metabolic flux analysis")OpenFLUX development teamBioinformatics - Interactions/Biopathways/Bionetworks
OpenFOAMOpenCFD Ltd, ESI GroupExposure/Risk Analysis - Microenvironmental/LCA Modeling
OpenGL ("developing portable, interactive 2D and 3D graphics applications")Silicon Graphics International Corp. (SGI) and Khronos GroupGeneral Development Tools - Data Visualization
OpenModelThe University of NottinghamGeneral Development Tools - Development and Programming
OpenStreetMap ("OpenStreetMap is [...] data about roads, trails, cafés, railway stations, and much more, all over the world")OpenStreetMap teamEnviroinformatics - Spatiotemporal Mapping/Analysis
OpenToxOpenTox project teamComputational Toxicology - Toxicoinformatics
OpenWormOpenWorm development teamComputational Toxicology - Virtual Cells, Tissues, Organs; Computational Toxicology - Virtual Model Organisms
OptiRNAUniversity of NebraskaBioinformatics - Biomolecular Sequences/Structures
OracleOracleGeneral Development Tools - Development and Programming
OrangeBioinformatics Laboratory, University of Ljubljana, SloveniaData/Simulation Pattern Analysis - Data Mining/Pattern Recognition; Data/Simulation Pattern Analysis - Classification/Clustering; Data/Simulation Pattern Analysis - Machine Learning Algorithms
ORDB - Olfactory Receptor DataBaseYale UniversityBioinformatics - Biomolecular Sequences/Structures
OriginOriginLab CorporationGeneral Development Tools - Development and Programming; General Development Tools - Data Visualization
OriginProOriginLab CorporationGeneral Development Tools - Development and Programming; General Development Tools - Data Visualization
Ortelius (mapping software for Mac OS X)Mapdiva, LLCEnviroinformatics - Spatiotemporal Mapping/Analysis; General Development Tools - Data Visualization
OrthoDBUniversity of Geneva Medical School, SwitzerlandBioinformatics - Interactions/Biopathways/Bionetworks
OspreySamuel Lunenfeld Research Institute, CanadaBioinformatics - Interactions/Biopathways/Bionetworks
P2P - Pollution Prevention Progress (see TRACI)USEPAEnviroinformatics - Environmental Fate and Transport; Exposure/Risk Analysis - Microenvironmental/LCA Modeling; Exposure/Risk Analysis - Ecological Risks
P3M - Physiological Parameters for PBPK ModelingThe LifeLine GroupComputational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
PAC - Protective Action CriteriaUSDOECheminformatics - Property/Activity Prediction
PaGE - Patterns from Gene ExpressionPaGE development team, University of PennsylvaniaBioinformatics - Biomolecular Sequences/Structures
PajekBatagelj et al., University of Ljubljana, SloveniaExposure/Risk Analysis - Socioeconomic/LSB Modeling; General Development Tools - Development and Programming
PAM - Prediction Analysis for MicroarraysStanford UniversityBioinformatics - Biomolecular Sequences/Structures
Pan Asian SNP DatabasePan-Asian SNP ConsortiumBioinformatics - Biomolecular Sequences/Structures; Exposure/Risk Analysis - Biomarkers
Pandora ("HPC Agent-Based Modelling framework")Barcelona Supercomputing CenterExposure/Risk Analysis - Socioeconomic/LSB Modeling; General Development Tools - Development and Programming
PANTHER - Protein ANalysis THrough Evolutionary RelationshipsPANTHER development team (Paul Thomas)Bioinformatics - Interactions/Biopathways/Bionetworks; Bioinformatics - Data Integration
ParaViewParaView project teamGeneral Development Tools - Data Visualization
PATCH - Program to Assist in Tracking Critical Habitat (see HexSim)USEPAExposure/Risk Analysis - Ecological Risks
PathArtJubilant BiosysBioinformatics - Interactions/Biopathways/Bionetworks
PathCase Pathways Database SystemCase Western Reserve UniversityBioinformatics - Interactions/Biopathways/Bionetworks
Pathogen PortalPathogen Portal Project TeamExposure/Risk Analysis - Biomarkers
Pathophysiology of the Digestive SystemColorado State UniversityComputational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
Pathophysiology of the Endocrine SystemColorado State UniversityComputational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
PathVisio ("a tool to edit and analyze biological pathways")PathVisio development teamBioinformatics - Interactions/Biopathways/Bionetworks
Pathway CommonsMemorial Sloan-Kettering Cancer Center and University of TorontoBioinformatics - Interactions/Biopathways/Bionetworks
Pathway DatabaseProtein LoungeBioinformatics - Interactions/Biopathways/Bionetworks
Pathway Map CreatorThomson ReutersBioinformatics - Interactions/Biopathways/Bionetworks
Pathway ProcessorIstituto Agrario di San Michele all’Adige, ItalyBioinformatics - Interactions/Biopathways/Bionetworks
Pathway StudioPathway StudioBioinformatics - Interactions/Biopathways/Bionetworks; Bioinformatics - Biological Dose-Response; Computational Toxicology - Toxicoinformatics
Pathway ToolsPathway Tools development teamBioinformatics - Interactions/Biopathways/Bionetworks
PathwayLab - in silico pathway analysis toolInneticsCheminformatics - Interaction/Reaction Modeling; Bioinformatics - Interactions/Biopathways/Bionetworks
PatientsLikeMe (network of patients sharing experiences on diseases)PatientsLikeMe teamExposure/Risk Analysis - Human Health Risks
PATRIC - Pathosystems Resource Integration CenterPATRIC Project TeamBioinformatics - Data Integration; Exposure/Risk Analysis - Biomarkers
PAYAOLOGUESBI and OIST, Japan; PathTextBioinformatics - Interactions/Biopathways/Bionetworks
PCRAMMETUSEPAEnviroinformatics - Environmental Fate and Transport
PCS-ICIS - Permit Compliance System and Integrated Compliance Information SystemUSEPAEnviroinformatics - Release Mapping/Modeling
PD map - Parkinson’s disease mapLCSB and Hiroaki Kitano team at SBI, TokyoBioinformatics - Interactions/Biopathways/Bionetworks; Computational Toxicology - Toxicoinformatics; Computational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics; Exposure/Risk Analysis - Biomarkers
PDB - Protein Data BankRCSB PDB (Rutgers University, UCSD)Bioinformatics - Biomolecular Sequences/Structures
PDP - Pesticide Data ProgramUSDA ARSExposure/Risk Analysis - Microenvironmental/LCA Modeling
PEARL - Pesticide Emission Assessment at Regional and Local scales, GeoPEARLAlterra, PBL and RIVMEnviroinformatics - Environmental Fate and Transport; Exposure/Risk Analysis - Ecological Risks
pepgrepUniversity of EssexBioinformatics - Biomolecular Sequences/Structures
Peptide AtlasPeptideAtlas team, Institute for Systems BiologyBioinformatics - Biomolecular Sequences/Structures
PerlPerl development teamGeneral Development Tools - Development and Programming
PERPEST - Predicts the Ecological Risks of PESTicides in freshwater ecosystemsAlterra and Wageningen UR, The NetherlandsExposure/Risk Analysis - Ecological Risks
Persephone ("Genome Visualization & Exploration Software")Ceres, Inc. Bioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Biological Dose-Response
Personalized Medicine Research Project population-based bio-bankMarshfield Clinic Research FoundationBioinformatics - Biological Dose-Response; Bioinformatics - Data Integration
PEST - Parameter ESTimationPEST development teamData/Simulation Pattern Analysis - Sensitivity/Uncertainty Analysis
PFAAT - Protein Family Alignment Annotation ToolPFAAT development teamBioinformatics - Biomolecular Sequences/Structures
PFAM - Pesticides in Flooded Application ModelUSEPAEnviroinformatics - Environmental Fate and Transport; Exposure/Risk Analysis - Ecological Risks
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, USBioinformatics - Biomolecular Sequences/Structures
PharmGKB - Pharmacogenomics KnowledgebaseUS Dept of Health and Human ServicesBioinformatics - Data Integration; Computational Toxicology - Toxicoinformatics
PhoenicsCHAMExposure/Risk Analysis - Microenvironmental/LCA Modeling
PHS - Public Health StatementsATSDR, CDCCheminformatics - Property/Activity Prediction
PHYLIP - PHYLogeny Inference PackageUniversity of WashingtonBioinformatics - Interactions/Biopathways/Bionetworks
PhyMLS. Guindon, et al., CNRSBioinformatics - Biomolecular Sequences/Structures
PhyreStructural Bioinformatics Group, Imperial College, LondonBioinformatics - Biomolecular Sequences/Structures
PhysioDesignerPhysioDesigner development teamComputational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics; Computational Toxicology - Virtual Cells, Tissues, Organs
PHYSPROP - Physical Properties DatabaseSRCCheminformatics - Property/Activity Prediction
picard ("A set of Java command line tools for manipulating high-throughput sequencing data (HTS) data and formats")Broad Institute and picard development teamBioinformatics - Biomolecular Sequences/Structures
PID - Pathway Interaction DatabaseNCI (National Cancer Institute), NIHBioinformatics - Interactions/Biopathways/Bionetworks
PID - Physiological Information DatabaseUSEPAComputational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
PIRAT - Pesticide Inert Risk Assessment ToolUSEPAExposure/Risk Analysis - Microenvironmental/LCA Modeling; Exposure/Risk Analysis - Cumulative/Aggregate Exposures
PK SolutionsSummit ResearchComputational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
PKQuestDavid Levitt, University of MinnesotaComputational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
PK-SimBayer TechnologyComputational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
PLINK ("Whole genome association analysis toolset")PLINK development team, CHGR - Massachusetts General Hospital, Boston, MABioinformatics - Biomolecular Sequences/Structures; Exposure/Risk Analysis - Biomarkers
Pollen.com (National Allergy Forecast & Information About Allergies)IMS Health Inc.Enviroinformatics - Release Mapping/Modeling
PollenLibraryIMS Health Inc.Enviroinformatics - Release Mapping/Modeling
PolyBayes ("automated analysis of single-nucleotide polymorphism (SNP) discovery in redundant DNA sequences")Washington University Genome Sequencing CenterBioinformatics - Biomolecular Sequences/Structures; Exposure/Risk Analysis - Biomarkers
Polyphred (single nucleotide substitution identification)University of Washington (Brent Ewing, Phil Green, David Gordon et al.)Bioinformatics - Biomolecular Sequences/Structures; Exposure/Risk Analysis - Biomarkers
PostGIS ("Spatial and Geographic objects for PostgreSQL")OSGeo ProjectEnviroinformatics - Spatiotemporal Mapping/Analysis
PostgreSQLPostgreSQL Global Development GroupGeneral Development Tools - Development and Programming
PPDB - Pesticide Properties DataBaseUniversity of HertfordshireExposure/Risk Analysis - Ecological Risks
PRED-GPCRUniversity of Athens, GreeceBioinformatics - Biomolecular Sequences/Structures
PredictProteinROSTLABBioinformatics - Biomolecular Sequences/Structures
Primate Info NetNational Primate Research Center, University of WisconsinComputational Toxicology - Virtual Model Organisms
PRIMET - Pesticides RIsks in the tropics to Man, Environment and TradeAlterra and Wageningen UR, The NetherlandsExposure/Risk Analysis - Ecological Risks
PRINTSBioinformatics at Manchester, University of Manchester
ProcessIt NMRBio-Rad LaboratoriesCheminformatics - Structure Elucidation
ProfileAnalysisBruker DaltonicsExposure/Risk Analysis - Biomarkers
Progenetix ("genomic copy number aberrations in cancer")Baudis Laboratory, University of ZurichExposure/Risk Analysis - Biomarkers
PROSITESIB - Swiss Institute of Bioinformatics
Protective Action CriteriaEMI SIGCheminformatics - Property/Activity Prediction
PRoTEGE - Prioritization/Ranking of Toxic Exposures with GIS ExtensionComputational Chemodynamics LaboratoryExposure/Risk Analysis - Microenvironmental/LCA Modeling
Protein DatabaseNational Center for Biotechnology Information, NLM, NIH
Protein ProspectorUCSFBioinformatics - Biomolecular Sequences/Structures
Protein Sequence DatabaseUniversity of Delaware and Georgetown University
ProteinScapeBruker DaltonicsExposure/Risk Analysis - Biomarkers
ProteoIQ ("qualitative and quantitative suite for proteomics")Premier BiosoftBioinformatics - Biological Dose-Response; Exposure/Risk Analysis - Biomarkers
Proteome Bioknowledge LibraryUniversity of Manchester
PRS - Pesticide Reregistration StatusUSEPACheminformatics - Property/Activity Prediction
PRZM - Pesticide Root Zone ModelUSEPAEnviroinformatics - Environmental Fate and Transport
PRZM/EXAMS ShellUSEPAEnviroinformatics - Environmental Fate and Transport; Exposure/Risk Analysis - Ecological Risks
PRZM-GWUSEPAEnviroinformatics - Environmental Fate and Transport; Exposure/Risk Analysis - Ecological Risks
PSAP - Priority Substances Assessment ProgramHealth CanadaCheminformatics - Property/Activity Prediction
Ps-iLustick ConsultingGeneral Development Tools - Development and Programming
PSI-BLAST - Protein Similarity Search BLASTEMBL-EBIBioinformatics - Biomolecular Sequences/Structures
PubChemNational Center for Biotechnology Information, NLM, NIHCheminformatics - Property/Activity Prediction
PubMedNational Center for Biotechnology Information, NLM, NIHCheminformatics - Property/Activity Prediction; Bioinformatics - Biological Dose-Response; Computational Toxicology - Toxicoinformatics; Computational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
PubMethBioBix, Laboratory for Bioinformatics and Computational Genomics, Ghent University, BelgiumBioinformatics - Biological Dose-Response; Bioinformatics - Data Integration; Exposure/Risk Analysis - Biomarkers
PUMAdb - Princeton University MicroArray database (supersedes SMD)Princeton UniversityBioinformatics - Biological Dose-Response
PyDSToolRobert Clewley, GSUGeneral Development Tools - Development and Programming
PyMOLPyMOL TeamCheminformatics - Property/Activity Prediction; Bioinformatics - Biomolecular Sequences/Structures
PythonPython Software FoundationGeneral Development Tools - Development and Programming
QGIS (“Create, edit, visualise, analyse and publish geospatial information”)QGIS development teamEnviroinformatics - Spatiotemporal Mapping/Analysis; General Development Tools - Data Visualization
QiKPropSchrodinger, LLCCheminformatics - Property/Activity Prediction
QSAR ToolboxOrganisation for Economic Co-operation and Development and European Chemicals AgencyCheminformatics - Property/Activity Prediction
QTDT (Linkage Disequilibrium Analyses for Quantitative and Discrete Traits)Abecasis Lab, University of MichiganBioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Data Integration
QTXQTX development teamBioinformatics - Biomolecular Sequences/Structures
QUAL2E (Enhanced Stream Water Quality model)Tufts University and USEPAEnviroinformatics - Environmental Fate and Transport; Exposure/Risk Analysis - Ecological Risks
QUAL2K - River and Stream Water Quality ModelUSEPAEnviroinformatics - Environmental Fate and Transport; Exposure/Risk Analysis - Ecological Risks
QuEST - Quantitative Enrichment of Sequence TagsStanford UniversityBioinformatics - Biomolecular Sequences/Structures
QUIC - Quick Urban & Industrial ComplexLos Alamos National LaboratoryEnviroinformatics - Environmental Fate and Transport
R packageR package development teamGeneral Development Tools - Development and Programming
R/maanovaChurchill Group, Jackson LaboratoryBioinformatics - Biological Dose-Response
RaidarCEMC, CanadaExposure/Risk Analysis - Microenvironmental/LCA Modeling
RAMAS GISApplied BiomathematicsExposure/Risk Analysis - Ecological Risks
RAMS - Regional Atmospheric Modeling SystemATMET, LLCEnviroinformatics - Environmental Fate and Transport
Rapid Minerrapid-iData/Simulation Pattern Analysis - Data Mining/Pattern Recognition
RasMol ("Molecular Graphics Visualisation Tool")RasMOL development teamCheminformatics - Structure Elucidation
Rational RoseIBMGeneral Development Tools - Development and Programming
RatMineUniversity of Cambridge, Cambridge, UKBioinformatics - Bio-Ontologies; Bioinformatics - Interactions/Biopathways/Bionetworks; Bioinformatics - Biological Dose-Response; Computational Toxicology - Virtual Model Organisms
Ray (Assembly of reads obtained with sequencing technologies) S. Boisvert, F. Laviolette, J. CorbeilBioinformatics - Biomolecular Sequences/Structures
RCRAInfoUSEPAEnviroinformatics - Release Mapping/Modeling
REACH - Registration, Evaluation, Authorisation and Restriction of Chemical substancesEuropean Chemicals AgencyCheminformatics - Property/Activity Prediction
ReachScanUSEPAExposure/Risk Analysis - Ecological Risks
ReactomeReactome teamBioinformatics - Interactions/Biopathways/Bionetworks; Exposure/Risk Analysis - Biomarkers
READY - Real-time Environmental Applications and Display sYstem (Current and forecast meteorological data; Archived data also available)Air Resources Laboratory, NOAAEnviroinformatics - Spatiotemporal Mapping/Analysis
RealTimeDesign SoftwareBiosearch TechnologiesBioinformatics - Biological Dose-Response
Reaxys Chemistry DatabaseReaxysCheminformatics - Property/Activity Prediction
Reaxys system (Search substances, reactions, citations, patents, etc.)Reaxys development teamCheminformatics - Property/Activity Prediction; Bioinformatics - Biomolecular Sequences/Structures
REBASE - The Restriction Enzyme dataBASENew England Biolabs, Inc. (Roberts, R.J., Macelis, D.)Bioinformatics - Biological Dose-Response; Bioinformatics - Data Integration
REDUCEHarmen Bussemaker Laboratory, Columbia UniversityBioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Interactions/Biopathways/Bionetworks
RefSeq - NCBI Reference Sequence DatabaseNational Center for Biotechnology Information, NLM, NIHBioinformatics - Biomolecular Sequences/Structures; Exposure/Risk Analysis - Biomarkers
REMSAD - Regional Modeling System for Aerosols and DepositionICF ConsultingEnviroinformatics - Environmental Fate and Transport
RepastArgonne National LaboratoryExposure/Risk Analysis - Socioeconomic/LSB Modeling; General Development Tools - Development and Programming
RESRAD - RESidual RADioactiveArgonne National LaboratoryEnviroinformatics - Environmental Fate and Transport; Exposure/Risk Analysis - Cumulative/Aggregate Exposures
RETIGO - REal TIme GeOspatial viewer ("web-based tool for researchers and citizen scientists to explore their air measurements")USEPAEnviroinformatics - Spatiotemporal Mapping/Analysis
RetroMEXCompuDrugCheminformatics - Interaction/Reaction Modeling
RExcel (Excel add-in to use R from Microsoft Excel)RExcel development teamGeneral Development Tools - Data Visualization
RGD - Rat Genome DatabaseMedical College of WisconsinBioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Interactions/Biopathways/Bionetworks; Bioinformatics - Data Integration; Computational Toxicology - Virtual Model Organisms
RIOPA - Relationships of Indoor, Outdoor, and Personal AirEOHSI and Health Effects InstituteExposure/Risk Analysis - Microenvironmental/LCA Modeling; Exposure/Risk Analysis - Cumulative/Aggregate Exposures
RIVM e-toxBase ("ecotoxicity data on both terrestrial and aquatic species")RIVM (Netherlands National Institute for Public Health and the Environment)Computational Toxicology - Toxicoinformatics; Exposure/Risk Analysis - Ecological Risks
RIVM reportsRIVMCheminformatics - Property/Activity Prediction
RMAP (next-generation sequencing read mapper)Cold Spring Harbor Laboratory, NY and USC, CABioinformatics - Biomolecular Sequences/Structures
RNA CoMPASS - RNA Comprehensive Multi-Processor Analysis System for SequencingGuorong Xu and RNA CoMPASS development teamBioinformatics - Biomolecular Sequences/Structures
RNA World ("collection of links to RNA-related information")Leibniz Institute for Age Research, FLI, Germany and RNA World teamBioinformatics - Biomolecular Sequences/Structures
RNAi databaseNYU's Center for Genomics & Systems BiologyBioinformatics - Biological Dose-Response; Bioinformatics - Data Integration
Roadmap Epigenomics Project DataNIEHSBioinformatics - Biological Dose-Response; Bioinformatics - Data Integration
RPM-AERO (Modelling platform for studying photochemical gaseous and aerosol phase processes)Computational Chemodynamics LaboratoryEnviroinformatics - Environmental Fate and Transport
RS-HDMR - Random-Sampling High Dimensional Model RepresentationRabitz Laboratory, Princeton University and Computational Chemodynamics LaboratoryData/Simulation Pattern Analysis - Data Mining/Pattern Recognition; Data/Simulation Pattern Analysis - Sensitivity/Uncertainty Analysis
RTECS - Registry of Toxic Effects of Chemical SubstancesCDCCheminformatics - Property/Activity Prediction
RubyRuby development team (Yukihiro “Matz” Matsumoto)General Development Tools - Development and Programming
RUCDR - Rutgers University Cell and DNA RepositoryRUCDR TeamBioinformatics - Biological Dose-Response; Bioinformatics - Data Integration
R-UNSATUSGSEnviroinformatics - Environmental Fate and Transport; Exposure/Risk Analysis - Ecological Risks
SAMBAShamir Laboratory, Tel Aviv UniversityBioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Interactions/Biopathways/Bionetworks
SAMtools - Sequence Alignment/MapLi et al., Wellcome Trust Sanger Institute, UK and Broad Institute of MIT and Harvard, USABioinformatics - Biomolecular Sequences/Structures
SANDYGerstein Laboratory, Yale UniversityBioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Interactions/Biopathways/Bionetworks
SAS - Statistical Analysis System SAS Institute Inc.General Development Tools - Development and Programming
SAS-EM - SAS Enterprise MinerSAS Institute Inc.Data/Simulation Pattern Analysis - Data Mining/Pattern Recognition; General Development Tools - Development and Programming
SAS-SDS - SAS Scientific Discovery SolutionsSAS Institute Inc.General Development Tools - Development and Programming
SBGN-ED ("Edit, translation and validation of SBGN Maps")Plant Bioinformatics Group, Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben, GermanyBioinformatics - Interactions/Biopathways/Bionetworks
SBKB - Structural Biology KnowledgebaseProtein Structure Initiative and Nature Publishing GroupBioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Data Integration
SBML - Systems Biology Markup LanguageSBML TeamComputational Toxicology - Virtual Cells, Tissues, Organs
SBML ConverterSBML TeamComputational Toxicology - Virtual Cells, Tissues, Organs
SBML Test SuiteSBML TeamComputational Toxicology - Virtual Cells, Tissues, Organs
SBMLeditorSBML teamComputational Toxicology - Virtual Cells, Tissues, Organs
SBMLToolbox (for MATLAB and Octave)SBML TeamComputational Toxicology - Virtual Cells, Tissues, Organs
SBPOP Package ("Support for Model Based Drug Development – From Mechanistic Models to Complex Trial Simulation")SBPOP Package development team at Novartis Pharma AG Modeling & SimulationBioinformatics - Biological Dose-Response; Computational Toxicology - Toxicoinformatics; Computational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
SCAMPI ("Prediction of membrane protein topology")Stockholm Bioinformatics Center, Stockholm UniversityBioinformatics - Biomolecular Sequences/Structures
SCAN ("SNP and CNV Annotation Database")The University of ChicagoBioinformatics - Biomolecular Sequences/Structures; Exposure/Risk Analysis - Biomarkers
SCan-MarK Explorer ("Sophic’s Cancer Biomarker Knowledge Environment")Sophic Alliance Inc.Exposure/Risk Analysis - Biomarkers
SCI-GROW - Screening Concentration In GROund WaterUSEPAEnviroinformatics - Environmental Fate and Transport; Exposure/Risk Analysis - Ecological Risks
Scilab ("software for numerical computation")Scilab Enterprises, former Scilab Consortium and Scilab contributorsGeneral Development Tools - Development and Programming
SCiLS ("Statistical analysis of MALDI imaging data")SCiLS GmbH and Bruker DaltonicsExposure/Risk Analysis - Biomarkers
SCIPUFF - Second-order Closure Integrated PUFF ModelTitan ProductsEnviroinformatics - Environmental Fate and Transport
SCoP - Simulation Control ProgramSimulation Resources IncGeneral Development Tools - Development and Programming
SCOP - Structural Classification of ProteinsMRC Laboratory of Molecular BiologyBioinformatics - Biomolecular Sequences/Structures
Scorecard Chemical ProfilesGoodGuideCheminformatics - Property/Activity Prediction
SDBS - Spectral Database for Organic CompoundsNational Institute of Advanced Industrial Science and Technology (AIST), JapanCheminformatics - Structure Elucidation
SDWIS - Safe Drinking Water Information SystemUSEPAExposure/Risk Analysis - Microenvironmental/LCA Modeling
See5/ C5.0RuleQuestData/Simulation Pattern Analysis - Data Mining/Pattern Recognition
SEQUESTYates Laboratory, University of WashingtonBioinformatics - Biomolecular Sequences/Structures
SERAFM - Spreadsheet-based Ecological Risk Assessment for the Fate of MercuryUSEPAExposure/Risk Analysis - Ecological Risks
SeSAm - Shell for Simulated Agent SystemsSeSAm development teamGeneral Development Tools - Development and Programming
Sets2NetworksSBCNY and Mount Sinai School of MedicineBioinformatics - Interactions/Biopathways/Bionetworks
SEVENS database ("summarizes GPCR (G-protein coupled receptor) genes that are identified [...] from [...] eukaryote genomes")Computational Biology Research Center, AIST, JapanBioinformatics - Biomolecular Sequences/Structures
SGD - Saccharomyces Genome DatabaseStanford UniversityBioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Interactions/Biopathways/Bionetworks; Bioinformatics - Biological Dose-Response; Computational Toxicology - Virtual Model Organisms
Shape SignaturesWelsh Laboratory, RWJMSBioinformatics - Biomolecular Sequences/Structures
SHEDS Multimedia - Stochastic Human Exposure and Dose Simulation modelUSEPAExposure/Risk Analysis - Cumulative/Aggregate Exposures
SHEDS-AIRTOXICS - Stochastic Human Exposure and Dose Simulation for Air ToxicsUSEPAExposure/Risk Analysis - Cumulative/Aggregate Exposures
SHEDS-Pesticides - Stochastic Human Exposure and Dose Simulation Model for PesticidesUSEPAExposure/Risk Analysis - Cumulative/Aggregate Exposures
SHEDS-PM - Stochastic Human Exposure and Dose Simulation for Particulate MatterUSEPAExposure/Risk Analysis - Cumulative/Aggregate Exposures
SHEDS-WOOD - Stochastic Human Exposure and Dose Simulation Model for Wood PreservativesUSEPAExposure/Risk Analysis - Cumulative/Aggregate Exposures
SICER ("clustering approach for identification of enriched domains from histone modification ChIP-Seq data")W. Peng lab, George Washington UniversityBioinformatics - Biomolecular Sequences/Structures; Exposure/Risk Analysis - Biomarkers
SIDS - Screening Information DatasetUNEPEnviroinformatics - Release Mapping/Modeling
Sigma-Aldrich - Chemical searchSigma-Aldrich Co. LLC.Cheminformatics - Structure Elucidation; Cheminformatics - Property/Activity Prediction
Sigma-Aldrich Structure Search (search chemical structures)Sigma-Aldrich Co. LLC.Cheminformatics - Structure Elucidation; Cheminformatics - Property/Activity Prediction
SigmaPlotSystat Software Inc.General Development Tools - Data Visualization
SigmaStatSystat Software Inc.General Development Tools - Data Visualization
SimBiology app for MATLAB ("Model, simulate, and analyze biological systems")The MathWorks, Inc.Bioinformatics - Interactions/Biopathways/Bionetworks; Bioinformatics - Biological Dose-Response; Computational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
SIMCAUmetricsGeneral Development Tools - Development and Programming
SimCLIM ("software package [...] to facilitate climate risk and adaptation assessments")CLIMsystems Ltd.Enviroinformatics - Spatiotemporal Mapping/Analysis
SimCLIM for ArcGIS / Climate ("add-in [...] to produce spatial images of climate change")CLIMsystems Ltd.Enviroinformatics - Spatiotemporal Mapping/Analysis
SimCLIM for ArcGIS / Marine ("add-in [...] to explore the impacts of climate change on marine biogeochemical cycles")CLIMsystems Ltd.Enviroinformatics - Spatiotemporal Mapping/Analysis
SimcypSimcyp LtdComputational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
Simul8Simul8 CorpGeneral Development Tools - Development and Programming
SimulinkThe Mathworks, Inc.General Development Tools - Development and Programming
SIP - Screening Imbibition Program ("model to estimate chemical exposure from drinking water alone in birds and mammals")USEPAEnviroinformatics - Environmental Fate and Transport; Exposure/Risk Analysis - Ecological Risks
Skin Deep DatabaseEnvironmental Working GroupExposure/Risk Analysis - Microenvironmental/LCA Modeling
SKY/M-FISH and CGH DatabaseNational Center for Biotechnology Information, NLM, NIH and National Cancer Institute, NIHBioinformatics - Data Integration; Exposure/Risk Analysis - Biomarkers
SMART-BS-Seq - Specific Methylation Analysis and Report Tool for BS-Seq dataPython Software FoundationBioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Biological Dose-Response; Exposure/Risk Analysis - Biomarkers
SMBioNetUniversity of Nice, FranceBioinformatics - Interactions/Biopathways/Bionetworks
SMD - Stanford Microarray Database (see PUMAdb)Stanford UniversityBioinformatics - Biological Dose-Response; Exposure/Risk Analysis - Biomarkers
SMOKE - Sparse Matrix Operator Kernel EmissionsCMAS Center, UNC-Chapel HillEnviroinformatics - Release Mapping/Modeling
SMS - Surface Water Modeling SystemCoastal and Hydraulics LaboratoryEnviroinformatics - Environmental Fate and Transport
SNAP - Screening for Non-Acceptable PolymorphismsRost Lab, Columbia University, New YorkBioinformatics - Biomolecular Sequences/Structures; Exposure/Risk Analysis - Biomarkers
SNAP - SNP Annotation and Proxy SearchSNAP Development TeamBioinformatics - Biomolecular Sequences/Structures; Exposure/Risk Analysis - Biomarkers
SNIP - S-Space Network Inference ProcedureRabitz Laboratory, Princeton UniversityBioinformatics - Interactions/Biopathways/Bionetworks
SNP500CancerSAIC-Frederick, NCI-FCRDC, MDBioinformatics - Biomolecular Sequences/Structures; Exposure/Risk Analysis - Biomarkers
SNPinfo Web ServerNIEHSBioinformatics - Biomolecular Sequences/Structures; Exposure/Risk Analysis - Biomarkers
SNP-o-matic (analysis of Solexa reads and comparison with reference)Sanger InstituteBioinformatics - Biomolecular Sequences/Structures; Exposure/Risk Analysis - Biomarkers
SNPTrackUSFDABioinformatics - Biomolecular Sequences/Structures; Exposure/Risk Analysis - Biomarkers
SOAP - Short Oligonucleotide Analysis PackageBeijing Genomics InstituteBioinformatics - Biomolecular Sequences/Structures
SOAPdenovo2 (Large-size genome de-novo assembler)Ruibang Luo, et al., Tai Po Industrial EstateBioinformatics - Biomolecular Sequences/Structures
SOARS - Spot Oriented Agent Role SimulatorSOARS Project and Deguchi Lab, Tokyo Institute of TechnologyExposure/Risk Analysis - Socioeconomic/LSB Modeling; General Development Tools - Development and Programming
SocDynamics.org (Modeling Social Dynamics)SocDynamics.org development teamExposure/Risk Analysis - Microenvironmental/LCA Modeling; Exposure/Risk Analysis - Socioeconomic/LSB Modeling
Soil Data Mart (see Web Soil Survey)USDA NRCSEnviroinformatics - Spatiotemporal Mapping/Analysis
SOPRA - Scaffolding algorithm for paired reads via statistical optimizationA. Sengupta lab, Rutgers UniversityBioinformatics - Biomolecular Sequences/Structures
SOSUI ("predicts a part of the secondary structure of proteins from a given amino acid sequence")Tokyo UniversityBioinformatics - Biomolecular Sequences/Structures
SoundcitiesStanza teamGeneral Development Tools - Data Visualization
SPAD - Signaling Pathway DatabaseKyushu UniversityBioinformatics - Interactions/Biopathways/Bionetworks
SPADE - Smart Python multi-Agent Development EnvironmentSPADE development teamExposure/Risk Analysis - Socioeconomic/LSB Modeling; General Development Tools - Development and Programming
SPARC - SPARC Performs Automated Reasoning in ChemistryUSEPACheminformatics - Property/Activity Prediction
SPARK - Simple Platform for Agent-based Representation of KnowledgeSPARK development teamExposure/Risk Analysis - Socioeconomic/LSB Modeling; General Development Tools - Development and Programming
Spark ("engine for large-scale data processing")The Apache Software FoundationGeneral Development Tools - Development and Programming
SPARTAN - Surface PARTiculate mAtter NetworkSPARTAN Network teamExposure/Risk Analysis - Microenvironmental/LCA Modeling; Exposure/Risk Analysis - Cumulative/Aggregate Exposures
Spartan (molecular modeling package)WaveFunctionCheminformatics - Structure Elucidation; Cheminformatics - Property/Activity Prediction; Cheminformatics - Interaction/Reaction Modeling
SPEAR - SPEcies At Risk Calculator/ TU - Toxic-Unit CalculatorUFZ LeipzigExposure/Risk Analysis - Ecological Risks
SpecInfoJohn Wiley & Sons, Inc.Cheminformatics - Structure Elucidation
Spectral databaseUSEPA and US Air ForceCheminformatics - Structure Elucidation
SPELL - Serial Pattern of Expression Levels LocatorPrinceton UniversityBioinformatics - Biological Dose-Response
Spin Trap DatabaseNIEHSCheminformatics - Property/Activity Prediction
SPLS - Sparse partial least squaresKeles Research Group, University of WisconsinBioinformatics - Biological Dose-Response; Data/Simulation Pattern Analysis - Data Mining/Pattern Recognition
Spotfire Decision Site SoftwareTIBCO SpotfireData/Simulation Pattern Analysis - Data Mining/Pattern Recognition; General Development Tools - Development and Programming
Spotfire S-PlusTIBCO SpotfireGeneral Development Tools - Development and Programming
SpringerProtocolsSpringer-VerlagBioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Interactions/Biopathways/Bionetworks; Bioinformatics - Biological Dose-Response; Bioinformatics - Data Integration
SRD - Source Ranking DatabaseUSEPAEnviroinformatics - Release Mapping/Modeling
SRS - Substance Registry ServicesUSEPACheminformatics - Property/Activity Prediction
SRSM - Stochastic Response Surface MethodComputational Chemodynamics LaboratoryData/Simulation Pattern Analysis - Sensitivity/Uncertainty Analysis
SSEARCH (sequence similarity search)SSEARCH teamBioinformatics - Biomolecular Sequences/Structures
SSTS - Section Seven Tracking SystemUSEPAEnviroinformatics - Release Mapping/Modeling
SSURGO - Soil Survey Geographic DatabaseUSDA NRCSEnviroinformatics - Spatiotemporal Mapping/Analysis
StarLogo/ OpenStarLogoMITExposure/Risk Analysis - Socioeconomic/LSB Modeling; General Development Tools - Development and Programming
StarNet 2 ("query and visualization tool for precomputed correlation data derived from [...] published microarray data")VanBuren laboratory, Texas A&M Health Science CenterBioinformatics - Interactions/Biopathways/Bionetworks
Statistica (with Data and Text Miner)StatSoftData/Simulation Pattern Analysis - Data Mining/Pattern Recognition; General Development Tools - Development and Programming
Statistical AbstractUS Census BureauEnviroinformatics - Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis - Socioeconomic/LSB Modeling
STATSGO/ U.S. General Soil MapUSDA NRCSEnviroinformatics - Spatiotemporal Mapping/Analysis
STELLAisee systemsGeneral Development Tools - Development and Programming
StellaRStellaR development teamGeneral Development Tools - Development and Programming
STEM - Spatiotemporal Epidemiological ModelerEclipseEnviroinformatics - Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis - Human Health Risks
StemBase (gene expression data obtained from stem cells)Canadian Stem Cell NetworkBioinformatics - Biological Dose-Response; Exposure/Risk Analysis - Biomarkers
STIR - Screening Tool for Inhalation RiskUSEPAExposure/Risk Analysis - Ecological Risks
STITCH - Search Tool for Interactions of ChemicalsSTITCH development teamBioinformatics - Interactions/Biopathways/Bionetworks
STORET - STOrage and RETrievalUSEPAEnviroinformatics - Spatiotemporal Mapping/Analysis; Enviroinformatics - Release Mapping/Modeling
STRING - Search Tool for the Retrieval of Interacting Genes/ProteinsSTRING TeamBioinformatics - Biomolecular Sequences/Structures
Structural Biology Software DatabaseTheoretical and Computational Biophysics Group, University of IllinoisBioinformatics - Biomolecular Sequences/Structures
Structure-Activity RelationshipsUSEPA
SubMAP - Subnetwork Mappings in Alignment of PathwaysBioinformatics Lab, University of FloridaBioinformatics - Interactions/Biopathways/Bionetworks
SUCcESS (Integration of quantitative information from ChIP-chip experiments into motif finding)Keles Research Group, University of WisconsinBioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Biological Dose-Response; Exposure/Risk Analysis - Biomarkers
SugarscapeSugarscape development teamExposure/Risk Analysis - Socioeconomic/LSB Modeling; General Development Tools - Development and Programming
SwarmSwarm Development GroupExposure/Risk Analysis - Socioeconomic/LSB Modeling; General Development Tools - Development and Programming
SWASH - Surface WAter Scenarios HelpAlterra and Wageningen UR, The NetherlandsExposure/Risk Analysis - Ecological Risks
SWCC - Surface Water Concentration CalculatorUSEPAEnviroinformatics - Environmental Fate and Transport
SWIMODEL - Swimmer Exposure Assessment ModelUSEPAExposure/Risk Analysis - Microenvironmental/LCA Modeling
SYBYL ("Molecular Modeling from Sequence through Lead Optimization")Certara, L.P. and TriposCheminformatics - Structure Elucidation; Cheminformatics - Property/Activity Prediction; Bioinformatics - Biomolecular Sequences/Structures
SYSTATSystat Software, Inc.Data/Simulation Pattern Analysis - Data Mining/Pattern Recognition; General Development Tools - Development and Programming
SystemsRealityUSEPAExposure/Risk Analysis - Microenvironmental/LCA Modeling
TableauTableau SoftwareGeneral Development Tools - Data Visualization
TANKSUSEPAEnviroinformatics - Release Mapping/Modeling
TargetPCenter for Biological Sequence Analysis, Technical University of DenmarkBioinformatics - Interactions/Biopathways/Bionetworks
TavernamyGrid, University of ManchesterBioinformatics - Data Integration
Taxonomic Data CenterBiota of North America Program (BONAP)Enviroinformatics - Spatiotemporal Mapping/Analysis
TB Drug Target DatabaseTB Drug Target Database development teamExposure/Risk Analysis - Biomarkers
T-CoffeeEMBL-EBIBioinformatics - Biomolecular Sequences/Structures
TDS - Total Diet StudyUSFDAExposure/Risk Analysis - Microenvironmental/LCA Modeling
TEACH - Toxicity and Exposure Assessment for Children's HealthUSEPACheminformatics - Property/Activity Prediction; Exposure/Risk Analysis - Cumulative/Aggregate Exposures
TEAM - Total Exposure Assessment Methodology StudyUSEPAExposure/Risk Analysis - Microenvironmental/LCA Modeling; Exposure/Risk Analysis - Biomarkers
TEAM - Trade and Environment Assessment ModelAbt Associates, Inc. and USEPA
TecplotTecplot IncGeneral Development Tools - Data Visualization
TerraMETerraME Develppment Team, Federal University of Ouro PretoGeneral Development Tools - Development and Programming
TerrPLANTUSEPAEnviroinformatics - Environmental Fate and Transport; Exposure/Risk Analysis - Ecological Risks
The Interactive FlyThe Interactive Fly development team (Thomas B. Brody)Computational Toxicology - Virtual Cells, Tissues, Organs
The NanodatabaseThe Ecological Council, DTU Environment and Danish Consumer Council, DenmarkExposure/Risk Analysis - Microenvironmental/LCA Modeling
T-HERPS - Terrestrial Herpetofaunal Exposure Residue Program Simulation ("to estimate dietary exposure and risk to terrestrial-phase amphibians and reptiles from pesticide use")USEPAExposure/Risk Analysis - Ecological Risks
THREADER (Protein Structure Prediction tool)Bioinformatics Group, University College LondonCheminformatics - Structure Elucidation; Bioinformatics - Biomolecular Sequences/Structures
Tier 1 Rice Model ("estimate surface water exposure from the use of pesticides in rice paddies")USEPAEnviroinformatics - Environmental Fate and Transport; Exposure/Risk Analysis - Ecological Risks
TIGER - Topologically Integrated Geographic Encoding and ReferencingUS Census BureauEnviroinformatics - Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis - Socioeconomic/LSB Modeling
TileHGMM (Mixture modeling for genome-wide localization of transcription factors)Keles Research Group, University of WisconsinBioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Biological Dose-Response; Exposure/Risk Analysis - Biomarkers
TissueDistributionDBsGerman Cancer Research Center, DKFZ, HeidelbergBioinformatics - Biological Dose-Response; Computational Toxicology - Virtual Cells, Tissues, Organs
TitaniumAppcelerator IncGeneral Development Tools - Development and Programming
TMFinder ("Trans-Membrane protein prediction tool")TM-Finder development team and The Hospital for Sick Children (SickKids)Bioinformatics - Biomolecular Sequences/Structures
TMVA - Toolkit for Multivariate Data Analysis with ROOTTMVA development teamData/Simulation Pattern Analysis - Data Mining/Pattern Recognition; Data/Simulation Pattern Analysis - Machine Learning Algorithms
TopHat (spliced read mapper for RNA-Seq)JHU Center for Computational BiologyBioinformatics - Biomolecular Sequences/Structures
TOPKAT - TOxicity Prediction by Komputer Assisted TechnologyaccelrysCheminformatics - Property/Activity Prediction
TopoToolbox ("MATLAB program for the analysis of digital elevation models")TopoToolbox development teamEnviroinformatics - Spatiotemporal Mapping/Analysis
TopPred ("Topology prediction of membrane proteins")TopPred development teamBioinformatics - Biomolecular Sequences/Structures
TOPS - Topology of Protein StructureUniversity of Leeds
TopSpin (NMR data analysis and acquisition and processing of NMR spectra)Bruker CorporationCheminformatics - Structure Elucidation; Bioinformatics - Biomolecular Sequences/Structures; Exposure/Risk Analysis - Biomarkers
Tox TownU.S. National Library of MedicineComputational Toxicology - Toxicoinformatics
ToxCast - Toxicity ForecasterUSEPACheminformatics - Property/Activity Prediction; Bioinformatics - Biological Dose-Response; Computational Toxicology - Toxicoinformatics
ToxFAQsATSDR, CDCCheminformatics - Property/Activity Prediction; Computational Toxicology - Toxicoinformatics
ToxFXNIEHSBioinformatics - Biological Dose-Response; Computational Toxicology - Toxicoinformatics
ToxGuides™ATSDR, CDCCheminformatics - Property/Activity Prediction; Computational Toxicology - Toxicoinformatics; Exposure/Risk Analysis - Human Health Risks
Toxic Substances PortalATSDR, CDCComputational Toxicology - Toxicoinformatics; Exposure/Risk Analysis - Human Health Risks
TOXLINE - Toxicology Literature OnlineNational Library of MedicineCheminformatics - Property/Activity Prediction; Computational Toxicology - Toxicoinformatics
TOXMAPDivision of Specialized Information Services, US National Library of MedicineEnviroinformatics - Release Mapping/Modeling; Computational Toxicology - Toxicoinformatics
ToxmatchJoint Research Centre, IHCPBioinformatics - Biomolecular Sequences/Structures; Computational Toxicology - Toxicoinformatics
ToxNetNational Library of MedicineCheminformatics - Property/Activity Prediction; Computational Toxicology - Toxicoinformatics
ToxProfilesATSDR, CDCCheminformatics - Property/Activity Prediction; Computational Toxicology - Toxicoinformatics
ToxRefDB - Toxicity Reference DatabaseUSEPACheminformatics - Property/Activity Prediction; Computational Toxicology - Toxicoinformatics
ToxRTool - Toxicological data Reliability Assessment ToolEuropean CommissionComputational Toxicology - Toxicoinformatics
TOXSWA - TOXic substances in Surface WAtersTOXSWA teamEnviroinformatics - Environmental Fate and Transport; Exposure/Risk Analysis - Ecological Risks
Toxtree (Estimatation of toxic hazard by applying a decision tree approach)Ideaconsult LtdCheminformatics - Property/Activity Prediction; Computational Toxicology - Toxicoinformatics
TRA - Targeted Risk Assessment ToolECETOCExposure/Risk Analysis - Human Health Risks; Exposure/Risk Analysis - Ecological Risks
TRACI - Tool for the Reduction and Assessment of Chemical and other Environmental Impacts (previously, P2P)USEPAEnviroinformatics - Environmental Fate and Transport; Exposure/Risk Analysis - Microenvironmental/LCA Modeling; Exposure/Risk Analysis - Ecological Risks
TransFacGene RegulationBioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Interactions/Biopathways/Bionetworks
TransPathGene RegulationBioinformatics - Interactions/Biopathways/Bionetworks
T-REX - Terrestrial Residue Exposure ("model to calculate the residues on avian and mammalian food items")USEPAExposure/Risk Analysis - Ecological Risks
trex2-agent ("A formal framework for situated agent deliberation and execution")trex2-agent development teamGeneral Development Tools - Development and Programming
TRI - Toxics Release InventoryUSEPAEnviroinformatics - Release Mapping/Modeling
Trinity RNA-Seq Assembly Broad Institute, Hebrew University of Jerusalem and Trinity Developers GroupBioinformatics - Biomolecular Sequences/Structures
Trinotate ("Transcriptome Functional Annotation and Analysis")Trinotate development teamBioinformatics - Biomolecular Sequences/Structures; Exposure/Risk Analysis - Biomarkers
truPKStrand GenomicsComputational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
TSCAInv - TSCA InventoryUSEPACheminformatics - Property/Activity Prediction
TSCATS - Toxic Substance Control Act Test Submission DatabaseSRC IncCheminformatics - Property/Activity Prediction
Tute ("web application [...] in the cloud and [...] analyze and annotate entire human genomes")Tute GenomicsBioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Data Integration; Exposure/Risk Analysis - Biomarkers
Tweet ArchivistTweet ArchivistData/Simulation Pattern Analysis - Data Mining/Pattern Recognition
Twinscan/N-SCAN ("gene-structure prediction")Brent Lab, Washington University in St. LouisBioinformatics - Biomolecular Sequences/Structures
UAM-V - Urban Airshed Model-VICF International and USEPAEnviroinformatics - Environmental Fate and Transport
ubertool ("Cloud-based environmental models for evaluating pesticide risks to ecosystems")USEPAExposure/Risk Analysis - Ecological Risks
UCINET ("software package for the analysis of social network data")Analytic Technologies.Exposure/Risk Analysis - Socioeconomic/LSB Modeling
UCSC Genome BrowserGenome Bioinformatics Group, UC Santa CruzBioinformatics - Biological Dose-Response
Ullmann's Encyclopedia of Industrial ChemistryJohn Wiley & Sons, IncCheminformatics - Property/Activity Prediction
UniProtKB - Universal Protein Resource KnowledgebaseUniProt Consortium
UniSTS ("database of sequence tagged sites")National Center for Biotechnology Information, NLM, NIHBioinformatics - Biomolecular Sequences/Structures
United Nations Statistical YearbookUnited NationsExposure/Risk Analysis - Microenvironmental/LCA Modeling; Exposure/Risk Analysis - Socioeconomic/LSB Modeling; Exposure/Risk Analysis - Cumulative/Aggregate Exposures
UnmixUSEPAEnviroinformatics - Environmental Fate and Transport
Unregulated Contaminant Monitoring dataUSEPAEnviroinformatics - Release Mapping/Modeling; Enviroinformatics - Environmental Fate and Transport; Exposure/Risk Analysis - Human Health Risks
UR3M - Unified Radon Relative Risk ModelUSEPAExposure/Risk Analysis - Human Health Risks
US Census Population DatabaseUS Census BureauEnviroinformatics - Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis - Socioeconomic/LSB Modeling; Exposure/Risk Analysis - Human Health Risks
US Census SurveyUS Census BureauExposure/Risk Analysis - Microenvironmental/LCA Modeling; Exposure/Risk Analysis - Socioeconomic/LSB Modeling; Exposure/Risk Analysis - Human Health Risks
US Economic CensusUS Census BureauEnviroinformatics - Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis - Socioeconomic/LSB Modeling
US Health Map (Interactive Health Trends Map of US at County level for both Genders)Institute for Health Metrics and Evaluation (IHME)Enviroinformatics - Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis - Socioeconomic/LSB Modeling
USEtox - UNEP-SETAC (Life Cycle Initiative) ToxUSEtox development teamEnviroinformatics - Environmental Fate and Transport; Exposure/Risk Analysis - Microenvironmental/LCA Modeling; Exposure/Risk Analysis - Ecological Risks
USGS Pesticide Use DatabaseUS Geological SurveyEnviroinformatics - Release Mapping/Modeling
VANTED - Visualization and Analysis of Networks containing Experimental DataPlant Bioinformatics Group, Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben, GermanyBioinformatics - Interactions/Biopathways/Bionetworks
VCell - The Virtual CellCenter for Cell Analysis and Modeling (CCAM), University of ConnecticutComputational Toxicology - Virtual Cells, Tissues, Organs
VectorBase ("Bioinformatics Resource for Invertebrate Vectors of Human Pathogens")VectorBase Project teamBioinformatics - Data Integration
VEGA - Vertebrate Genome AnnotationHAVANA group, Wellcome Trust Sanger Institute, UKBioinformatics - Biomolecular Sequences/Structures
VEGAS - Versatile Gene-based Association StudyVEGAS development team, Queensland Institute of Medical Research, AustraliaBioinformatics - Biomolecular Sequences/Structures
VegScape - Vegetation Condition ExplorerUSDA National Agricultural Statistics ServiceEnviroinformatics - Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis - Microenvironmental/LCA Modeling; Exposure/Risk Analysis - Cumulative/Aggregate Exposures
Velvet ("Sequence assembler for very short reads")EMBL-EBIBioinformatics - Biomolecular Sequences/Structures
v-Embryo - Virtual Embryo ProjectUSEPAComputational Toxicology - Toxicoinformatics; Computational Toxicology - Virtual Cells, Tissues, Organs
VERDI - Visualization Environment Rich Data InterpretationArgonne National Laboratory, USEPA, and CMAS CenterEnviroinformatics - Spatiotemporal Mapping/Analysis
VIDA (molecular modeling software)OpenEye Scientific Software Inc.Cheminformatics - Structure Elucidation
ViPR - Virus Pathogen ResourceViPR Project teamBioinformatics - Biomolecular Sequences/Structures; Bioinformatics - Data Integration
VirtualLeaf ("cell-based computer-modeling framework for plant tissue morphogenesis")VirtualLeaf development teamComputational Toxicology - Virtual Cells, Tissues, Organs
visANTBoston UniversityBioinformatics - Interactions/Biopathways/Bionetworks
Visible Human ProjectNational Library of Medicine
Visio stencils for UML and SysMLSoftware Stencils development team (P. Hruby)General Development Tools - Data Visualization
Visual StudioMicrosoftGeneral Development Tools - Development and Programming
VLEACHDynamac Corporation and USEPAEnviroinformatics - Environmental Fate and Transport
v-Liver - Virtual Liver ProjectUSEPAComputational Toxicology - Toxicoinformatics; Computational Toxicology - Virtual Cells, Tissues, Organs
VT-KB - Virtual Tissues KnowledgebaseUSEPAComputational Toxicology - Toxicoinformatics; Computational Toxicology - Virtual Cells, Tissues, Organs
WashU Epigenome BrowserWashington UniversityBioinformatics - Biological Dose-Response; Bioinformatics - Data Integration
WASP - Water Quality Analysis Simulation ProgramUSEPAEnviroinformatics - Environmental Fate and Transport; Exposure/Risk Analysis - Ecological Risks
Water Quality Standards DatabaseUSEPAExposure/Risk Analysis - Ecological Risks
WATERS - Watershed Assessment, Tracking & Environmental Results SystemUSEPAExposure/Risk Analysis - Microenvironmental/LCA Modeling; Exposure/Risk Analysis - Ecological Risks
Watershed Plan BuilderUSEPAExposure/Risk Analysis - Ecological Risks
WATERSHEDSS - WATER, Soil, and Hydro- Environmental Decision Support SystemNorth Carolina State University and USEPAEnviroinformatics - Environmental Fate and Transport
WCIT - Water Contaminant Information ToolUSEPAExposure/Risk Analysis - Ecological Risks
Weather Underground (Current and historical weather forecasts and reports from across the world)The Weather Channel, LLCEnviroinformatics - Spatiotemporal Mapping/Analysis; Enviroinformatics - Environmental Fate and Transport
Web Soil SurveyUSDAEnviroinformatics - Spatiotemporal Mapping/Analysis
WebArrayWebArray project teamBioinformatics - Biological Dose-Response
WebGIS (A Geographic Information System Resource)Lakes Enviornmental SoftwareEnviroinformatics - Spatiotemporal Mapping/Analysis
Web-ICE - Web-based Interspecies Correlation EstimationUSEPAExposure/Risk Analysis - Ecological Risks
WebMDWebMD team
WekaMachine Learning Group, University of WaikatoData/Simulation Pattern Analysis - Data Mining/Pattern Recognition; Data/Simulation Pattern Analysis - Machine Learning Algorithms
WellCAD (combines "display, editing and analysis capabilities for well data")Advanced Logic TechnologyGeneral Development Tools - Data Visualization
WhAEM2000USEPAEnviroinformatics - Environmental Fate and Transport
WHATIF - Watershed Health Assessment Tools Investigating FisheriesCanaan Valley Institute and USEPAExposure/Risk Analysis - Ecological Risks
WhiteStar dataWhiteStar CorporationGeneral Development Tools - Data Visualization
WHO Global Health Observatory Map GalleryWorld Health Organization (WHO)Enviroinformatics - Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis - Socioeconomic/LSB Modeling
Whole Brain AtlasJohnson and Becker, Harvard Medical SchoolComputational Toxicology - Virtual Cells, Tissues, Organs
WholeCellKB-MG - Mycoplasma genitalium WholeCellKBStanford UniversityComputational Toxicology - Virtual Cells, Tissues, Organs; Computational Toxicology - Virtual Model Organisms
WinNonlinPharsightComputational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
WinNonMixPharsightComputational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
WinSAAMUniversity of PennsylvaniaGeneral Development Tools - Development and Programming
WISER - Wireless Information System for Emergency RespondersNational Library of MedicineCheminformatics - Property/Activity Prediction
WMS - Watershed Modeling SystemAquaveoEnviroinformatics - Environmental Fate and Transport
Wolfram SystemModelerWolfram ResearchGeneral Development Tools - Development and Programming
World Bank Open Data ("free and open access to data about development in countries around the globe")The World Bank GroupExposure/Risk Analysis - Socioeconomic/LSB Modeling
Worldmapper ("collection of world maps, where territories are re-sized on each map according to the subject of interest")Worldmapper TeamEnviroinformatics - Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis - Socioeconomic/LSB Modeling; General Development Tools - Data Visualization
WormAtlasAlbert Einstein College of MedicineComputational Toxicology - Virtual Cells, Tissues, Organs; Computational Toxicology - Virtual Model Organisms
WormBaseWormBase development teamBioinformatics - Biomolecular Sequences/Structures; Computational Toxicology - Virtual Cells, Tissues, Organs; Computational Toxicology - Virtual Model Organisms
WormBookWormBook development teamComputational Toxicology - Virtual Cells, Tissues, Organs; Computational Toxicology - Virtual Model Organisms
WQN - Water Quality NetworkUS Geological SurveyEnviroinformatics - Spatiotemporal Mapping/Analysis; Enviroinformatics - Release Mapping/Modeling
WRDB - Water Resources DatabaseGeorgia Environmental Protection Division and USEPAExposure/Risk Analysis - Ecological Risks
WRF - The Weather Research & Forecasting ModelWRF ConsortiumEnviroinformatics - Environmental Fate and Transport
WRF User's ForumWRF User's Forum TeamEnviroinformatics - Environmental Fate and Transport
WRF-Chem - WRF weather prediction coupled with chemistryWRF-Chem development teamEnviroinformatics - Environmental Fate and Transport
WWEIA - What We Eat In America, NHANESUSDA ARS and CDCExposure/Risk Analysis - Microenvironmental/LCA Modeling; Exposure/Risk Analysis - Socioeconomic/LSB Modeling
wwPDB - Worldwide Protein Data BankRCSB PDB, USA, PDBe, Europe, PDBj, Japan and BMRB, USABioinformatics - Biomolecular Sequences/Structures
X!TandemThe Global Proteome Machine OrganizationBioinformatics - Biomolecular Sequences/Structures
Xenbase ("Xenopus laevis and Xenopus tropicalis biology and genomics resource")University of Calgary, Alberta, CanadaComputational Toxicology - Virtual Model Organisms
Xpose (for NONMEM)Xpose development teamComputational Toxicology - Dosimetry, Toxicokinetics, Toxicodynamics
X-TileYale UniversityBioinformatics - Data Integration; Exposure/Risk Analysis - Biomarkers
Yeast GFP Fusion Localization DatabaseUniversity of California, San Francisco and SGDBioinformatics - Data Integration; Computational Toxicology - Virtual Model Organisms
YeastMine ("Search and retrieve S. cerevisiae data")SGD and Intermine project at Cambridge Systems Biology Centre, UKBioinformatics - Bio-Ontologies; Bioinformatics - Interactions/Biopathways/Bionetworks; Bioinformatics - Biological Dose-Response; Computational Toxicology - Virtual Model Organisms
YEASTNET ("A consensus reconstruction of yeast metabolism")Yeastnet development teamBioinformatics - Interactions/Biopathways/Bionetworks
ZebrafishMineZFIN at University of Oregon and InterMine project at Cambridge Systems Biology Centre, UKBioinformatics - Bio-Ontologies; Bioinformatics - Biomolecular Sequences/Structures; Computational Toxicology - Virtual Model Organisms
ZFIN (Zebrafish Model Organism Database)ZFIN Database development teamComputational Toxicology - Virtual Cells, Tissues, Organs; Computational Toxicology - Virtual Model Organisms
Zinc LibraryAuckland Bioengineering Institute, University of Auckland, NZComputational Toxicology - Virtual Cells, Tissues, Organs