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.
| Resource | Developer | Category |
|---|---|---|
| @RISK – At Risk (“risk analysis using Monte Carlo simulation”) | Palisade Corporation | Data/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 Transport | USEPA | Enviroinformatics – Environmental Fate and Transport |
| 7TMRmine (“hierarchical mining tool for 7TMRs”) | University of Nebraska | Bioinformatics – Biomolecular Sequences/Structures |
| ABySS – Assembly By Short Sequences | Michael Smith Genome Sciences Centre, Canada and BC Cancer Research Centre | Bioinformatics – Biomolecular Sequences/Structures |
| ABySS-Explorer – Assembly By Short Sequences Explorer | Michael Smith Genome Sciences Centre, Canada and BC Cancer Research Centre | Bioinformatics – Biomolecular Sequences/Structures |
| Accelerated Stochastic Simulation Algorithm for Reaction Networks | University of California, Irvine | Bioinformatics – Interactions/Biopathways/Bionetworks |
| Accelrys Discovery Studio (“predictive science application for the Life Sciences”) | Accelrys | Cheminformatics – Property/Activity Prediction |
| ACD/NMR Databases | ACD/Labs | Cheminformatics – Structure Elucidation |
| ACD/NMR Expert | ACD/Labs | Cheminformatics – Structure Elucidation |
| ACD/NMR Predictors | ACD/Labs | Cheminformatics – Structure Elucidation |
| ACD/NMR Processor Academic Edition (processing of 1D and 2D NMR data) | ACD/Labs | Cheminformatics – Structure Elucidation |
| ACD/Tox Suite | ACD/Labs | Cheminformatics – Property/Activity Prediction |
| ACE – Acute-to-Chronic Estimation with Time-Concentration-Effect Models | USEPA | Exposure/Risk Analysis – Ecological Risks |
| ACRES – Assessment, Cleanup and Redevelopment Exchange System | USEPA | Enviroinformatics – Release Mapping/Modeling |
| acslX (“modeling and simulation of dynamic systems and processes”) | AEgis Technologies | General Development Tools – Development and Programming |
| ACToR – Aggregated Computational Toxicology Resource | USEPA | Bioinformatics – Biological Dose-Response; Computational Toxicology – Toxicoinformatics |
| Acts/ Risk – Analytical Contaminant Transport Analysis System/ Health Risk Analysis Software | M. M. Aral et al., Georgia Institute of Technology, GA | Enviroinformatics – Environmental Fate and Transport |
| ADAPT (“computational modeling platform […] for pharmacokinetic and pharmacodynamic applications”) | Biomedical Simulations Resource, USC | Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics |
| ADB – Assessment Database (“database application for tracking water quality assessment data”) | USEPA | Enviroinformatics – Spatiotemporal Mapping/Analysis; Enviroinformatics – Environmental Fate and Transport |
| ADME Workbench (“pharmacokinetic modeling by integrating […] absorption, distribution, metabolism and excretion methods”) | The AEgis Technologies Group | Bioinformatics – Biological Dose-Response; Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics |
| ADMET Predictor – Absorption, Distribution, Metabolism, Elimination, Toxicity Predictor | Simulations Plus, Inc. | Cheminformatics – Property/Activity Prediction; Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics |
| ADZE – Allelic Diversity AnalyZEr | Stanford University | Bioinformatics – Data Integration |
| AEGL – Acute Exposure Guideline Levels | USEPA | Cheminformatics – Property/Activity Prediction |
| AERMOD – AMS/EPA Regulatory Model | USEPA | Enviroinformatics – Environmental Fate and Transport |
| AERONET – AErosol RObotic NETwork data | AERONET | Enviroinformatics – Spatiotemporal Mapping/Analysis |
| Affymetrix Expression Console | Affymetrix | Bioinformatics – Biological Dose-Response; Exposure/Risk Analysis – Biomarkers |
| Affymetrix GeneChip Sequence Analysis Software | Affymetrix | Bioinformatics – Biomolecular Sequences/Structures; Exposure/Risk Analysis – Biomarkers |
| Affymetrix Transcriptome Analysis Console | Affymetrix | Bioinformatics – 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 Vekemans | Bioinformatics – Data Integration |
| AGDISP – AGricultural DISPersal | USDA Forest Service | Enviroinformatics – Environmental Fate and Transport; Exposure/Risk Analysis – Ecological Risks |
| AgDRIFT | USEPA, USDA Forest Service and Spray Drift Task Force | Enviroinformatics – Environmental Fate and Transport; Exposure/Risk Analysis – Ecological Risks |
| Agent Analyst (“Agent Based Modeling Extension for ArcGIS”) | University of Redlands, Argonne National Laboratory | Enviroinformatics – Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis – Socioeconomic/LSB Modeling |
| Agricultural Chemical Use Database | National Agricultural Statistics Service | Enviroinformatics – Release Mapping/Modeling |
| AGWA – Automated Geospatial Watershed Assessment | USEPA, USDA and University of Arizona | Enviroinformatics – Environmental Fate and Transport |
| AHEAD – Alliance for Human Epigenomics and Disease | AHEAD Task Force | Bioinformatics – Biological Dose-Response; Exposure/Risk Analysis – Biomarkers |
| AHS – American Housing Survey | US Census Bureau | Enviroinformatics – Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis – Microenvironmental/LCA Modeling; Exposure/Risk Analysis – Socioeconomic/LSB Modeling |
| Air Liquide Gas Encyclopedia | Air Liquide | Cheminformatics – 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 |
| AirData | USEPA | Enviroinformatics – Release Mapping/Modeling |
| AIRMEX (European Indoor Air Monitoring and Exposure Assessment Project database) | European Commission, JRC, IHCP | Enviroinformatics – Spatiotemporal Mapping/Analysis; Enviroinformatics – Release Mapping/Modeling |
| AIRS/AFS – Air Facility System | USEPA | Enviroinformatics – Release Mapping/Modeling |
| Allergome | Allergome platform development team | Exposure/Risk Analysis – Microenvironmental/LCA Modeling |
| ALLPATHS-LG (“genome assembly from low cost data”) | Broad Institute | Bioinformatics – Biomolecular Sequences/Structures |
| ALOGPS (“provides interactive on-line prediction of logP, water solubility and pKa(s) of compounds”) | Virtual Computational Chemistry Laboratory | Cheminformatics – Property/Activity Prediction |
| ALOHA – Areal Locations of Hazardous Atmospheres | NOAA | Enviroinformatics – Release Mapping/Modeling; Enviroinformatics – Environmental Fate and Transport; Exposure/Risk Analysis – Human Health Risks |
| ALOHA (Areal Locations of Hazardous Atmospheres) ArcMap Import Tools | US NOAA Office of Response and Restoration | Enviroinformatics – 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 Oxford | Bioinformatics – Biomolecular Sequences/Structures |
| Alu Pairs Database | NIEHS | Bioinformatics – Biomolecular Sequences/Structures |
| AMDIS – Automated MS Deconvolution and Identification System | NIST | Cheminformatics – Structure Elucidation |
| AMEM – ADL Migration Estimation Model | USEPA | Exposure/Risk Analysis – Microenvironmental/LCA Modeling |
| American Cleaning Institute Cleaning Product Ingredient Inventory | American Cleaning Institute | Exposure/Risk Analysis – Microenvironmental/LCA Modeling |
| American Communities Project | American Communities Project, American University, Washington, DC | Enviroinformatics – Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis – Socioeconomic/LSB Modeling |
| AmiGO (Gene Ontology database search) | AmiGO development team | Bioinformatics – Bio-Ontologies; Computational Toxicology – Virtual Cells, Tissues, Organs |
| AMP – Agent Modeling Platform | Eclipse Foundation | Exposure/Risk Analysis – Socioeconomic/LSB Modeling; General Development Tools – Development and Programming |
| Analytica | Lumina Decision Systems | General Development Tools – Development and Programming |
| ANSYS CFD (Computational Fluid Dynamics) | ANSYS | General Development Tools – Development and Programming |
| ANSYS Fluent (“Flow Modeling Simulation Software”) | ANSYS | General Development Tools – Development and Programming |
| ANTHROPAC (“program for cultural domain analysis”) | Analytic Technologies | Enviroinformatics – Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis – Socioeconomic/LSB Modeling |
| Antigenicity Plot | Luca Toldo | Bioinformatics – Biomolecular Sequences/Structures |
| AnyLogic (“simulation tool that supports Discrete Event, Agent Based, and System Dynamics Simulation”) | AnyLogic Company | Exposure/Risk Analysis – Socioeconomic/LSB Modeling; General Development Tools – Development and Programming |
| AOPWiki – Adverse Outcome Pathway Wiki | AOPWiki team (includes European Commission JRC, USEPA ORD and OECD) | Bioinformatics – Biological Dose-Response; Computational Toxicology – Toxicoinformatics; Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics |
| AqQA | AqQA, LLC | General Development Tools – Data Visualization |
| AQS – Air Quality System | USEPA | Enviroinformatics – Spatiotemporal Mapping/Analysis; Enviroinformatics – Release Mapping/Modeling |
| AQTESOLV – AQuifer TEst SOLVer | HydroSOLVE, Inc. | Enviroinformatics – Environmental Fate and Transport |
| AQUATOX (“simulation model for aquatic systems”) | USEPA and R. Park, Ecomodeling | Enviroinformatics – Environmental Fate and Transport; Exposure/Risk Analysis – Ecological Risks |
| AquiferWin32 | ESI Ltd. | Enviroinformatics – Environmental Fate and Transport; Exposure/Risk Analysis – Ecological Risks |
| ARAGORN (tRNA and tmRNA detection) | ARAGORN development team | Bioinformatics – Biomolecular Sequences/Structures |
| Arc Hydro (ArcGIS add-in to support geospatial and temporal data analyses) | Esri | Enviroinformatics – Spatiotemporal Mapping/Analysis |
| ArcGIS (geographical information system mapping and visualization) | Esri | Enviroinformatics – 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 | |
| ArcPad | Esri | Enviroinformatics – Spatiotemporal Mapping/Analysis; General Development Tools – Data Visualization |
| Arcv2CAD | Guthrie CAD/GIS Software Pty Ltd. | General Development Tools – Data Visualization |
| ARES Commander Edition | Graebert GmbH | General Development Tools – Development and Programming; General Development Tools – Data Visualization |
| ArrayExpress | EMBL-EBI | Bioinformatics – Biological Dose-Response; Computational Toxicology – Toxicoinformatics; Exposure/Risk Analysis – Biomarkers |
| ArrayTrack/ebTrack | USFDA and ebCTC | Bioinformatics – Biological Dose-Response; Computational Toxicology – Toxicoinformatics |
| ARS Water database | USDA-ARS Hydrology Laboratory | Enviroinformatics – Environmental Fate and Transport |
| Artboard (“vector-based drawing software” for Mac OS X) | Mapdiva, LLC | General Development Tools – Data Visualization |
| ASAP – A Systematic Annotation Package For Community Analysis of Genomes | University of Wisconsin, Madison | Bioinformatics – Biomolecular Sequences/Structures |
| Ascape (“developing and exploring general-purpose agent-based models”) | Ascape development team | Exposure/Risk Analysis – Socioeconomic/LSB Modeling; General Development Tools – Development and Programming |
| ASOS/AWOS – Automated Surface and Weather Observing Systems | FAA | Enviroinformatics – Environmental Fate and Transport |
| ASPEN – Assessment System for Population Exposure Nationwide | USEPA | Enviroinformatics – Environmental Fate and Transport |
| ASTER – Assessment Tools for the Evaluation of Risk | USEPA | Exposure/Risk Analysis – Ecological Risks |
| atBioNet (“an Integrated Network Analysis Tool […] in Genomics and Proteomics”) | USFDA | Bioinformatics – Interactions/Biopathways/Bionetworks; Bioinformatics – Data Integration |
| Atlas of United States Mortality | CDC | Enviroinformatics – Spatiotemporal Mapping/Analysis |
| ATTAINS – Assessment, TMDL Tracking and ImplementatioN System | USEPA | Enviroinformatics – Release Mapping/Modeling |
| ATTILA – Analytical Tools Interface for Landscape Assessments | USEPA | Exposure/Risk Analysis – Ecological Risks |
| ATUS – American Time Use Survey | U.S. Bureau of Labor Statistics | Exposure/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, Germany | Bioinformatics – Biomolecular Sequences/Structures |
| AutoDock (docking tools suite) | The Scripps Research Institute | Cheminformatics – Property/Activity Prediction; Bioinformatics – Biomolecular Sequences/Structures |
| Automated Particle Tracking and Analysis Software | University of California, Irvine | Bioinformatics – 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 USEPA | Data/Simulation Pattern Analysis – Data Mining/Pattern Recognition; Data/Simulation Pattern Analysis – Sensitivity/Uncertainty Analysis |
| BANJO: Bayesian Network Inference with Java Objects | Duke University | Data/Simulation Pattern Analysis – Data Mining/Pattern Recognition |
| BASE – BioArray Software Environment | BASE development team | |
| BASINS – Better Assessment Science Integrating point & Non-point Sources | USEPA | Enviroinformatics – Environmental Fate and Transport |
| BASS – Bioaccumulation and Aquatic System Simulator | USEPA | Exposure/Risk Analysis – Ecological Risks |
| BBID – Biological Biochemical Image Database | NIA, Intramural Research Program | Bioinformatics – Interactions/Biopathways/Bionetworks |
| BCF database – Bio-concentration Factors Gold standard database | Cefic LRI and EURAS | Exposure/Risk Analysis – Human Health Risks; Exposure/Risk Analysis – Ecological Risks |
| BEACON – Beach Advisory and Closing On-line Notification | USEPA | Enviroinformatics – Release Mapping/Modeling; Exposure/Risk Analysis – Ecological Risks |
| bear (“data analysis tool for average bioequivalence (ABE) and bioavailability (BA) for useR”) | bear development team | Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics |
| behaviorsearch (“Adaptive search and exploration of agent-based model parameters”) | behaviorsearch development team | General Development Tools – Development and Programming |
| Behaviour Composer | Modelling4All project and University of Oxford | General Development Tools – Development and Programming |
| BEIS – Biogenic Emission Inventory System | USEPA | Enviroinformatics – Release Mapping/Modeling |
| BELD – Biogenic Emissions Landuse Database | USEPA | Enviroinformatics – Release Mapping/Modeling |
| BenMAP (“estimate the health impacts and economic benefits […] when populations experience changes in air quality”) | USEPA | Exposure/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 Project | Berkeley Drosophila Genome Project Consortium | Bioinformatics – Biomolecular Sequences/Structures; Bioinformatics – Biological Dose-Response; Computational Toxicology – Virtual Model Organisms |
| Berkeley Madonna (“modeling and analysis of dynamic systems”) | UC Berkeley | General Development Tools – Development and Programming |
| BEs – Biomonitoring Equivalents | Summit Toxicology, LLP | Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics; Exposure/Risk Analysis – Biomarkers |
| BetaBuster (“Bayesian Epidemiologic Screening” technique for “obtaining specific Beta prior distributions”) | BetaBuster team | Data/Simulation Pattern Analysis – Sensitivity/Uncertainty Analysis |
| BicAT – Biclustering Analysis Toolbox | ETH, Zurich | Bioinformatics – Biomolecular Sequences/Structures; Data/Simulation Pattern Analysis – Classification/Clustering |
| BIND – Biomolecular Interaction Network Database | Christopher Hogue’s Research Laboratory | Bioinformatics – Interactions/Biopathways/Bionetworks |
| BioCarta | BioCarta LLC | Bioinformatics – Interactions/Biopathways/Bionetworks; Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics; Exposure/Risk Analysis – Biomarkers |
| Biocatalysis/ Biodegradation Database | University of Minnesota | Bioinformatics – Interactions/Biopathways/Bionetworks; Bioinformatics – Data Integration |
| Biocellion (“Computer Simulation of Living Cell Systems”) | biocellion development team | Computational Toxicology – Virtual Cells, Tissues, Organs |
| Bioclipse (“workbench for the life sciences” based on Eclipse Rich Client Platform) | Bioclipse development team | Cheminformatics – 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 team | Bioinformatics – Bio-Ontologies; Bioinformatics – Biomolecular Sequences/Structures |
| BioDMET (“physiologically-based pharmacokinetic (PBPK) modeling and simulation tool”) | GE and DTRA | Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics |
| Bioeffects Program | Center for Coastal Monitoring and Assessment, National Ocean Service | Exposure/Risk Analysis – Ecological Risks |
| BioGPS (“gene annotation portal”) | BioGPS development team | Bioinformatics – Biomolecular Sequences/Structures |
| BioGRID – Biological General Repository for Interaction Datasets | BioGRID Team | Bioinformatics – Interactions/Biopathways/Bionetworks; Bioinformatics – Data Integration; Exposure/Risk Analysis – Biomarkers |
| Biokmod (“Mathematica toolbox […] with application for modeling Linear and Nonlinear Biokinetic Systems”) | Guillermo Sanchez | Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics |
| BiokmodWeb | Guillermo Sanchez | Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics |
| BioLayout Express3D (“visualization and analysis of network graphs”) | BioLayout Express3D Team | Bioinformatics – Interactions/Biopathways/Bionetworks; General Development Tools – Data Visualization |
| Biomarkers Database (last updated in August 2004) | USEPA | Bioinformatics – Biological Dose-Response; Computational Toxicology – Toxicoinformatics; Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics; Exposure/Risk Analysis – Biomarkers |
| BioModels (“repository of computational models of biological processes”) | EMBL-EBI | Computational Toxicology – Virtual Cells, Tissues, Organs |
| BioNumbers (“The Database of Useful Biological Numbers”) | Weizmann Institute, Israel | Bioinformatics – Biological Dose-Response; Bioinformatics – Data Integration; Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics |
| BioPAX – Biological Pathway Exchange | BioPAX development team | Bioinformatics – Interactions/Biopathways/Bionetworks |
| Bio-PEPA Workbench | Bio-PEPA development team | Bioinformatics – 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 USEPA | Exposure/Risk Analysis – Ecological Risks |
| Biopython (“tools for biological computation written in Python”) | Biopython development team | Bioinformatics – 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 Caltech | Bioinformatics – Interactions/Biopathways/Bionetworks |
| BiQ Analyzer (“software tool for DNA methylation analysis”) | Max Planck Institute for Informatics, Germany | Bioinformatics – Biomolecular Sequences/Structures; Exposure/Risk Analysis – Biomarkers |
| Bismark (tool to map bisulfite converted sequence reads and determine cytosine methylation states) | Babraham Bioinformatics | Bioinformatics – 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, NIH | Bioinformatics – Biomolecular Sequences/Structures |
| BLAT – BLAST-like Alignment Tool | Jim Kent | Bioinformatics – Biomolecular Sequences/Structures |
| BLM – Biotic Ligand Model | HydroQual | Exposure/Risk Analysis – Ecological Risks |
| Blocks Database (“sequence analysis”; no longer updated) | Fred Hutchinson Cancer Research Center | Bioinformatics – Biomolecular Sequences/Structures |
| BMDExpress (“analyze microarray dose-response data”) | BMDExpress team | Bioinformatics – Biological Dose-Response; Computational Toxicology – Toxicoinformatics |
| BMDS – Benchmark Dose Software | USEPA | Computational 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 Carolina | Enviroinformatics – Spatiotemporal Mapping/Analysis |
| BMRB – Biological Magnetic Resonance Data Bank | BMRB project team, University of Wisconsin | Cheminformatics – Structure Elucidation |
| BOND – Biomolecular Object Network Databank | Thomson | Bioinformatics – Biomolecular Sequences/Structures |
| Boomer (“Non-Linear Regression Program”) | D.W.A. Bourne | Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics |
| BOSS – Biomarkers of Oxidative Stress Study | NIEHS | Bioinformatics – Biological Dose-Response; Computational Toxicology – Toxicoinformatics; Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics; Exposure/Risk Analysis – Biomarkers |
| Bowtie (DNA sequence alignment tool) | Bowtie development team | Bioinformatics – Biomolecular Sequences/Structures |
| Bowtie 2 (sequencing reads to long reference sequences aligner) | Bowtie 2 development team | Bioinformatics – Biomolecular Sequences/Structures |
| Boxshade (“program for creating good looking printouts from multiple-aligned […] sequences”) | Boxshade Development Team | General Development Tools – Data Visualization |
| BRB-ArrayTools | Dr. Richard Simon and BRB-ArrayTools Development Team | Bioinformatics – Biological Dose-Response; Computational Toxicology – Toxicoinformatics |
| BRENDA – BRaunschweig ENzyme DAtabase | D. Schomburg, Technische Universität Braunschweig, Germany | Bioinformatics – Biomolecular Sequences/Structures |
| Breve (“build 3D simulations of multi-agent systems and artificial life”) | Jon Klein | Exposure/Risk Analysis – Socioeconomic/LSB Modeling; General Development Tools – Development and Programming |
| BRFSS – Behavioral Risk Factor Surveillance System | CDC | Exposure/Risk Analysis – Microenvironmental/LCA Modeling |
| bsim-bccs (“Models the stochastic interactions of bacteria and particles in a fluid based environment”) | bsim-bccs development team | Bioinformatics – Interactions/Biopathways/Bionetworks; Exposure/Risk Analysis – Ecological Risks |
| BUGS – Bayesian inference Using Gibbs Sampling (OpenBUGS/ WinBUGS) | BUGS project team | Data/Simulation Pattern Analysis – Sensitivity/Uncertainty Analysis |
| BugsXLA – A GUI for WinBugs | Phil Woodward | Data/Simulation Pattern Analysis – Sensitivity/Uncertainty Analysis |
| BWA – Burrows-Wheeler Aligner | BWA development team | Bioinformatics – Biomolecular Sequences/Structures |
| C++ | C++ development team | General Development Tools – Development and Programming |
| CAD Viewer | Tailor Made Software | General Development Tools – Data Visualization |
| CAD2Shape | Guthrie CAD/GIS Software Pty Ltd. | General Development Tools – Data Visualization |
| CAESAR – Computer Assisted Evaluation of industrial chemical Substances According to Regulations | VEGA | Cheminformatics – Property/Activity Prediction |
| Cain (“Stochastic Simulations for Chemical Kinetics”) | Cain development team (Sean Mauch et al.) | Bioinformatics – Interactions/Biopathways/Bionetworks |
| CalcuSyn | Biosoft | Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics |
| California Safe Cosmetics Program Product Database | California Safe Cosmetics Program, California Department of Public Health | Exposure/Risk Analysis – Microenvironmental/LCA Modeling; Exposure/Risk Analysis – Cumulative/Aggregate Exposures |
| CALPro (CALPUFF, CALMET) | Atmospheric Studies Group at TRC | Enviroinformatics – Environmental Fate and Transport |
| CalTOX | California DTSC | Enviroinformatics – Environmental Fate and Transport; Exposure/Risk Analysis – Microenvironmental/LCA Modeling; Exposure/Risk Analysis – Ecological Risks |
| Cambridge Structural Database | Cambridge Crystallographic Data Centre | Cheminformatics – Property/Activity Prediction; Bioinformatics – Biomolecular Sequences/Structures |
| CAMEO MARPLOT (Mapping applications for response, planning, and local operational tasks) | USEPA and NOAA | Enviroinformatics – Spatiotemporal Mapping/Analysis; Enviroinformatics – Release Mapping/Modeling |
| CAMx – Comprehensive Air Quality Model with Extensions | Environ | Enviroinformatics – Environmental Fate and Transport |
| caNanoLab – cancer Nanotechnology Laboratory | NCI (National Cancer Institute), NIH | Exposure/Risk Analysis – Microenvironmental/LCA Modeling |
| Cancer Mortality Maps | NCI (National Cancer Institute), NIH | Enviroinformatics – Spatiotemporal Mapping/Analysis |
| CARBDOSE | USEPA | Exposure/Risk Analysis – Human Health Risks |
| CARES – Cumulative and Aggregate Risk Evaluation System | CropLife America, ILSI Research Foundation | Exposure/Risk Analysis – Cumulative/Aggregate Exposures |
| CartoDB | Vizzuality team | Enviroinformatics – Spatiotemporal Mapping/Analysis; General Development Tools – Data Visualization |
| Cartographica | ClueTrust | Enviroinformatics – Spatiotemporal Mapping/Analysis; General Development Tools – Data Visualization |
| CartoMobile | ClueTrust | Enviroinformatics – Spatiotemporal Mapping/Analysis; General Development Tools – Data Visualization |
| CASCADE | Alterra and Plant Research International | Exposure/Risk Analysis – Ecological Risks |
| CASEUltra | MultiCase Inc. | Cheminformatics – Property/Activity Prediction |
| Cassandra database (“open source distributed database management system”) | Apache Cassandra development team and The Apache Software Foundation | General Development Tools – Development and Programming |
| CATH (“Protein Structure Classification Database”) | University College, London | Bioinformatics – Biomolecular Sequences/Structures |
| CATS – Contaminants in Aquatic and Terrestrial ecoSystems | RIVM | Enviroinformatics – Environmental Fate and Transport |
| CBECS – Commercial Buildings Energy Consumption Survey | U.S. Energy Information Administration | Exposure/Risk Analysis – Microenvironmental/LCA Modeling; Exposure/Risk Analysis – Socioeconomic/LSB Modeling |
| CCRIS – Chemical Carcinogenesis Research Information System | NLM | Cheminformatics – Property/Activity Prediction |
| CDC WONDER – Wide-ranging Online Data for Epidemiologic Research | CDC | Enviroinformatics – Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis – Microenvironmental/LCA Modeling |
| CD-HIT – Cluster Database at High Identity with Tolerance | Li group, University of California, San Diego (developed at Burnham Institute) | Bioinformatics – Biomolecular Sequences/Structures |
| CEBS – Chemical Effects in Biological Systems | NIEHS | Bioinformatics – Biological Dose-Response; Bioinformatics – Data Integration; Computational Toxicology – Toxicoinformatics; Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics |
| CEE-TV – Contaminant Exposure and Effects-Terrestrial Vertebrates | US Geological Survey | Exposure/Risk Analysis – Ecological Risks |
| Cefic LRI Toolbox – Long-range Research Initiative Toolbox | Cefic | Exposure/Risk Analysis – Human Health Risks |
| Cell Explorer | Cell Explorer team | Computational Toxicology – Virtual Cells, Tissues, Organs |
| CellDesigner | Systems Biology Institute, Japan | Bioinformatics – Interactions/Biopathways/Bionetworks; Computational Toxicology – Virtual Cells, Tissues, Organs |
| CellML | Auckland Bioengineering Institute, University of Auckland, NZ | Computational Toxicology – Virtual Cells, Tissues, Organs |
| CellNetAnalyzer / FluxAnalyzer | Max Planck Institute | Bioinformatics – Interactions/Biopathways/Bionetworks |
| CellNetOptimizer | CellNOpt development team | Bioinformatics – Interactions/Biopathways/Bionetworks |
| CellSys | Interdisciplinary Centre for Bioinformatics, University of Leipzig, Germany | Bioinformatics – Data Integration; Computational Toxicology – Virtual Cells, Tissues, Organs |
| Census of Agriculture | USDA NASS | Enviroinformatics – Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis – Microenvironmental/LCA Modeling |
| CEP – Cumulative Exposure Project | USEPA | Enviroinformatics – Spatiotemporal Mapping/Analysis |
| CEPST – Chemical Exposure Priority Setting Tool | The LifeLine Group | Exposure/Risk Analysis – Human Health Risks |
| CE-QUAL-ICM | U.S. Army Corps of Engineers | Exposure/Risk Analysis – Ecological Risks |
| CE-QUAL-W2 | U.S. Army Corps of Engineers and Portland State University | Enviroinformatics – Environmental Fate and Transport; Exposure/Risk Analysis – Ecological Risks |
| CERCLIS – Comprehensive Environmental Response, Compensation, and Liability Information System | USEPA | Enviroinformatics – Release Mapping/Modeling |
| C-FERST – Community-Focused Exposure and Risk Screening Tool | USEPA | Exposure/Risk Analysis – Cumulative/Aggregate Exposures; Exposure/Risk Analysis – Human Health Risks |
| CGAP – Cancer Genome Anatomy Project | NCI (National Cancer Institute), NIH | Bioinformatics – Biological Dose-Response; Exposure/Risk Analysis – Biomarkers |
| CGD – Customized Geographic Database | Biota of North America Program (BONAP) | Enviroinformatics – Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis – Socioeconomic/LSB Modeling |
| CHAD – Consolidated Human Activity Database | USEPA | Exposure/Risk Analysis – Microenvironmental/LCA Modeling; Exposure/Risk Analysis – Socioeconomic/LSB Modeling; Exposure/Risk Analysis – Cumulative/Aggregate Exposures |
| CHARM – Complex Hazardous Air Release Model | Dr. Mark Eltgroth | |
| CharProtDB – Characterized Protein Database | J. Craig Venter Institute | Bioinformatics – Bio-Ontologies; Bioinformatics – Biomolecular Sequences/Structures |
| Chaste (“general purpose simulation package […] in biology and physiology”) | Computational Biology Group, Dept. of Computer Science, University of Oxford | Bioinformatics – Data Integration |
| ChEBI – Chemical Entities of Biological Interest | EMBL-EBI | Bioinformatics – Bio-Ontologies |
| ChemBank | Broad Institute | Cheminformatics – Property/Activity Prediction; Bioinformatics – Biomolecular Sequences/Structures |
| ChemBioNavigator (visualization of chemical and biological space of molecular groups) | University of Hamburg and BioSolveIT | Cheminformatics – Property/Activity Prediction |
| ChemGate (chemical structure search) | John Wiley & Sons, Inc. and eMolecules, Inc. | Cheminformatics – Structure Elucidation |
| Chemical Data Reporting | USEPA | Enviroinformatics – Release Mapping/Modeling |
| Chemicalize (search chemical structures) | ChemAxon | Cheminformatics – Property/Activity Prediction |
| ChemIDplus Advanced | NLM | Cheminformatics – Property/Activity Prediction |
| ChemPoint (“Environmental Data Management System”) | Starpoint Software Inc. | General Development Tools – Data Visualization |
| ChemSpider | Royal Society of Chemistry, Cambridge | Cheminformatics – 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 Releases | USEPA | Exposure/Risk Analysis – Cumulative/Aggregate Exposures |
| ChemView | USEPA | Exposure/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 Handbook | USEPA | Exposure/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 Toolbox | University of Oxford | Data/Simulation Pattern Analysis – Sensitivity/Uncertainty Analysis |
| ChromDB – The Chromatin Database | BIO5 Institute | Bioinformatics – Biomolecular Sequences/Structures; Bioinformatics – Data Integration |
| CHSI – Community Health Status Indicators | CDC | Enviroinformatics – Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis – Socioeconomic/LSB Modeling |
| CICAD – Concise International Chemical Assessment Documents | IPCS INCHEM | Cheminformatics – Property/Activity Prediction |
| CLC Sequence Viewer | CLC bio | Bioinformatics – Biomolecular Sequences/Structures |
| CLCbio Genomics Workbench (analysis, comparison and visualization of next generation sequencing data) | CLCbio | Bioinformatics – Biomolecular Sequences/Structures |
| CLIP – Closed-Loop Identification Protocol | Rabitz Laboratory, Princeton University | Cheminformatics – Interaction/Reaction Modeling |
| Cloe PK | Cyprotex PLC | Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics |
| Cloe Predict | Cyprotex | Bioinformatics – Biological Dose-Response; Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics |
| Clustal Omega (Multiple DNA, RNA and protein sequence alignment program) | Conway Institute, UCD Dublin | Bioinformatics – Biomolecular Sequences/Structures |
| ClustalW2 (see Clustal Omega) | EMBL-EBI | Bioinformatics – Biomolecular Sequences/Structures |
| CluSTr | EMBL-EBI | Bioinformatics – Biomolecular Sequences/Structures |
| CMAQ – Community Multi-scale Air Quality modeling system | CMAS Center, UNC-Chapel Hill | Enviroinformatics – 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 Wisconsin | Bioinformatics – Biomolecular Sequences/Structures; Bioinformatics – Biological Dose-Response; Exposure/Risk Analysis – Biomarkers |
| Cmgui – Continuum Mechanics, Image Analysis, Signal Processing and System Identification Graphical User Interface | Auckland Bioengineering Institute, University of Auckland, NZ | Computational Toxicology – Virtual Cells, Tissues, Organs |
| CNV Project Data – Copy Number Variation Project Data | Wellcome Trust Sanger Institute, UK | Bioinformatics – Biomolecular Sequences/Structures; Exposure/Risk Analysis – Biomarkers |
| CNVFinder – Copy Number Variant Finder | Wellcome Trust Sanger Institute, UK | Bioinformatics – Biomolecular Sequences/Structures; Exposure/Risk Analysis – Biomarkers |
| COG – Clusters of Orthologous Groups of proteins | National Center for Biotechnology Information, NLM, NIH | Bioinformatics – Biomolecular Sequences/Structures; Bioinformatics – Data Integration |
| Cognoscente (“database and visualization tool for biomolecular interactions […] in the literature”) | VanBuren laboratory, Texas A&M Health Science Center | Bioinformatics – Interactions/Biopathways/Bionetworks |
| CombiTool | Leibniz Institute for Age Research – FLI, Germany | Bioinformatics – Biological Dose-Response |
| COMBO – COral Mortality and Bleaching Output | COMBO Team | Exposure/Risk Analysis – Ecological Risks |
| COMMUTER | USEPA | Enviroinformatics – Environmental Fate and Transport |
| Comparative Toxicogenomics Database | Mount Desert Island Biological Laboratory | Bioinformatics – Biological Dose-Response; Computational Toxicology – Toxicoinformatics; Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics |
| Compass | Bruker Daltonics | Exposure/Risk Analysis – Biomarkers |
| Compass OpenAccess | Bruker Daltonics | Exposure/Risk Analysis – Biomarkers |
| CompMoby (“detect over-represented motifs in the upstream or 3′ UTR sequences of co-expressed genes”) | QB3 and UCSF | Bioinformatics – Biomolecular Sequences/Structures |
| Comprehensive Cancer Information | NCI (National Cancer Institute), NIH | Computational Toxicology – Toxicoinformatics; Exposure/Risk Analysis – Human Health Risks |
| CompuCell 3D | Indiana University and Biocomplexity Institute | Computational Toxicology – Virtual Cells, Tissues, Organs |
| COMSOL MultiPhysics | COMSOL | General 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”) | RIVM | Exposure/Risk Analysis – Microenvironmental/LCA Modeling |
| Consumer Expenditure Survey | U.S. Bureau of Labor Statistics | Exposure/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 Nanotechnologies | Exposure/Risk Analysis – Microenvironmental/LCA Modeling |
| CONTAM | NIST | Exposure/Risk Analysis – Microenvironmental/LCA Modeling |
| Contrail – To assemble large genomes in the cloud | University of MD | Bioinformatics – Biomolecular Sequences/Structures |
| COPASI – Complex Pathway Simulator (“successor of Gepasi”) | Virginia Bioinformatics Institute, Virginia Tech | Cheminformatics – Interaction/Reaction Modeling; Bioinformatics – Interactions/Biopathways/Bionetworks |
| CORINA (“3D structure generator for small and medium sized, […] molecules”) | Molecular Networks GmbH | Cheminformatics – Property/Activity Prediction |
| Cormas | Cormas development team, Cirad | Exposure/Risk Analysis – Ecological Risks |
| COS.SIM (“Agent Based Traffic MicroSimulation”) | COS.SIM development team | Exposure/Risk Analysis – Microenvironmental/LCA Modeling |
| Cosmeticsinfo.org | Personal Care Products Council | Exposure/Risk Analysis – Cumulative/Aggregate Exposures |
| COSMIC – Catalogue Of Somatic Mutations In Cancer | Wellcome Trust Sanger Institute, UK | Exposure/Risk Analysis – Biomarkers |
| CPCat – Chemical and Product Categories | USEPA | Computational Toxicology – Toxicoinformatics; Exposure/Risk Analysis – Microenvironmental/LCA Modeling |
| CPDB – Carcinogenic Potency Database | CPDB development team | Computational 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 Database | CDC and DeLima Associates, Virginia, USA | Exposure/Risk Analysis – Microenvironmental/LCA Modeling; Exposure/Risk Analysis – Cumulative/Aggregate Exposures |
| CPS – Current Population Survey | US Census Bureau | Enviroinformatics – Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis – Socioeconomic/LSB Modeling |
| CRC Handbook of Chemistry and Physics | CRC Press | Cheminformatics – Property/Activity Prediction |
| CRC Handbook of Data on Organic Compounds | CRC Press | Cheminformatics – Property/Activity Prediction |
| Creme – RIFM Aggregate Exposure Model for Fragrance Materials | Creme Global and RIFM | Exposure/Risk Analysis – Microenvironmental/LCA Modeling |
| CREMOFAC – Chromatin Remodeling Factors | Chromatin Biology Lab, Jawaharlal Nehru Centre for Advanced Scientific Research, India | Bioinformatics – Biological Dose-Response; Bioinformatics – Data Integration |
| CropScape (“crop-specific land cover data layer created annually for the continental United States”) | USDA National Agricultural Statistics Service | Enviroinformatics – Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis – Cumulative/Aggregate Exposures |
| Crystal Ball | Decisioneering Inc./ Oracle | Data/Simulation Pattern Analysis – Sensitivity/Uncertainty Analysis |
| CSD – Cambridge Structural Database | Cambridge Crystallographic Data Centre | Cheminformatics – Structure Elucidation |
| CSD Linker Database | Chemical Computing Group | Cheminformatics – Structure Elucidation |
| CSDS – Cambridge Structural Database System | Cambridge Crystallographic Data Centre | Cheminformatics – Structure Elucidation |
| CSEM – Multi-read Allocation for ChIP-seq | Keles Research Group, University of Wisconsin | Bioinformatics – Biomolecular Sequences/Structures; Bioinformatics – Biological Dose-Response; Exposure/Risk Analysis – Biomarkers |
| CSFII – Continuing Survey of Food Intakes by Individuals | USDA | Exposure/Risk Analysis – Microenvironmental/LCA Modeling; Exposure/Risk Analysis – Socioeconomic/LSB Modeling |
| CTEPP – Children’s Total Exposure to Persistent Pesticides and Other Persistent Organic Pollutants | USEPA | Enviroinformatics – Release Mapping/Modeling |
| Cufflinks – Transcript assembly, differential expression and regulation for RNA-Seq samples | UC Berkeley, JHU, and Caltech | Bioinformatics – Biomolecular Sequences/Structures; Bioinformatics – Biological Dose-Response; Exposure/Risk Analysis – Biomarkers |
| CummeRbund – To analyze Cufflinks RNA-Seq output | MIT and Harvard | Bioinformatics – Biomolecular Sequences/Structures; Exposure/Risk Analysis – Biomarkers |
| CureTogether (a blog where “patients […] share quantitative information on over 500 medical conditions”) | CureTogether team | Exposure/Risk Analysis – Biomarkers |
| CVSim | CVSim development team | Bioinformatics – Biological Dose-Response; Computational Toxicology – Virtual Cells, Tissues, Organs |
| Cyber Patient | Michael B. Bolger, USC | Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics |
| CySBGN (“SBGN diagrams in Cytoscape”) | CySBGN development team, Saez-Rodriguez Group, EMBL-EBI | Bioinformatics – Interactions/Biopathways/Bionetworks |
| Cytoscape | Cytoscape Consortium and Institut Pasteur | General Development Tools – Data Visualization |
| DALY Calculator – Disability-Adjusted Life Year Calculator | DALY Calculator development team | Exposure/Risk Analysis – Human Health Risks |
| DART – Developmental and Reproductive Toxicology Database | NLM, NIH | Cheminformatics – Property/Activity Prediction; Computational Toxicology – Toxicoinformatics |
| Database of Macromolecular Movement | Mark Gerstein, et al., Yale University | Cheminformatics – Structure Elucidation; Bioinformatics – Biomolecular Sequences/Structures |
| DAVID – Database for Annotation, Visualization and Integrated Discovery | National Institute of Allergy and Infectious Diseases, NIH | Bioinformatics – Biomolecular Sequences/Structures; Bioinformatics – Data Integration |
| DBCAT – DataBase of CpG islands and Analytical Tool | Research Center for Medical Excellence National Taiwan University | Bioinformatics – Biomolecular Sequences/Structures |
| DBChIP – program to detect differentially bound sharp binding sites across multiple conditions | Keles Research Group, University of Wisconsin | Bioinformatics – Biomolecular Sequences/Structures; Bioinformatics – Biological Dose-Response; Exposure/Risk Analysis – Biomarkers |
| dbGaP – Database of Genotypes and Phenotypes | National Center for Biotechnology Information, NLM, NIH | Bioinformatics – Biomolecular Sequences/Structures; Bioinformatics – Data Integration; Exposure/Risk Analysis – Biomarkers |
| dbSNP | National Center for Biotechnology Information, NLM, NIH | Bioinformatics – Biomolecular Sequences/Structures; Exposure/Risk Analysis – Biomarkers |
| dbZach | Zacharewski Laboratory, Michigan State University | |
| DCAL – Dose and Risk Calculation Software | Oak Ridge National Laboratory and USEPA | Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics |
| dChip – DNA-Chip Analyzer | Harvard University and Stanford University | Bioinformatics – Biological Dose-Response |
| DDI Predict | Aureus Sciences | Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics |
| DEBTox | University of Amsterdam | Exposure/Risk Analysis – Ecological Risks |
| Decision Forest | USFDA | Bioinformatics – Biological Dose-Response; Computational Toxicology – Toxicoinformatics |
| DEEM-FCID/ Calendex – Dietary Exposure Evaluation Model-Food Commodity Intake Database/ Calendex | USEPA | Exposure/Risk Analysis – Microenvironmental/LCA Modeling; Exposure/Risk Analysis – Cumulative/Aggregate Exposures |
| Defra Risk Assessment | Defra team and Department for Environment, Food & Rural Affairs | Exposure/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 Model | USEPA | Exposure/Risk Analysis – Cumulative/Aggregate Exposures |
| Derek Nexus | Lhasa Limited | Cheminformatics – Property/Activity Prediction |
| DEVS-Suite | DEVS-Suite development team | General Development Tools – Development and Programming |
| DFCI Gene Index | Gene Index Project, Harvard University | |
| DFLOW | USEPA | Enviroinformatics – Environmental Fate and Transport; Exposure/Risk Analysis – Ecological Risks |
| Diabetes Public Health Resource | CDC | |
| Didger (“geoprocessing and data conversion tool”) | Golden Software Inc. | Enviroinformatics – Spatiotemporal Mapping/Analysis; General Development Tools – Data Visualization |
| Digital Elevation Data | USDA NRCS | Enviroinformatics – Spatiotemporal Mapping/Analysis |
| DIP – Database of Interacting Proteins | David Eisenberg, UCLA | |
| DIPPR 801 Database | DIPPR, AIChE | Cheminformatics – Property/Activity Prediction |
| DISCOVAR – genome assembler and variant caller | Broad Institute | Bioinformatics – Biomolecular Sequences/Structures |
| DISCOVAR de novo – Assembler for large genomes up to human size | Broad Institute | Bioinformatics – Biomolecular Sequences/Structures |
| Discrete Dynamics Lab (“Tools for researching Cellular Automata, Random Boolean Networks, multi-value Discrete Dynamical Networks, and beyond”) | DDLab development team | Bioinformatics – Interactions/Biopathways/Bionetworks; General Development Tools – Development and Programming |
| Disease Maps 2012 | US Geological Survey | Enviroinformatics – Spatiotemporal Mapping/Analysis |
| Disease/ Phenotype web-PAGE (“disease based gene set analysis of microarray gene expression”) | Gene Expression and Genomics Unit, NIA, NIH | Bioinformatics – Biological Dose-Response; Exposure/Risk Analysis – Biomarkers; Exposure/Risk Analysis – Human Health Risks |
| DiseaseMeth – human disease methylation database | College of Bioinformatics Sci. and Tech., Harbin Medical U., China | Bioinformatics – Biomolecular Sequences/Structures; Bioinformatics – Data Integration |
| DisEBML (“Intrinsic Protein Disorder Prediction”) | DisEBML development team, EMBL | Bioinformatics – Biomolecular Sequences/Structures; Bioinformatics – Interactions/Biopathways/Bionetworks |
| DIVA-GIS (“mapping and geographic data analysis”) | DIVA-GIS development team | Enviroinformatics – Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis – Socioeconomic/LSB Modeling; General Development Tools – Data Visualization |
| DIVA-GIS (GIS data by country) | DIVA-GIS development team | Enviroinformatics – Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis – Socioeconomic/LSB Modeling |
| DMR Pollutant Loading Tool – Discharge Monitoring Report Pollutant Loading Tool | USEPA | Enviroinformatics – 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 system | Computational Chemodynamics Laboratory | Bioinformatics – Biological Dose-Response; Computational Toxicology – Toxicoinformatics; Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics |
| DoseSim | SCB Research Group, Colorado State University | Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics |
| Downhole Explorer (“drillhole presentation and plotting program”) | Downhole Explorer development team | General Development Tools – Data Visualization |
| DRINK – Drinking Water Research Information Network | USEPA | |
| DROPLET | Alterra and Wageningen UR, The Netherlands | Exposure/Risk Analysis – Ecological Risks |
| Drug Information Portal | NLM, NIH | Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics |
| DrugMatrix | NIEHS | Bioinformatics – Biological Dose-Response; Computational Toxicology – Toxicoinformatics; Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics |
| DSID – Dietary Supplement Ingredient Database | USDA Nutrient Data Laboratory and Office of Dietary Supplements, NIH | Exposure/Risk Analysis – Microenvironmental/LCA Modeling |
| DSSTox – Distributed Structure-Searchable Toxicity | USEPA | Cheminformatics – Property/Activity Prediction |
| DUST (“model to calculate the dermal uptake of pesticides by birds and mammals”) | USEPA | Exposure/Risk Analysis – Ecological Risks |
| DWS – Drinking Water Standards | USEPA | Exposure/Risk Analysis – Microenvironmental/LCA Modeling |
| Dynamic Signaling Maps | Hippron Physiomics Inc | Cheminformatics – Interaction/Reaction Modeling; Bioinformatics – Interactions/Biopathways/Bionetworks |
| Dynetica | Duke University | Bioinformatics – Interactions/Biopathways/Bionetworks |
| EADB – Estrogenic Activity Database | USFDA | Bioinformatics – Biological Dose-Response; Computational Toxicology – Toxicoinformatics; Exposure/Risk Analysis – Biomarkers |
| EAFUS – Everything Added to Food in the United States | USFDA | Exposure/Risk Analysis – Microenvironmental/LCA Modeling |
| E-Cell | E-Cell Project Team | Computational Toxicology – Virtual Cells, Tissues, Organs |
| ECETOC Science Areas – European Centre for Ecotoxicology and Toxicology of Chemicals Science Areas | ECETOC | Exposure/Risk Analysis – Microenvironmental/LCA Modeling; Exposure/Risk Analysis – Human Health Risks; Exposure/Risk Analysis – Ecological Risks |
| ECHO – Enforcement and Compliance History Online | USEPA | Enviroinformatics – Release Mapping/Modeling |
| Ecolab (“software package […] looking at the dynamics of evolution”) | Ecolab development team | Bioinformatics – Interactions/Biopathways/Bionetworks |
| Ecolego | Swedish Radiation Safety Authority, Sweden and Norwegian Radiation Protection Authority | General Development Tools – Development and Programming |
| ECOSAR – Ecological Structure Activity Relationships | Syracuse Research Corporation and USEPA | Exposure/Risk Analysis – Ecological Risks |
| ECOTOX – ECOTOXicology | USEPA | Cheminformatics – Property/Activity Prediction; Exposure/Risk Analysis – Ecological Risks |
| Edinburgh Pathway Editor | EPE development team | Bioinformatics – Interactions/Biopathways/Bionetworks |
| EDKB – Endocrine Disruptor Knowledge Base | USFDA | Bioinformatics – Biological Dose-Response; Computational Toxicology – Toxicoinformatics; Exposure/Risk Analysis – Biomarkers |
| E-FAST – Exposure and Fate Assessment Screening Tool | USEPA | Exposure/Risk Analysis – Cumulative/Aggregate Exposures; Exposure/Risk Analysis – Ecological Risks |
| EFDB – Environmental Fate Data Base | SRC Inc | Enviroinformatics – Environmental Fate and Transport; Cheminformatics – Property/Activity Prediction |
| EFDC – Environmental Fluid Dynamics Code | Virginia Institute of Marine Science, The College of William and Mary (J. M. Hamrick) and USEPA | Enviroinformatics – Environmental Fate and Transport |
| eggNOG – evolutionary genealogy of genes: Non-supervised Orthologous Groups | EMBL, Germany | Bioinformatics – Interactions/Biopathways/Bionetworks |
| EIGENSOFT (“combines functionality from our population genetics methods […] and our EIGENSTRAT stratification correction method”) | EIGENSOFT development team, Harvard School of Public Health | Bioinformatics – Biomolecular Sequences/Structures; Exposure/Risk Analysis – Biomarkers |
| EIO-LCA – Economic Input-Output Life Cycle Assessment | Green Design Institute, Carnegie Mellon University, PA | Exposure/Risk Analysis – Socioeconomic/LSB Modeling |
| EJView (“mapping tool […] to create maps and generate detailed reports based on the geographic areas and data sets”) | USEPA | Enviroinformatics – Spatiotemporal Mapping/Analysis |
| ELECANS – A Computational Cancer Systems Biology Simulation Studio | Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Korea | Bioinformatics – Biological Dose-Response; Bioinformatics – Data Integration |
| EMA – e-Mouse Atlas | EMA team | Bioinformatics – Data Integration; Computational Toxicology – Virtual Model Organisms |
| EMAGE – e-Mouse Atlas of Gene Expression | EMAGE team | Bioinformatics – Biological Dose-Response; Computational Toxicology – Toxicoinformatics |
| EMAP – Environmental Monitoring and Assessment Program | USEPA | Enviroinformatics – Spatiotemporal Mapping/Analysis; Enviroinformatics – Release Mapping/Modeling |
| EMBER | University of Chicago | Bioinformatics – Biological Dose-Response |
| EMBOSS – European Molecular Biology Open Software Suite | EMBOSS 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 Medicine | Bioinformatics – Biomolecular Sequences/Structures |
| EMI – Exposure Model for Individuals | USEPA | Exposure/Risk Analysis – Microenvironmental/LCA Modeling; Exposure/Risk Analysis – Cumulative/Aggregate Exposures |
| EMS-HAP – Emissions Modeling System for Hazardous Pollutants | USEPA | Enviroinformatics – Release Mapping/Modeling |
| EMSOFT – Exposure Model for Soil-Organic Fate and Transport | RTP | Enviroinformatics – Environmental Fate and Transport; Exposure/Risk Analysis – Ecological Risks |
| ENA – European Nucleotide Archive | EMBL-EBI | Bioinformatics – Biomolecular Sequences/Structures |
| ENCODE – Encyclopedia Of DNA Elements | NHGRI, NIH | Bioinformatics – Biomolecular Sequences/Structures; Exposure/Risk Analysis – Biomarkers |
| Encom Discover (“desktop Geographical Information System”) | Encom and Pitney Bowes | Enviroinformatics – Spatiotemporal Mapping/Analysis; General Development Tools – Data Visualization |
| Encom Discover PA – Encom Discover Profile Analyst | Encom and Pitney Bowes | Enviroinformatics – Spatiotemporal Mapping/Analysis |
| Encom QuickMag (“magnetic modeling package”) | Encom and Pitney Bowes | Enviroinformatics – Spatiotemporal Mapping/Analysis |
| E-Net (“software for analyzing ego network data”) | Analytic Technologies | Exposure/Risk Analysis – Socioeconomic/LSB Modeling; General Development Tools – Data Visualization |
| Ensembl Genome Browser | EMBL-EBI and Wellcome Trust Sanger Institute, UK | Bioinformatics – Biomolecular Sequences/Structures |
| Entorama | Branimir Cace | General Development Tools – Development and Programming |
| Envirofacts (provides environmental information at a local area of interest) | USEPA | Enviroinformatics – Release Mapping/Modeling |
| Enviromapper for Envirofacts (“provides […] information about environmental activities that may affect air, water, and land anywhere in the US”) | USEPA | Enviroinformatics – Release Mapping/Modeling |
| Environmental Genome Project/ SNPs Program | NIEHS and University of Washington | Computational Toxicology – Toxicoinformatics |
| Envision (“A spatially explicit, distributed, multiagent-based framework for policy assessment and alternative futuring”) | Envision development team, Oregon State University | Enviroinformatics – Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis – Socioeconomic/LSB Modeling |
| EnvStats – Package for Environmental Statistics, including US EPA Guidance | S.P. Millard | Enviroinformatics – 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 Database | EMBL-EBI | |
| EP_GOS_Clust | Floudas Research Group, Princeton University | Data/Simulation Pattern Analysis – Classification/Clustering |
| EPA-Expo-Box – EPA’s EXPOsure toolBOX (“A Toolbox for Exposure Assessors”) | USEPA | Computational 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”) | USEPA | Enviroinformatics – Environmental Fate and Transport; Exposure/Risk Analysis – Microenvironmental/LCA Modeling |
| EPI – Estimation Program Interface Suite – suite of physical/chemical property and environmental fate estimation programs | USEPA | Enviroinformatics – Environmental Fate and Transport; Cheminformatics – Property/Activity Prediction |
| EpiGRAPH – for advanced (epi-) genome analysis and prediction | EpiGRAPH development team | Bioinformatics – Biomolecular Sequences/Structures; Bioinformatics – Biological Dose-Response; Exposure/Risk Analysis – Biomarkers |
| EpiSIM Platform | TIGA Center Heidelberg, Germany | Bioinformatics – 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 Registry | NIEHS | Computational 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 Geospatial | Enviroinformatics – Spatiotemporal Mapping/Analysis |
| ERDEM – Exposure Related Dose Estimating Model | USEPA | Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics |
| ERPG – Emergency Response Planning Guidelines | AIHA | Cheminformatics – Property/Activity Prediction |
| ESCAPE – Embryonic Stem Cells Atlas of Pluripotency Evidence | SBCNY and Mount Sinai School of Medicine | Bioinformatics – Data Integration |
| Esri Business Analyst | Esri | Enviroinformatics – Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis – Microenvironmental/LCA Modeling; Exposure/Risk Analysis – Socioeconomic/LSB Modeling |
| EuPathDB – Eukaryotic Pathogen Database Resources | EuPathDB Project Team | Exposure/Risk Analysis – Biomarkers; Exposure/Risk Analysis – Human Health Risks |
| European AirBase reporting stations | European Environment Agency | Enviroinformatics – Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis – Microenvironmental/LCA Modeling; Exposure/Risk Analysis – Cumulative/Aggregate Exposures |
| EUSES – European Union System for the Evaluation of Substances | European Commission, JRC, IHCP | Exposure/Risk Analysis – Microenvironmental/LCA Modeling |
| EVS Pro – Environmental Visualization System Pro – 3D Mapping | C Tech | Enviroinformatics – Spatiotemporal Mapping/Analysis; General Development Tools – Data Visualization |
| EwE – Ecopath with Ecosim | International Center for Living Aquatic Resources Management, Philippines | Exposure/Risk Analysis – Ecological Risks |
| EXAMS – Exposure Analysis Modeling System | USEPA | Enviroinformatics – Environmental Fate and Transport; Exposure/Risk Analysis – Ecological Risks |
| exaptive | Exaptive, Inc. | General Development Tools – Development and Programming |
| ExPASy (“SIB Bioinformatics Resource Portal”) | SIB – Swiss Institute of Bioinformatics | |
| ExpoCastDB – Exposure Forecaster Database | USEPA | Exposure/Risk Analysis – Microenvironmental/LCA Modeling; Exposure/Risk Analysis – Cumulative/Aggregate Exposures; Exposure/Risk Analysis – Biomarkers |
| ExpoFacts – European Exposure Factors Sourcebook | European Commission, JRC, IHCP | Exposure/Risk Analysis – Human Health Risks |
| EXPOLIS Database | Matti Jantunen, KTL Air Hygiene Laboratory, Finland | Exposure/Risk Analysis – Cumulative/Aggregate Exposures |
| Exposure Factors Handbook | USEPA | Exposure/Risk Analysis – Cumulative/Aggregate Exposures; Exposure/Risk Analysis – Human Health Risks |
| EXTOXNET – EXTension TOXicology NETwork | University of California, Davis, Oregon State University, Michigan State University, Cornell University, and University of Idaho | Computational Toxicology – Toxicoinformatics |
| FACET – Flavourings, Additives and food Contact materials Exposure Task | Creme Global and collaborators | Exposure/Risk Analysis – Microenvironmental/LCA Modeling |
| FACT – Flow And Contaminant Transport | Savannah River Technology Center and US DOE | Enviroinformatics – 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 Microbial | Exponent, Inc. and USFDA | Exposure/Risk Analysis – Human Health Risks |
| FASCAT – Food and Agriculture Sector Criticality Assessment Tool | National Center for Food Protection and Defense | |
| Fast Numerical Algorithms for Stiff Reaction-Diffusion Equations | University of California, Irvine | General Development Tools – Development and Programming |
| FASTA – DNA and protein sequence alignment software package | EMBL-EBI | Bioinformatics – Biomolecular Sequences/Structures |
| FastQC – Quality control tool for high throughput sequence data | Babraham Bioinformatics | Bioinformatics – Biomolecular Sequences/Structures |
| FDA-iRISK | USFDA | Exposure/Risk Analysis – Human Health Risks |
| FDALabel – Full-Text Search of Drug Label Database | USFDA | Bioinformatics – Biological Dose-Response |
| FGENESH – “Program for predicting multiple genes in genomic DNA sequences” | Softberry, Inc. and The Sanger Centre, Cambridge, UK | Bioinformatics – Biomolecular Sequences/Structures |
| FGETS – Food and Gill Exchange of Toxic Substances | USEPA | Exposure/Risk Analysis – Ecological Risks |
| FieldML | Auckland Bioengineering Institute, University of Auckland, NZ | Computational Toxicology – Virtual Cells, Tissues, Organs |
| FileMaker | Filemaker, Inc | General Development Tools – Development and Programming |
| FIRST – FQPA Index Reservoir Screening Tool | USEPA | Enviroinformatics – Environmental Fate and Transport; Exposure/Risk Analysis – Ecological Risks |
| FLAME – Flexible Large-scale Agent-based Modeling Environment | Software Engineering Group, CSED, STFC | Exposure/Risk Analysis – Socioeconomic/LSB Modeling; General Development Tools – Development and Programming |
| flexImaging | Bruker Daltonics | Exposure/Risk Analysis – Biomarkers |
| FlexX | BioSolveIT | Cheminformatics – 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, Germany | Bioinformatics – Interactions/Biopathways/Bionetworks |
| FlyBase – “A Database of Drosophila Genes & Genomes” | FlyBase development team | Computational Toxicology – Virtual Model Organisms |
| FlyMine – “integrated database for Drosophila and Anopheles genomics” | University of Cambridge, Cambridge, UK | Bioinformatics – 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 USe | FOCUS team, EU Commission | Enviroinformatics – Environmental Fate and Transport; Exposure/Risk Analysis – Ecological Risks |
| Food Environment Atlas | USDA | Exposure/Risk Analysis – Socioeconomic/LSB Modeling |
| Fortran | Free Software Foundation, Inc | General Development Tools – Development and Programming |
| FoundationOne | Foundation Medicine | Bioinformatics – Biomolecular Sequences/Structures; Bioinformatics – Data Integration |
| FRAMES-3MRA – Multimedia, Multi-pathway, Multi-receptor Exposure and Risk Assessment | USEPA | Enviroinformatics – Environmental Fate and Transport; Exposure/Risk Analysis – Cumulative/Aggregate Exposures; Exposure/Risk Analysis – Ecological Risks |
| freshwaterecology.info | Institute of Hydrobiology & Aquatic Ecosystem Management, Vienna | Exposure/Risk Analysis – Ecological Risks |
| FRS – Facility Registry System | USEPA | Enviroinformatics – Release Mapping/Modeling |
| FunDO (“Exploring Genes Using Functional Disease Ontology Annotations”) | Northwestern University Biomedical Informatics Center | Bioinformatics – Bio-Ontologies; Exposure/Risk Analysis – Biomarkers |
| GAC – Genetic Alterations in Cancer | NIEHS | Bioinformatics – 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 Areas | GADM development team | Enviroinformatics – 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 |
| GAMA | IRD/UPMC International Research Unit, UMMISCO | General Development Tools – Development and Programming |
| GARR – Gross Alpha Radium Regulation | USEPA | Enviroinformatics – 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 Wales | Enviroinformatics – Environmental Fate and Transport; Data/Simulation Pattern Analysis – Sensitivity/Uncertainty Analysis |
| GastroPlus | Simulations Plus Inc | Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics |
| GATK – Genome Analysis Toolkit | Broad Institute | Bioinformatics – Biomolecular Sequences/Structures |
| GBPCALC – Gross Beta Photon Calculator | USEPA | Enviroinformatics – Environmental Fate and Transport; Exposure/Risk Analysis – Ecological Risks |
| GBrowse (Generic Genome Browser) | GBrowse development team | Bioinformatics – Biomolecular Sequences/Structures |
| GeMDBJ – Genome Medicine Database of Japan | SGMGP (The Study Groups of Millennium Genome Project for Alzheimer’s disease, Cancer, Diabetes Mellitus, Hypertension, Asthma and Pharmacogenetics) | Bioinformatics – Biological Dose-Response; Exposure/Risk Analysis – Biomarkers; Exposure/Risk Analysis – Human Health Risks |
| GenAge Database | HAGR – Human Ageing Genomic Resources | Computational Toxicology – Virtual Model Organisms; Exposure/Risk Analysis – Biomarkers |
| GenBank | National Center for Biotechnology Information, NLM, NIH | Bioinformatics – Biomolecular Sequences/Structures; Exposure/Risk Analysis – Biomarkers |
| Gene Expression Atlas | EMBL-EBI | Bioinformatics – Biological Dose-Response; Exposure/Risk Analysis – Biomarkers |
| Gene Finder | NCI (National Cancer Institute), NIH | Exposure/Risk Analysis – Biomarkers |
| Gene Network Inference Tool | University of California, Irvine | Bioinformatics – Interactions/Biopathways/Bionetworks; Bioinformatics – Data Integration |
| Gene Weaver | Jackson Laboratory, ME and collaborators | Bioinformatics – Bio-Ontologies; Bioinformatics – Biological Dose-Response |
| GENEEC2 – Generic Estimated Environmental Concentration | USEPA | Enviroinformatics – Environmental Fate and Transport; Exposure/Risk Analysis – Ecological Risks |
| GeneLoc | Weizmann Institute of Science | Exposure/Risk Analysis – Biomarkers |
| GeneMANIA – “predict the function of […] genes and gene sets” | Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Canada | Bioinformatics – Biomolecular Sequences/Structures; Exposure/Risk Analysis – Biomarkers |
| Genes2FANs | SBCNY and Mount Sinai School of Medicine | Bioinformatics – Interactions/Biopathways/Bionetworks |
| GeneSpring | Agilent Technologies | Bioinformatics – Biomolecular Sequences/Structures; Exposure/Risk Analysis – Biomarkers |
| GeneTalk – “Analyze human sequence variants” | GeneTalk development team | Bioinformatics – Biomolecular Sequences/Structures |
| Genetic Association Database | GAD development team and NIH | Bioinformatics – Biomolecular Sequences/Structures |
| GeneTox | NLM | Cheminformatics – Property/Activity Prediction; Bioinformatics – Biological Dose-Response; Computational Toxicology – Toxicoinformatics; Exposure/Risk Analysis – Biomarkers |
| GenMAPP – Gene Map Annotator and Pathway Profiler | Gladstone Institutes, UCSF | Bioinformatics – Biomolecular Sequences/Structures; Bioinformatics – Interactions/Biopathways/Bionetworks |
| Genomatix Suite | Genomatix Software GmbH | Bioinformatics – Biomolecular Sequences/Structures; Bioinformatics – Biological Dose-Response; Exposure/Risk Analysis – Biomarkers |
| Genotyping Console | Affymetrix Inc | Bioinformatics – Biomolecular Sequences/Structures; Exposure/Risk Analysis – Biomarkers |
| GENSAT – Gene Expression Nervous System ATlas database | Rockefeller University | Bioinformatics – Biological Dose-Response; Exposure/Risk Analysis – Biomarkers |
| GENSCAN | Stanford University (C. Burge and S. Karlin) | Bioinformatics – Biomolecular Sequences/Structures |
| GeoLytics Demographics Estimates/ Projections | GeoLytics, Inc. | Enviroinformatics – Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis – Socioeconomic/LSB Modeling |
| GEON Integrated Data Viewer | UNAVCO | General Development Tools – Data Visualization |
| Geospiza GeneSifter Analysis Edition | Perkin Elmer | Bioinformatics – Biomolecular Sequences/Structures |
| Gepasi (see COPASI) | Virginia Bioinformatics Institute, Virginia Tech | Cheminformatics – 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 team | General Development Tools – Development and Programming |
| GerES – German Environmental Survey | The Federal Environment Agency, Germany | Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics; Exposure/Risk Analysis – Cumulative/Aggregate Exposures |
| GESTIS – International limit values for chemical agents | IFA – Institut fur Arbeitsschutz | Cheminformatics – Property/Activity Prediction |
| geWorkBench – Genomics Workbench | NCI (National Cancer Institute), NIH | Bioinformatics – Biomolecular Sequences/Structures; Bioinformatics – Interactions/Biopathways/Bionetworks; Data/Simulation Pattern Analysis – Classification/Clustering |
| GFBio – German Federation for the curation of Biological data | GFBio | Bioinformatics – Bio-Ontologies |
| GLEAMviz – Global Epidemic and Mobility model | Northeastern University, ISI Foundation and Indiana University | Exposure/Risk Analysis – Microenvironmental/LCA Modeling |
| GLIDA – GPCR-Ligand Database | Kyoto University | Bioinformatics – Biomolecular Sequences/Structures |
| GlimmerHMM | Center for Bioinformatics and Computational Biology, University of Maryland | Bioinformatics – Biomolecular Sequences/Structures |
| Globally Optimal Biclustering | Androulakis Laboratory, Rutgers University | Data/Simulation Pattern Analysis – Classification/Clustering |
| GMAP – Genomic Mapping and Alignment Program for mRNA and EST Sequences | Genentech, Inc., CA | Bioinformatics – Biomolecular Sequences/Structures |
| GMC impute – Gaussian mixture clustering impute | Computational Chemodynamics Laboratory | Bioinformatics – Biological Dose-Response; Data/Simulation Pattern Analysis – Classification/Clustering; Data/Simulation Pattern Analysis – Machine Learning Algorithms |
| GME – Geospatial Modelling Environment | Spatial Ecology LLC | Enviroinformatics – Spatiotemporal Mapping/Analysis |
| GMS – Groundwater Modeling System | Aquaveo | Enviroinformatics – Environmental Fate and Transport |
| GNA – Genetic Network Analyzer | Ibis | Bioinformatics – Interactions/Biopathways/Bionetworks |
| GNPD – Mintel Global New Products Database | Mintel Group Ltd. | Exposure/Risk Analysis – Microenvironmental/LCA Modeling |
| GO Database – Gene Ontology Database | Gene Ontology Consortium | Bioinformatics – Bio-Ontologies |
| GOFFA – Gene Ontology for Functional Analysis | USFDA | Bioinformatics – Bio-Ontologies; Computational Toxicology – Virtual Cells, Tissues, Organs |
| GOLD – Genomes Online Database | GOLD Team | Bioinformatics – Biomolecular Sequences/Structures |
| GoMiner | NCI (National Cancer Institute), NIH | Bioinformatics – Biomolecular Sequences/Structures |
| GoodGuide (“source of information on health, environmental, and social impacts of consumer products”) | GoodGuide team | Exposure/Risk Analysis – Microenvironmental/LCA Modeling |
| Google Earth Pro (“3D interactive globe that can be used to aid planning, analysis and decision making”) | Enviroinformatics – 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”) | Enviroinformatics – Spatiotemporal Mapping/Analysis; General Development Tools – Data Visualization | |
| GPCR NaVa database – G Protein-Coupled Receptors Natural Variants database | Leiden/Amsterdam Center for Drug Research and Leiden Institute of Advanced Computer Science | Bioinformatics – Biomolecular Sequences/Structures |
| GPCR SARfari (“integrated chemogenomics research and discovery workbench for Class A G Protein Coupled Receptors”) | EMBL-EBI | Bioinformatics – Biomolecular Sequences/Structures |
| GPCRDB – G Protein-Coupled Receptor Data Base | GPCRDB development team | Cheminformatics – Structure Elucidation; Bioinformatics – Biomolecular Sequences/Structures |
| GPCRHMM – “GPCR detection method” | Stockholm Bioinformatics Centre | Bioinformatics – Biomolecular Sequences/Structures |
| GPCR-OKB – G Protein Coupled Receptor – Oligomer Knowledge Base | GPCR-OKB development team | Bioinformatics – Biomolecular Sequences/Structures |
| GPCR-PD (“database for G protein-coupled receptors”) | Incyte Genomics | Bioinformatics – Biomolecular Sequences/Structures |
| GPCRTree – “hierarchical classification of GPCR function” | University of Oxford, UK | Bioinformatics – Biomolecular Sequences/Structures |
| gpDB – “database of GPCRs, G-proteins, effectors and their interactions” | University of Athens, Greece | Bioinformatics – Interactions/Biopathways/Bionetworks; Bioinformatics – Data Integration |
| GPU Codes for 3D Model of Epidermal Development | University of California, Irvine | Computational Toxicology – Virtual Cells, Tissues, Organs |
| GPUFRAGFOLD – Protein Structure Prediction tool | Bioinformatics Group, University College London | Cheminformatics – Structure Elucidation; Bioinformatics – Biomolecular Sequences/Structures |
| GRAM – Genetic RegulAtory Modules | Gifford Laboratory, MIT | Bioinformatics – Biomolecular Sequences/Structures; Bioinformatics – Interactions/Biopathways/Bionetworks |
| Grapher – “Graphing software” | Golden Software Inc. | General Development Tools – Data Visualization |
| GraphPad Prism | GraphPad Software, Inc. | General Development Tools – Data Visualization |
| Graphviz (“Graph Visualization Software”) | Graphviz Development Team | General Development Tools – Data Visualization |
| GRASS GIS – Geographic Resources Analysis Support System Geographic information system | Open Source Geospatial Foundation | Enviroinformatics – Spatiotemporal Mapping/Analysis |
| GRNN_Impute | Computational Chemodynamics Laboratory | Data/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 team | Enviroinformatics – Environmental Fate and Transport; Exposure/Risk Analysis – Ecological Risks |
| GS+ (“Geostatistics for the Environmental Sciences”) | Gamma Design Software | Enviroinformatics – Spatiotemporal Mapping/Analysis |
| GSEA – Gene Set Enrichment Analysis | Broad Institute | Bioinformatics – Biological Dose-Response |
| GSLIB – Geostatistical Software Library | Stanford University | Enviroinformatics – Spatiotemporal Mapping/Analysis |
| GSNAP – Genomic Short-read Nucleotide Alignment Program | Genentech, Inc., CA | Bioinformatics – Biomolecular Sequences/Structures |
| GUTS – General Unified Threshold model for Survival | GUTS team | Exposure/Risk Analysis – Ecological Risks |
| GVS – Genome Variation Server | University of Washington | Bioinformatics – Biomolecular Sequences/Structures; Exposure/Risk Analysis – Biomarkers |
| GWA – Ground Water Atlas | US Geological Survey | Enviroinformatics – Release Mapping/Modeling |
| GWAS Catalog – Genome-Wide Association Studies Catalog | NHGRI Division of Genomic Medicine, NIH | Bioinformatics – Data Integration; Exposure/Risk Analysis – Biomarkers |
| GWASdb | GWASdb team | Bioinformatics – Data Integration; Exposure/Risk Analysis – Biomarkers |
| Gwyddion (“a modular program for SPM (scanning probe microscopy) data visualization and analysis”) | Gwyddion development team | Bioinformatics – Data Integration; General Development Tools – Data Visualization |
| HADCM3 – Hadley Centre Coupled Model | The Hadley Centre for Climate Prediction and Research and USEPA | Enviroinformatics – Spatiotemporal Mapping/Analysis |
| Hadoop (“open-source software for […] scalable, distributed computing”) | The Apache Software Foundation | General Development Tools – Development and Programming |
| HAIR – HArmonized environmental Indicators for pesticide Risk | Alterra and Wageningen UR, The Netherlands | Exposure/Risk Analysis – Ecological Risks |
| HAPEM – Hazardous Air Pollutant Exposure Model | USEPA | Exposure/Risk Analysis – Cumulative/Aggregate Exposures |
| HapMap | International HapMap Project | Bioinformatics – Biomolecular Sequences/Structures; Exposure/Risk Analysis – Biomarkers |
| HazardExpert Pro | CompuDrug | Cheminformatics – Property/Activity Prediction |
| HCA – Hydrophobic Cluster Analysis | MobyleNet | |
| HDMFinder (“Methylation prediction software”) | Zhang Lab, Cold Spring Harbor Laboratory, NY | Bioinformatics – Biomolecular Sequences/Structures; Exposure/Risk Analysis – Biomarkers |
| Health Indicators Warehouse | National Center for Health Statistics | Enviroinformatics – Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis – Socioeconomic/LSB Modeling |
| HealthMap | Boston Children’s Hospital | Enviroinformatics – Spatiotemporal Mapping/Analysis |
| HEDS – Human Exposure Database System | USEPA | Exposure/Risk Analysis – Microenvironmental/LCA Modeling; Exposure/Risk Analysis – Cumulative/Aggregate Exposures; Exposure/Risk Analysis – Human Health Risks |
| HEP – Human Epigenome Project | HEP Consortium | Bioinformatics – Biological Dose-Response; Exposure/Risk Analysis – Biomarkers |
| HERO – Health and Environmental Research Online database | USEPA | Exposure/Risk Analysis – Human Health Risks; Exposure/Risk Analysis – Ecological Risks |
| HEROIC – High-Throughput Epigenetic Regulatory Organization in Chromatin Project | HEROIC Project Consortium | Bioinformatics – Biological Dose-Response; Exposure/Risk Analysis – Biomarkers |
| HexSim (previously PATCH) | USEPA | Exposure/Risk Analysis – Ecological Risks |
| HGMD – Human Gene Mutation Database (integrated with Ingenuity Variant Analysis) | BIOBASE | Bioinformatics – Biomolecular Sequences/Structures; Bioinformatics – Biological Dose-Response; Computational Toxicology – Toxicoinformatics; Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics; Exposure/Risk Analysis – Biomarkers |
| Histone Database | NHGRI Division of Intramural Research, NIH | Bioinformatics – Biomolecular Sequences/Structures; Bioinformatics – Data Integration |
| HIV Molecular Immunology Database | Los Alamos National Laboratory | Exposure/Risk Analysis – Biomarkers |
| HIV Sequence database | Los Alamos National Laboratory | Bioinformatics – Biomolecular Sequences/Structures; Exposure/Risk Analysis – Biomarkers |
| Hive (“data warehouse software”) | Apache Hive development team and The Apache Software Foundation | General Development Tools – Development and Programming |
| HLM – Hierarchical Linear and Nonlinear Modeling | Scientific 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 team | Bioinformatics – Biomolecular Sequences/Structures |
| HMMTOP (“Prediction of transmembrane helices and topology of proteins”) | HMMTOP team, Institute of Enzymology, Hungary | Bioinformatics – Biomolecular Sequences/Structures |
| HMPDACC Data Browser (Human Microbiome Project DACC Data Portal) | NIH Human Microbiome Project DACC | Exposure/Risk Analysis – Biomarkers |
| HomoloGene | National Center for Biotechnology Information, NLM, NIH | Bioinformatics – Biomolecular Sequences/Structures |
| Howard’s Handbook of Environmental Fate and Exposure Data for Organic Chemicals | Philip Hall Howard | Cheminformatics – Property/Activity Prediction |
| HPAC – Hazard Prediction and Assessment Capability | DTRA – Defense Threat Reduction Agency | Enviroinformatics – Environmental Fate and Transport |
| HPD – Household Products Database | National Library of Medicine | Enviroinformatics – Release Mapping/Modeling; Exposure/Risk Analysis – Microenvironmental/LCA Modeling |
| HPVIS – High Production Volume Information System | USEPA | Exposure/Risk Analysis – Microenvironmental/LCA Modeling |
| HSDB – Hazardous Substances Data Bank | National Library of Medicine | Cheminformatics – Property/Activity Prediction; Computational Toxicology – Toxicoinformatics |
| HSPF – Hydrological Simulation Program – FORTRAN | USEPA | Enviroinformatics – Environmental Fate and Transport |
| Human Anatomy Online | HowToMedia Inc | |
| Human DNA Polymerase Gamma Mutation Database | NIEHS | Bioinformatics – Biomolecular Sequences/Structures; Exposure/Risk Analysis – Biomarkers |
| Human Epigenome Atlas | Bioinformatics Research Laboratory, Baylor College of Medicine | Bioinformatics – Biological Dose-Response; Bioinformatics – Data Integration |
| Human Genome Browser | Genome Bioinformatics Group, UC Santa Cruz. | Bioinformatics – Biomolecular Sequences/Structures |
| HumanCyc | SRI International | Bioinformatics – Interactions/Biopathways/Bionetworks |
| Human-gpDB (“database of human GPCRs, G-proteins, Effectors and their interactions”) | Human-gpDB team | Bioinformatics – Interactions/Biopathways/Bionetworks; Bioinformatics – Data Integration |
| HuRef Genome Browser (Individual Human Genome Browser) | J. Craig Venter Institute | Bioinformatics – Biomolecular Sequences/Structures |
| HYPACT – Hybrid Particle And Concentration Transport Model | ATMET | Enviroinformatics – Environmental Fate and Transport |
| Hypertable (“open source database system”) | Hypertable Inc. | General Development Tools – Development and Programming |
| HYSPLIT – Hybrid Single Particle Lagrangian Integrated Trajectory Model | NOAA Air Resources Laboratory | Enviroinformatics – Environmental Fate and Transport |
| IAQX – Simulation Tool Kit for Indoor Air Quality and Inhalation Exposure | USEPA | Enviroinformatics – Environmental Fate and Transport |
| IARC Monographs- Classifications | IARC, WHO | Computational Toxicology – Toxicoinformatics; Exposure/Risk Analysis – Human Health Risks |
| IARC TP53 Database | IARC, WHO | Computational Toxicology – Toxicoinformatics; Exposure/Risk Analysis – Biomarkers |
| IBM SPSS Modeler | SPSS Inc. and IBM | Data/Simulation Pattern Analysis – Data Mining/Pattern Recognition |
| IBM SPSS Statistics | SPSS Inc. and IBM | General Development Tools – Development and Programming |
| ICIS – Integrated Compliance Information System | USEPA | Enviroinformatics – Release Mapping/Modeling |
| ICRP – International Commission on Radiological Protection – Database of Dose Coefficients | ICRP | Bioinformatics – Biological Dose-Response; Computational Toxicology – Toxicoinformatics; Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics; Exposure/Risk Analysis – Human Health Risks |
| ICSC – International Chemical Safety Cards | International Labour Organization | Cheminformatics – Property/Activity Prediction |
| icsiboost | icsiboost project team | Data/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 Depth | The Bioinformatics Research Group, University of Hong Kong | Bioinformatics – Biomolecular Sequences/Structures |
| IDEA – Infusing satellite Data into Environmental air quality Applications | NASA- EPA-NOAA partnership | Enviroinformatics – Spatiotemporal Mapping/Analysis; Enviroinformatics – Release Mapping/Modeling |
| iemHUB (“online community resource for those involved in the development, evaluation, and application of environmental models”) | iemHUB team | Enviroinformatics – Environmental Fate and Transport; Exposure/Risk Analysis – Microenvironmental/LCA Modeling; Exposure/Risk Analysis – Cumulative/Aggregate Exposures |
| IGSM – Integrated Global System Model | MIT Joint Program on the Science and Policy of Global Change and USEPA | Enviroinformatics – Environmental Fate and Transport |
| IGV – Integrative Genomics Viewer | Broad Institute | Bioinformatics – Biomolecular Sequences/Structures; Bioinformatics – Biological Dose-Response |
| IIPP – Inert Ingredients in Pesticide Products | USEPA | Cheminformatics – Property/Activity Prediction |
| Illumina GenomeStudio | Illumina Software | Bioinformatics – Biomolecular Sequences/Structures |
| ImageJ | ImageJ development team | General Development Tools – Data Visualization |
| IMGT – ImMunoGeneTics information system | Marie-Paule Lefranc | Bioinformatics – Biomolecular Sequences/Structures |
| IMGT/3Dstructure-DB – ImMunoGeneTics | Marie-Paule Lefranc | Bioinformatics – Biomolecular Sequences/Structures |
| Index Mundi – Maps | IndexMundi development team | Enviroinformatics – 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 ALignment | Eddy group, HHMI Janelia Farm Research Campus, VA | Bioinformatics – Biomolecular Sequences/Structures |
| Information Collection Rule Drinking Water Microbial And Disinfection Byproduct Information | USEPA | Enviroinformatics – Release Mapping/Modeling; Exposure/Risk Analysis – Microenvironmental/LCA Modeling |
| Ingenuity Variant Analysis | Qiagen | Bioinformatics – Biomolecular Sequences/Structures; Computational Toxicology – Toxicoinformatics; Exposure/Risk Analysis – Biomarkers |
| Integr8 | EMBL-EBI | Bioinformatics – Biomolecular Sequences/Structures |
| Interactive Lyme Disease Map | CDC | Enviroinformatics – Spatiotemporal Mapping/Analysis |
| InterNano | National Nanomanufacturing Network | Exposure/Risk Analysis – Microenvironmental/LCA Modeling; Exposure/Risk Analysis – Cumulative/Aggregate Exposures |
| InterPro | EMBL-EBI | Bioinformatics – Biomolecular Sequences/Structures |
| IONEX – Ion Exchange | USEPA | Exposure/Risk Analysis – Ecological Risks |
| IPA – Ingenuity Pathway Analysis | Qiagen N.V. | Bioinformatics – Interactions/Biopathways/Bionetworks; Bioinformatics – Biological Dose-Response; Computational Toxicology – Toxicoinformatics; Exposure/Risk Analysis – Biomarkers |
| iPathwayGuide | Advaita Corporation | Bioinformatics – Interactions/Biopathways/Bionetworks |
| iPathways | The Systems Biology Institute, Japan | Bioinformatics – Interactions/Biopathways/Bionetworks |
| iProClass | PIR – Protein Information Resource | Bioinformatics – Biomolecular Sequences/Structures |
| IPython – Shell interface for interactive computing in multiple programming languages | IPython development team | General Development Tools – Data Visualization |
| IRD – Influenza Research Database | IRD Project Team | Bioinformatics – Biomolecular Sequences/Structures; Exposure/Risk Analysis – Biomarkers |
| IRIS – Integrated Risk Information System | USEPA | Bioinformatics – Biological Dose-Response; Computational Toxicology – Toxicoinformatics; Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics; Exposure/Risk Analysis – Human Health Risks |
| ISDD – In vitro Sedimentation, Diffusion and Dosimetry model | PNNL | Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics |
| isee NetSim (Web-based Simulation Sharing for STELLA and iThink models) | isee Systems, Inc. | General Development Tools – Development and Programming |
| IsoConc | USEPA | Enviroinformatics – Environmental Fate and Transport; Exposure/Risk Analysis – Ecological Risks |
| IsoError | USEPA | Exposure/Risk Analysis – Ecological Risks |
| IsoSource | USEPA | Enviroinformatics – Environmental Fate and Transport; Exposure/Risk Analysis – Ecological Risks |
| iSTREEM | American Cleaning Institute | Exposure/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”) | USEPA | Enviroinformatics – Release Mapping/Modeling; Enviroinformatics – Environmental Fate and Transport; Exposure/Risk Analysis – Microenvironmental/LCA Modeling |
| Italian demographics data | ISTAT | Enviroinformatics – Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis – Socioeconomic/LSB Modeling |
| ITER – International Toxicity Estimates for Risk | National Library of Medicine | Cheminformatics – Property/Activity Prediction |
| iTOL – Interactive Tree Of Life | EMBL, Germany | Bioinformatics – Interactions/Biopathways/Bionetworks |
| IUPHAR-DB – International Union of Basic and Clinical Pharmacology Database | IUPHAR-DB development team | Bioinformatics – Data Integration; Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics; Exposure/Risk Analysis – Biomarkers |
| IUR data – Inventory Update Reporting data | USEPA | Enviroinformatics – Release Mapping/Modeling |
| J/maanova | Churchill Group, Jackson Laboratory | Bioinformatics – Biological Dose-Response |
| Jaguar (“ab initio electronic structure package”) | Schrödinger, LLC | Cheminformatics – Structure Elucidation; Cheminformatics – Property/Activity Prediction; Cheminformatics – Interaction/Reaction Modeling |
| Jason | Jason development team | General Development Tools – Development and Programming |
| Java | Oracle | General 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 team | Bioinformatics – Biological Dose-Response; General Development Tools – Data Visualization |
| JigCell | Virgina Tech | Computational Toxicology – Virtual Cells, Tissues, Organs |
| JILDT – Jason Induction of Logical Decison Trees | JILDT development team | General Development Tools – Development and Programming |
| J-MADeM – Multi-modal Agent Decision Making (library integrated into Jason) | MADeM development team | Exposure/Risk Analysis – Socioeconomic/LSB Modeling; General Development Tools – Development and Programming |
| jMOSAiCS – Joint Analysis of Multiple ChIP-seq Datasets | Keles Research Group, University of Wisconsin | Bioinformatics – Biomolecular Sequences/Structures; Bioinformatics – Biological Dose-Response; Exposure/Risk Analysis – Biomarkers |
| JPred | Barton Group, University of Dundee | Bioinformatics – Biomolecular Sequences/Structures |
| Jsim | Physiome Project, University of Washington | General Development Tools – Development and Programming |
| JSNP – Japanese Single Nucleotide Polymorphisms | University of Tokyo and the Japan Science and Technology Agency (JST) | Bioinformatics – Biomolecular Sequences/Structures; Exposure/Risk Analysis – Biomarkers |
| JSoar | Soar Technology, Inc. and Dave Ray | General Development Tools – Development and Programming |
| KABAM – Kow (based) Aquatic BioAccumulation Model | USEPA | Enviroinformatics – Environmental Fate and Transport; Exposure/Risk Analysis – Ecological Risks |
| Kalign | EMBL-EBI | Bioinformatics – Biomolecular Sequences/Structures |
| KEGG – Kyoto Encyclopedia of Genes and Genomes | Kanehisa Laboratories, Japan | Bioinformatics – Interactions/Biopathways/Bionetworks; Bioinformatics – Data Integration; Exposure/Risk Analysis – Biomarkers |
| KEGG DRUG | Kanehisa Laboratories, Japan | Exposure/Risk Analysis – Biomarkers |
| KEGG GENES database | Kanehisa Laboratories, Japan | Bioinformatics – Biomolecular Sequences/Structures; Bioinformatics – Interactions/Biopathways/Bionetworks |
| KEGG LIGAND database | Kanehisa Laboratories, Japan | Cheminformatics – Interaction/Reaction Modeling |
| KEGG MEDICUS | Kanehisa Laboratories, Japan | Computational Toxicology – Toxicoinformatics; Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics |
| KELVIN | Battelle Center for Mathematical Medicine, Nationwide Children’s Hospital, Ohio | Bioinformatics – Biomolecular Sequences/Structures; Bioinformatics – Data Integration |
| Kelviz | Battelle Center for Mathematical Medicine, Nationwide Children’s Hospital, Ohio | Bioinformatics – Biomolecular Sequences/Structures; Bioinformatics – Data Integration |
| Keyplayer (“Finding sets of key players in a network”) | Analytic Technologies | Exposure/Risk Analysis – Socioeconomic/LSB Modeling |
| Kirk-Othmer Encyclopedia of Chemical Technology | Wiley Online Library | Cheminformatics – Property/Activity Prediction |
| KNB – Knowledge Network for Biocomplexity | KNB team | Exposure/Risk Analysis – Ecological Risks |
| KNIME – Konstanz Information Miner | KNIME development team | General Development Tools – Development and Programming |
| KNN_Impute | Computational Chemodynamics Laboratory | Data/Simulation Pattern Analysis – Classification/Clustering |
| Krackplot (“Network visualization”) | Analytic Technologies | Exposure/Risk Analysis – Socioeconomic/LSB Modeling; General Development Tools – Data Visualization |
| KUPKB – The Kidney and Urinary Pathway Knowledge Base | INSERM, France and University of Manchester, UK | Bioinformatics – Interactions/Biopathways/Bionetworks; Bioinformatics – Data Integration; Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics; Exposure/Risk Analysis – Biomarkers |
| LandGEM – Landfill Gas Emissions Model | USEPA | Enviroinformatics – Release Mapping/Modeling |
| LandScan USA | Oak Ridge National Laboratory | Enviroinformatics – Spatiotemporal Mapping/Analysis |
| LandView | US Census Bureau | Enviroinformatics – Spatiotemporal Mapping/Analysis |
| Lange’s Handbook of Chemistry | McGraw-Hill | Cheminformatics – Property/Activity Prediction |
| Lazar – chemical toxicity prediction | In Silico Toxicology GmBH | Cheminformatics – Property/Activity Prediction |
| LibSBML/ JSBML – Programming library for C++, Java, Python and others | SBML Team | Computational Toxicology – Virtual Cells, Tissues, Organs |
| Lifeline | LifeLine Group | Exposure/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 Lab | Acumenta Biotech | Bioinformatics – Data Integration |
| LIVERTOX™ | NIDDK and NLM | Bioinformatics – Biological Dose-Response; Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics |
| LMPD – LIPID MAPS Proteome Database | University of California, San Diego | Bioinformatics – Biomolecular Sequences/Structures; Bioinformatics – Data Integration |
| LMSD – LIPID MAPS Structure Database | University of California, San Diego | Bioinformatics – Biomolecular Sequences/Structures; Bioinformatics – Data Integration |
| LOGKOW database | Sangster Research Laboratories, Canada | Cheminformatics – Property/Activity Prediction |
| LONI Atlases | Laboratory of Neuro Imaging, UCLA | |
| LSD (“platform for the development, use and distribution of simulations”) | Laboratory for Simulation Development | General Development Tools – Development and Programming |
| LSPC – Loading Simulation Program in C++ | USEPA | Enviroinformatics – Environmental Fate and Transport |
| LTKB – Liver Toxicity Knowledge Base | USFDA | Bioinformatics – Biological Dose-Response; Computational Toxicology – Toxicoinformatics |
| Lucene (“text search engine library”) | Apache Software Foundation | General Development Tools – Development and Programming |
| LUDEP – Lung Dose Evaluation Program | National Radiological Protection Board, UK | Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics |
| LULC – Land Use and Land Cover | US Geological Survey | Enviroinformatics – Spatiotemporal Mapping/Analysis |
| Mackay’s Handbook of Physical-Chemical Properties and Environmental Fate for Organic Chemicals | CRC Press | Cheminformatics – Property/Activity Prediction |
| Macromodel (“program for molecular modeling”) | Schrödinger, LLC | Cheminformatics – Interaction/Reaction Modeling |
| MACS – Model-based Analysis of ChIP-Seq data | Harvard University | Bioinformatics – Biomolecular Sequences/Structures |
| MADARA – Multi-Agent Distributed Adaptive Resource Allocation | madara development team | General Development Tools – Development and Programming |
| MADr-BMD – Model Averaging for Dichotomous Response Benchmark Dose | Wheeler and Bailer | Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics |
| MAExplorer – Microarray Explorer | MAExplorer development team | Bioinformatics – Biomolecular Sequences/Structures |
| MAGICC/SCENGEN – Model for the Assessment of Greenhouse Gas Induced Climate Change/Scenario Generator | National Center for Atmospheric Research | Enviroinformatics – Environmental Fate and Transport |
| MAKER (“portable and […] configurable genome annotation pipeline”) | Yandell Laboratory, University of Utah | Bioinformatics – Biomolecular Sequences/Structures |
| Mammalian Protein-Protein Interaction Database | Munich Information Center for Protein Sequences (MIPS), Institute of Bioinformatics and Systems Biology (IBIS), Germany | Bioinformatics – Biological Dose-Response |
| MapBox | MapBox team | Enviroinformatics – Spatiotemporal Mapping/Analysis; General Development Tools – Data Visualization |
| MapInfo Professional (“desktop mapping application”) | MapInfo and Pitney Bowes | Enviroinformatics – Spatiotemporal Mapping/Analysis; General Development Tools – Data Visualization |
| MapInfo Vertical Mapper (“tool for geospatial data analysis”) | MapInfo and Pitney Bowes | Enviroinformatics – Spatiotemporal Mapping/Analysis; General Development Tools – Data Visualization |
| Maple | MapleSoft | General Development Tools – Development and Programming |
| MapTales | MapTales team | General Development Tools – Data Visualization |
| MapUSA – Human mapping project | John Logan | Enviroinformatics – Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis – Socioeconomic/LSB Modeling |
| Maq – Mapping and Assembly with Quality | Maq development team | Bioinformatics – Biomolecular Sequences/Structures |
| MAQC – MicroArray Quality Control | USFDA | Bioinformatics – Biological Dose-Response |
| Maqview – graphical read alignment viewer | Maqview development team (Ruan et al.) | Bioinformatics – Biomolecular Sequences/Structures |
| Marathon | University of California, Irvine | Data/Simulation Pattern Analysis – Data Mining/Pattern Recognition |
| MariaDB | MariaDB Foundation | General Development Tools – Development and Programming |
| Marker Maps | NCI (National Cancer Institute), NIH | |
| MarkerView | AB Sciex | Exposure/Risk Analysis – Biomarkers |
| Mascot | Matrix Science | Bioinformatics – Biomolecular Sequences/Structures; Exposure/Risk Analysis – Biomarkers |
| MASON – Multi-Agent Simulator Of Neighborhoods | GMU Evolutionary Computation Laboratory and GMU Center for Social Complexity | Exposure/Risk Analysis – Socioeconomic/LSB Modeling; General Development Tools – Development and Programming |
| MASS – Multi-Agent Simulation Suite | AITIA International Inc | Exposure/Risk Analysis – Socioeconomic/LSB Modeling; General Development Tools – Development and Programming |
| MASTEP – Metapopulation model for Assessing Spatial and Temporal Effects of Pesticides | Alterra and Wageningen UR, The Netherlands | Exposure/Risk Analysis – Ecological Risks |
| MASyV – Multi-Agent System Visualization | MASyV development team | Exposure/Risk Analysis – Socioeconomic/LSB Modeling; General Development Tools – Development and Programming |
| Mathcad | PTC | General Development Tools – Development and Programming |
| Mathematica | Wolfram Research | General Development Tools – Development and Programming |
| MATLAB | The Mathworks, Inc. | General Development Tools – Development and Programming |
| MATLAB Bioinformatics Toolbox | The 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 Simulation | I.L.S.T.S., Technische Universität Berlin; I.T.P.S., Swiss Federal Institute of Technology, Zurich and Senozon | Enviroinformatics – Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis – Socioeconomic/LSB Modeling |
| maxdView | Manchester Bioinformatics | Bioinformatics – Biological Dose-Response; Computational Toxicology – Toxicoinformatics |
| Maximally Informative Genes | Androulakis Laboratory, Rutgers University | Bioinformatics – Interactions/Biopathways/Bionetworks |
| MCCEM – Multi-Chamber Concentration and Exposure Model | Versar Inc. and USEPA | Exposure/Risk Analysis – Microenvironmental/LCA Modeling |
| MCell – Monte Carlo cell | Pittsburgh Supercomputing Center and Computational Neurobiology Laboratory, Salk Institute | Computational Toxicology – Virtual Cells, Tissues, Organs |
| MCIP – Meteorology-Chemistry Interface Processor | USEPA | Enviroinformatics – Release Mapping/Modeling |
| MCSim | Free Software Foundation, Inc | Data/Simulation Pattern Analysis – Sensitivity/Uncertainty Analysis |
| MDscan – Motif Discovery scan | Stanford Medical Informatics, Stanford University | Bioinformatics – Biomolecular Sequences/Structures |
| MEANSIM – Mean Similarity Analysis | USEPA | Data/Simulation Pattern Analysis – Data Mining/Pattern Recognition |
| MEASURE – Mobile Emissions Assessment System for Urban and Regional Evaluation | Georgia Institute of Technology and USEPA | Enviroinformatics – Environmental Fate and Transport |
| MEGA – Molecular Evolutionary Genetics Analysis | MEGA team | Bioinformatics – Biomolecular Sequences/Structures |
| MEGAN – Model of Emissions of Gases and Aerosols from Nature | NCAR Earth System Laboratory | Enviroinformatics – Release Mapping/Modeling |
| MeInfoText | National Taiwan University | Bioinformatics – Biological Dose-Response; Bioinformatics – Data Integration; Exposure/Risk Analysis – Biomarkers |
| MEMSAT3 – MEMbrane protein Structure And Topology | MEMSAT team, University College London, UK | Bioinformatics – Biomolecular Sequences/Structures |
| MENTOR – Modeling ENvironment for TOtal Risk studies | Computational Chemodynamics Laboratory | Exposure/Risk Analysis – Biomarkers |
| MENTOR-1A – Modeling ENvironment for TOtal Risk studies in a One Atmosphere setting | Computational Chemodynamics Laboratory | Enviroinformatics – Environmental Fate and Transport |
| MENTOR-2E – Modeling ENvironment for TOtal Risk studies for Emergency Event applications | Computational Chemodynamics Laboratory | Exposure/Risk Analysis – Cumulative/Aggregate Exposures |
| MENTOR-3P – Modeling ENvironment for TOtal Risk studies using Physiologically-based Pharmacokinetic modeling tools for Population assessments | Computational Chemodynamics Laboratory | Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics |
| MENTOR-4M – Modeling ENvironment for TOtal Risk studies for Multiple co-occurring contaminants and Multimedia, Multipathway, Multiroute exposures | Computational Chemodynamics Laboratory | Enviroinformatics – Environmental Fate and Transport; Exposure/Risk Analysis – Cumulative/Aggregate Exposures |
| MENTOR-DOT – Modeling ENvironment for TOtal Risk studies Diagnostic and Optimization Tools | Computational Chemodynamics Laboratory | Data/Simulation Pattern Analysis – Data Mining/Pattern Recognition; Data/Simulation Pattern Analysis – Sensitivity/Uncertainty Analysis |
| MEPAS – Multimedia Environmental Pollutant Assessment System | Pacific Northwest National Laboratory | Enviroinformatics – Environmental Fate and Transport; Exposure/Risk Analysis – Cumulative/Aggregate Exposures |
| Merck Index | Merck & Co Inc | Cheminformatics – Property/Activity Prediction |
| Mercury Maps | USEPA | Exposure/Risk Analysis – Ecological Risks |
| MESOPUFF – Mesoscale Puff Model | USEPA | Enviroinformatics – Environmental Fate and Transport |
| MesoWest (Current and archived weather observations and summaries from across the United States) | Dept. of Atmos. Sci., University of Utah | Enviroinformatics – Spatiotemporal Mapping/Analysis; Enviroinformatics – Environmental Fate and Transport |
| MetaboliteTools | Bruker Daltonics | Exposure/Risk Analysis – Biomarkers |
| MetaCore | Thomson Reuters | Bioinformatics – Interactions/Biopathways/Bionetworks |
| MetaCyc | SRI International | Bioinformatics – Interactions/Biopathways/Bionetworks |
| MetaMerge (reconcile differences in existing metabolic network models) | MetaMerge development team | Bioinformatics – Interactions/Biopathways/Bionetworks |
| METAPC | Multicase Inc | Cheminformatics – Interaction/Reaction Modeling |
| MetaQTL | MetaQTL development team | Bioinformatics – Biomolecular Sequences/Structures |
| MetaSD (“A system dynamics model archive”) | MetaSD development team | General Development Tools – Development and Programming |
| MetaSite | Molecular Discovery | Cheminformatics – Interaction/Reaction Modeling |
| Meteor | Lhasa Limited | Cheminformatics – Interaction/Reaction Modeling; Bioinformatics – Interactions/Biopathways/Bionetworks |
| MethBase – a reference methylome database | Smith lab, Molecular and Computational Biology, U. of Southern California | Bioinformatics – Biomolecular Sequences/Structures |
| MethDB – database for DNA methylation and environmental epigenetic effects | MethDB team | Bioinformatics – Biological Dose-Response; Bioinformatics – Data Integration |
| MethPrimerDB | Ghent University, Belgium | Bioinformatics – Biological Dose-Response; Bioinformatics – Data Integration |
| MethTools | Leibniz Institute for Age Research – Fritz Lipmann Institute, Germany | Bioinformatics – Biological Dose-Response |
| MethyCancer – Database for studying human DNA Methylation and Cancer | Chinese Academy of Sciences | Bioinformatics – Biological Dose-Response; Exposure/Risk Analysis – Biomarkers |
| Methylator (“An SVM Based Method for DNA Methylation Prediction”) | Methylator Development Team | Bioinformatics – Biomolecular Sequences/Structures; Exposure/Risk Analysis – Biomarkers |
| MethyLogiX DNA methylation database | Epigenetics Group, Technical University of Munich, Germany (A. Schumacher) | Bioinformatics – Biological Dose-Response |
| MethylomeDB – Brain Methylome Database | Haghighi lab, Columbia University | Bioinformatics – Biomolecular Sequences/Structures |
| MetNetDB – MetNet Database | Iowa State University | Bioinformatics – Interactions/Biopathways/Bionetworks |
| MetNetGE | Iowa State University | Bioinformatics – Interactions/Biopathways/Bionetworks |
| Metworks | Thermo Scientific | Cheminformatics – Structure Elucidation |
| MeV – MultiExperiment Viewer | MeV development team | Bioinformatics – Biomolecular Sequences/Structures |
| MEXAlert | CompuDrug | Cheminformatics – Interaction/Reaction Modeling |
| MFFRST – Metal Finishing Facility Risk Screening Tool | USEPA | Exposure/Risk Analysis – Human Health Risks |
| Mgenome | Gu Laboratory, Iowa State University | Bioinformatics – Interactions/Biopathways/Bionetworks |
| MGI – Mouse Genome Informatics | The Jackson Laboratory, Maine and MGI team | Bioinformatics – 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 Search | NIEHS | Bioinformatics – Biomolecular Sequences/Structures |
| microBEnet – microbiology of the Built Environment network | Eisen Lab at University of California, Davis and Building Ecology Research Group | Bioinformatics – Data Integration; Exposure/Risk Analysis – Ecological Risks |
| microRNA.org | Bioinformatics – Biological Dose-Response; Exposure/Risk Analysis – Biomarkers | |
| MIDAS – Multi Instance Data Acquisition System | Science and Technology Facilities Council, UK | Bioinformatics – Biomolecular Sequences/Structures; Exposure/Risk Analysis – Biomarkers |
| MIEP – Modeling Immunity to Enteric Pathogens | Center for Modeling Immunity to Enteric Pathogens, Virginia Tech | Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics |
| Mimosa (“modeling and simulation platform”) | Mimosa development team and Cirad | General Development Tools – Development and Programming |
| Minitab | Minitab Inc. | General Development Tools – Development and Programming |
| MINT – Molecular INTeraction database | University of Rome Tor Vergata, Italy | Bioinformatics – Biomolecular Sequences/Structures; Bioinformatics – Interactions/Biopathways/Bionetworks |
| MINTEQA2 | USEPA and Jerry Allison, Computer Sciences Corp. | Enviroinformatics – Environmental Fate and Transport |
| MIRA – Whole Genome Shotgun and EST Sequence Assembler | Bastien Chevreux | Bioinformatics – Biomolecular Sequences/Structures |
| miRBase – microRNA database | Griffiths-Jones lab, U. of Manchester and Wellcome Trust Sanger Institute | Bioinformatics – Biomolecular Sequences/Structures |
| miRBase (“the microRNA database”) | University of Manchester, UK | Bioinformatics – 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 University | Bioinformatics – Biomolecular Sequences/Structures |
| Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer | University Hospital, Lund, Sweden | Exposure/Risk Analysis – Biomarkers |
| MLC++ | Silicon Graphics International Corp., CA | Data/Simulation Pattern Analysis – Machine Learning Algorithms |
| MM5 or PSU/NCAR mesoscale model | Pennsylvania State University National Center for Atmospheric Research | Enviroinformatics – Environmental Fate and Transport |
| MMDB – Molecular Modeling Database (NCBI Structure) | National Center for Biotechnology Information, NLM, NIH | Cheminformatics – Structure Elucidation; Bioinformatics – Biomolecular Sequences/Structures |
| MMG – Medical Management Guidelines | ATSDR, CDC | Cheminformatics – Property/Activity Prediction |
| MOABS – MOdel based Analysis of Bisulfite Sequencing data | Deqiang Sun, Baylor College of Medicine | Bioinformatics – Biomolecular Sequences/Structures; Bioinformatics – Biological Dose-Response; Exposure/Risk Analysis – Biomarkers |
| Mobidyc – MOdelling Based on Individuals for the DYnamics of Communities | Mobidyc development team | Exposure/Risk Analysis – Socioeconomic/LSB Modeling; General Development Tools – Development and Programming |
| MOBILE | USEPA | Enviroinformatics – Release Mapping/Modeling |
| MobyDick | The Rockefeller University | Bioinformatics – Biomolecular Sequences/Structures |
| Model Builder | Flavio Coelho | General Development Tools – Development and Programming |
| ModelAssist (for @RISK and Crystal Ball) | Vose Software, Belgium | Data/Simulation Pattern Analysis – Sensitivity/Uncertainty Analysis |
| ModelMaker | The University of Nottingham and FamilyGenetix | General Development Tools – Development and Programming |
| ModelMaker Tools | ModelMaker Tools | General Development Tools – Development and Programming |
| ModelRisk | Vose Software, Belgium | Data/Simulation Pattern Analysis – Sensitivity/Uncertainty Analysis |
| Models-3 Technical Support Forum | CMAS Center | Enviroinformatics – Environmental Fate and Transport |
| modENCODE – Model Organism ENCyclopedia Of DNA Elements | modENCODE Project Consortium | Bioinformatics – Biomolecular Sequences/Structures; Computational Toxicology – Virtual Model Organisms |
| Modflow | US Geological Survey | Enviroinformatics – Environmental Fate and Transport |
| Modgen – Model generator | Statistics Canada | General Development Tools – Development and Programming |
| MODIS Satellite Land, Ocean, Atmosphere Products | NASA | Enviroinformatics – Spatiotemporal Mapping/Analysis |
| modMine (“data warehouse for the modENCODE project”) | University of Cambridge, Cambridge, UK | Bioinformatics – Biomolecular Sequences/Structures; Computational Toxicology – Virtual Model Organisms |
| MOE – Molecular Operating Environment | Chemical Computing Group | Cheminformatics – Property/Activity Prediction |
| MoKa | Molecular Discovery Ltd | Cheminformatics – Property/Activity Prediction |
| Mold2 | USFDA | Bioinformatics – Biomolecular Sequences/Structures |
| MonetDB (“open source column-oriented database management system”) | MonetDB development team | General 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 Exactly | MONGOOSE development team, MIT | Bioinformatics – Interactions/Biopathways/Bionetworks |
| Monocle – toolkit for analyzing single-cell gene expression experiments | Cole Trapnell | Bioinformatics – Biological Dose-Response; Exposure/Risk Analysis – Biomarkers |
| Moose – Multiscale Neuroscience and Systems Biology Simulator | Moose team | Bioinformatics – 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, Germany | Bioinformatics – Data Integration; Computational Toxicology – Virtual Cells, Tissues, Organs |
| MOSAiCS – MOdel-based one and two Sample Analysis and Inference for ChIP-Seq Data | Keles Research Group, University of Wisconsin | Bioinformatics – Biomolecular Sequences/Structures; Bioinformatics – Biological Dose-Response; Exposure/Risk Analysis – Biomarkers |
| Mouse Genome Resequencing Project | NIEHS | Bioinformatics – Biomolecular Sequences/Structures; Computational Toxicology – Virtual Model Organisms |
| MouseMine | MGI at The Jackson Laboratory and InterMine project at Cambridge Systems Biology Centre, UK | Bioinformatics – Bio-Ontologies; Bioinformatics – Interactions/Biopathways/Bionetworks; Bioinformatics – Biological Dose-Response; Computational Toxicology – Virtual Model Organisms |
| MOVES – Motor Vehicle Emission Simulator | USEPA | Enviroinformatics – Release Mapping/Modeling |
| MPPD – Multiple-Path Particle Dosimetry Model | Applied Research Associates | Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics |
| MrBayes | MrBayes development team | Bioinformatics – Biomolecular Sequences/Structures |
| mrsFAST (short-read mapper) | mrsFAST development team | Bioinformatics – Biomolecular Sequences/Structures |
| MSDS – Material Safety Data Sheets | 3E Company | Cheminformatics – Property/Activity Prediction |
| MT3DMS – Modular 3-D Multi-Species Transport model (previously MT3D) | S.S. Papadopulos & Associates, Inc. and USEPA | Enviroinformatics – Environmental Fate and Transport |
| MUSCLE – MUltiple Sequence Comparison by Log- Expectation | EMBL-EBI | Bioinformatics – Biomolecular Sequences/Structures |
| Mussel Watch Program | Center for Coastal Monitoring and Assessment, National Ocean Service | Exposure/Risk Analysis – Ecological Risks |
| MySQL | Oracle | General Development Tools – Development and Programming |
| mzMINE | MZmine team (open-source) | Exposure/Risk Analysis – Biomarkers |
| NACJD – National Archive of Criminal Justice Data | ICPSR, University of Michigan | Enviroinformatics – Spatiotemporal Mapping/Analysis |
| NADP – National Atmospheric Deposition Program | National Atmospheric Deposition Program | Enviroinformatics – Spatiotemporal Mapping/Analysis |
| Nanomaterial Registry | RTI International | Exposure/Risk Analysis – Microenvironmental/LCA Modeling |
| Nanowerk Nanotechnology Products and Applications | Nanowerk | Exposure/Risk Analysis – Microenvironmental/LCA Modeling |
| NAPA – North American Plant Atlas | Biota of North America Program (BONAP) | Enviroinformatics – Spatiotemporal Mapping/Analysis |
| NASQAN – National Stream Quality Accounting Network | US Geological Survey | Enviroinformatics – Release Mapping/Modeling |
| NATA – National Air Toxics Assessments | USEPA | Enviroinformatics – 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 Interior | Enviroinformatics – Spatiotemporal Mapping/Analysis |
| National Geochemical Survey | US Geological Survey | Enviroinformatics – Spatiotemporal Mapping/Analysis; Enviroinformatics – Release Mapping/Modeling |
| National Lake Fish Tissue Study | USEPA | Exposure/Risk Analysis – Ecological Risks |
| National Listing of Fish Advisories Database | USEPA | Exposure/Risk Analysis – Ecological Risks |
| National Nutrient Database for Standard Reference | USDA | Exposure/Risk Analysis – Microenvironmental/LCA Modeling |
| National Status & Trends in Coastal Zones | Center for Coastal Monitoring and Assessment, National Ocean Service | Exposure/Risk Analysis – Ecological Risks |
| National Toxicology Program Technical Reports | NIEHS | Computational Toxicology – Toxicoinformatics; Exposure/Risk Analysis – Human Health Risks |
| NAWQA – National Water-Quality Assessment Program | US Geological Survey | Enviroinformatics – Spatiotemporal Mapping/Analysis; Enviroinformatics – Release Mapping/Modeling |
| NCAR Graphics | University Corporation for Atmospheric Research | General Development Tools – Data Visualization |
| NCBI Epigenomics | National Center for Biotechnology Information, NLM, NIH | Bioinformatics – Biological Dose-Response; Bioinformatics – Data Integration |
| NCBI Gene | National Center for Biotechnology Information, NLM, NIH | Bioinformatics – Biomolecular Sequences/Structures |
| NCBI GEO – NCBI Gene Expression Omnibus database | National Center for Biotechnology Information, NLM, NIH | Bioinformatics – Biological Dose-Response; Exposure/Risk Analysis – Biomarkers |
| NCBI Model Organisms Guide | National Center for Biotechnology Information, NLM, NIH | Bioinformatics – Biomolecular Sequences/Structures; Computational Toxicology – Virtual Model Organisms |
| NCBI Nucleotide Sequence Database | National Center for Biotechnology Information, NLM, NIH | Bioinformatics – Biomolecular Sequences/Structures |
| NCBI/ Primer-BLAST | National Center for Biotechnology Information, NLM, NIH | Bioinformatics – Biomolecular Sequences/Structures |
| NCDC – NOAA National Climatic Data Center | NOAA | Enviroinformatics – Environmental Fate and Transport |
| NCFAP Pesticide Use Database | National Center for Food and Agricultural Policy (NCFAP) | Enviroinformatics – Release Mapping/Modeling |
| NCHS – National Center for Health Statistics Data | CDC | Enviroinformatics – Spatiotemporal Mapping/Analysis |
| NCI DIS 3D – National Cancer Institute Drug Information System 3D structure database | NCI (National Cancer Institute), NIH | Cheminformatics – Structure Elucidation; Bioinformatics – Biomolecular Sequences/Structures |
| NCI State Cancer Profiles | NCI (National Cancer Institute), NIH | Enviroinformatics – Spatiotemporal Mapping/Analysis |
| NCOD – National Contaminant Occurrence Database | USEPA | Exposure/Risk Analysis – Microenvironmental/LCA Modeling |
| NCTRlcdb – NCTR Liver Cancer Database | USFDA | Computational 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 University | Bioinformatics – Biomolecular Sequences/Structures |
| NED – National Elevation Dataset | US Geological Survey | Enviroinformatics – Spatiotemporal Mapping/Analysis |
| NEI – National Emissions Inventory | USEPA | Enviroinformatics – 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 Technologies | Exposure/Risk Analysis – Socioeconomic/LSB Modeling; General Development Tools – Data Visualization |
| NetLogo | Uri Wilensky, Center for Connected Learning | Exposure/Risk Analysis – Socioeconomic/LSB Modeling; General Development Tools – Development and Programming |
| NetRecodon | NetRecodon development team | Bioinformatics – Biomolecular Sequences/Structures |
| Network | Fluxus Technology Ltd. | Bioinformatics – Interactions/Biopathways/Bionetworks; General Development Tools – Development and Programming |
| Neurodatabase | Weill Medical College, Cornell University | |
| NEURON (“for empirically-based simulations of neurons and networks of neurons”) | NEURON development team | Bioinformatics – Interactions/Biopathways/Bionetworks; Computational Toxicology – Virtual Cells, Tissues, Organs |
| Newbler (“software package for de novo DNA sequence assembly”) | 454 Life Sciences, Roche Diagnostics Corporation | Bioinformatics – Biomolecular Sequences/Structures |
| NewHybrids | NewHybrids development team | Bioinformatics – Data Integration |
| NGA – National Geochemical Atlas | USGS | Enviroinformatics – Spatiotemporal Mapping/Analysis |
| NGSmethDB – A database for next-generation sequencing single-cytosine-resolution DNA methylation database | Computational Genomics and Bioinformatics Group, U. Granada, Spain | Bioinformatics – Biomolecular Sequences/Structures |
| NHANES – National Health and Nutrition Examination Survey | CDC | Computational 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 Survey | USEPA | Enviroinformatics – Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis – Socioeconomic/LSB Modeling |
| NHATS – National Human Adipose Tissue Survey | USEPA | Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics; Exposure/Risk Analysis – Biomarkers |
| NHEXAS – National Human Exposure Assessment Survey (project completed) | USEPA | Exposure/Risk Analysis – Microenvironmental/LCA Modeling; Exposure/Risk Analysis – Cumulative/Aggregate Exposures; Exposure/Risk Analysis – Biomarkers |
| NHPN – National Highway Planning Network | US Department of Transportation | Enviroinformatics – Spatiotemporal Mapping/Analysis |
| NIEHS SNPs Exome Variant Server | NIEHS and University of Washington | Bioinformatics – Biomolecular Sequences/Structures; Exposure/Risk Analysis – Biomarkers |
| NIH Human Microbiome Project (HMP) Roadmap Project | National Center for Biotechnology Information, NLM, NIH | Exposure/Risk Analysis – Biomarkers |
| NIH Model Organisms for Biomedical Research | NIH | Computational Toxicology – Virtual Model Organisms |
| NIH Roadmap Epigenomics Project Data | National Center for Biotechnology Information, NLM, NIH | Bioinformatics – Biological Dose-Response |
| NIMH-RGR Data Explorer | NIMH Center for Collaborative Genomic Studies on Mental Disorders | Bioinformatics – Data Integration; Exposure/Risk Analysis – Biomarkers |
| NIST Chemistry WebBook | NIST | Cheminformatics – Structure Elucidation; Cheminformatics – Property/Activity Prediction |
| NJ-HSFS – Right to Know Hazardous Substance Fact Sheets | NJ Department of Health | Cheminformatics – Property/Activity Prediction |
| NJ-RTKHSL – Right to Know Hazardous Substance List | NJ Department of Health | Cheminformatics – Property/Activity Prediction |
| NLCD – National Land Cover Dataset | US Geological Survey | Enviroinformatics – Spatiotemporal Mapping/Analysis |
| NLM ChemIDplus Advanced | National Library of Medicine | Cheminformatics – Property/Activity Prediction |
| NMFS – National Marine Fisheries Service | NOAA | Enviroinformatics – Spatiotemporal Mapping/Analysis |
| NMPDR – National Microbial Pathogen Data Resource (no longer maintained; see PATRIC) | NMPDR Project Team | Exposure/Risk Analysis – Biomarkers |
| NMRShiftDB | nmrshiftdb2 development team | Cheminformatics – Structure Elucidation |
| NOES – National Occupational Exposure Survey | CDC – NIOSH | Exposure/Risk Analysis – Microenvironmental/LCA Modeling |
| Nonhuman Primate HIV/SIV Vaccine Trials Database | Los Alamos National Laboratory | Exposure/Risk Analysis – Biomarkers |
| NONMEM | ICON Development Solutions and Regents of the University of California | Computational Toxicology – Toxicoinformatics; Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics |
| Novoalign | Novocraft Technologies | Bioinformatics – Biomolecular Sequences/Structures |
| NPDWR – National Primary Drinking Water Regulations | USEPA | Exposure/Risk Analysis – Microenvironmental/LCA Modeling |
| NPG – NIOSH Pocket Guide to Chemical Hazards | CDC – NIOSH | Cheminformatics – Property/Activity Prediction |
| NPIRS – National Pesticide Information Retrieval System | Purdue University | Enviroinformatics – Release Mapping/Modeling |
| NRWQC – National Recommended Water Quality Criteria | USEPA | Enviroinformatics – Release Mapping/Modeling |
| NSL – Neural Simulation Language | NSL Development Team | Bioinformatics – Interactions/Biopathways/Bionetworks |
| NSQS – National Sediment Quality Survey | USEPA | Enviroinformatics – 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 data | Keles Research Group, University of Wisconsin | Bioinformatics – Biomolecular Sequences/Structures; Bioinformatics – Biological Dose-Response; Exposure/Risk Analysis – Biomarkers |
| NuPoP – Nucleosome Positioning Prediction Engine | Northwestern University (J.-P. Wang) | Bioinformatics – Biomolecular Sequences/Structures |
| NWIS – National Water Information System | US Geological Survey | Enviroinformatics – Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis – Microenvironmental/LCA Modeling |
| NWPCAM – Nation Water Pollution Control Assessment Model | USEPA | Enviroinformatics – Environmental Fate and Transport; Exposure/Risk Analysis – Ecological Risks |
| NWS – National Weather Service | NOAA | Enviroinformatics – Environmental Fate and Transport |
| Objective C | Apple | General Development Tools – Development and Programming |
| OChD – OSHA Occupational Chemical Database | OSHA | Cheminformatics – Property/Activity Prediction |
| OChem – Online Chemical database | eADMET GmbH, Germany | Cheminformatics – Property/Activity Prediction; Bioinformatics – Biomolecular Sequences/Structures |
| Octave | John W. Eaton | General Development Tools – Development and Programming |
| OECD Existing Chemicals Database | OECD Secretariat | Enviroinformatics – Release Mapping/Modeling |
| OmicBrowse | Genome-Phenome Superbrain Project | Bioinformatics – Data Integration |
| OmicsOffice for Microarrays | Integromics | Bioinformatics – 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, NIH | Bioinformatics – Data Integration; Exposure/Risk Analysis – Biomarkers |
| Omix | Peter Droste | Cheminformatics – Interaction/Reaction Modeling; Bioinformatics – Interactions/Biopathways/Bionetworks |
| OncoLogic – Evaluate the carcinogenic potential of chemicals | USEPA | Cheminformatics – Property/Activity Prediction |
| Oncomine | Life Technologies Corporation | Bioinformatics – Biological Dose-Response; Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics; Exposure/Risk Analysis – Biomarkers |
| Online SMILES Translator and Structure File Generator | CADD Group, Chemical Biology Laboratory, NCI | Cheminformatics – Structure Elucidation |
| OpenCell (for CellML models) | Auckland Bioengineering Institute, University of Auckland, NZ | Computational Toxicology – Virtual Cells, Tissues, Organs |
| OpenCMISS/CM – Open Continuum Mechanics, Imaging, Signal processing and System identification | Auckland Bioengineering Institute, University of Auckland, NZ | Computational Toxicology – Virtual Cells, Tissues, Organs |
| OpenFLUX (“MATLAB-based modelling software for 13C metabolic flux analysis”) | OpenFLUX development team | Bioinformatics – Interactions/Biopathways/Bionetworks |
| OpenFOAM | OpenCFD Ltd, ESI Group | Exposure/Risk Analysis – Microenvironmental/LCA Modeling |
| OpenGL (“developing portable, interactive 2D and 3D graphics applications”) | Silicon Graphics International Corp. (SGI) and Khronos Group | General Development Tools – Data Visualization |
| OpenModel | The University of Nottingham | General Development Tools – Development and Programming |
| OpenStreetMap (“OpenStreetMap is […] data about roads, trails, cafés, railway stations, and much more, all over the world”) | OpenStreetMap team | Enviroinformatics – Spatiotemporal Mapping/Analysis |
| OpenTox | OpenTox project team | Computational Toxicology – Toxicoinformatics |
| OpenWorm | OpenWorm development team | Computational Toxicology – Virtual Cells, Tissues, Organs; Computational Toxicology – Virtual Model Organisms |
| OptiRNA | University of Nebraska | Bioinformatics – Biomolecular Sequences/Structures |
| Oracle | Oracle | General Development Tools – Development and Programming |
| Orange | Bioinformatics Laboratory, University of Ljubljana, Slovenia | Data/Simulation Pattern Analysis – Data Mining/Pattern Recognition; Data/Simulation Pattern Analysis – Classification/Clustering; Data/Simulation Pattern Analysis – Machine Learning Algorithms |
| ORDB – Olfactory Receptor DataBase | Yale University | Bioinformatics – Biomolecular Sequences/Structures |
| Origin | OriginLab Corporation | General Development Tools – Development and Programming; General Development Tools – Data Visualization |
| OriginPro | OriginLab Corporation | General Development Tools – Development and Programming; General Development Tools – Data Visualization |
| Ortelius (mapping software for Mac OS X) | Mapdiva, LLC | Enviroinformatics – Spatiotemporal Mapping/Analysis; General Development Tools – Data Visualization |
| OrthoDB | University of Geneva Medical School, Switzerland | Bioinformatics – Interactions/Biopathways/Bionetworks |
| Osprey | Samuel Lunenfeld Research Institute, Canada | Bioinformatics – Interactions/Biopathways/Bionetworks |
| P2P – Pollution Prevention Progress (see TRACI) | USEPA | Enviroinformatics – Environmental Fate and Transport; Exposure/Risk Analysis – Microenvironmental/LCA Modeling; Exposure/Risk Analysis – Ecological Risks |
| P3M – Physiological Parameters for PBPK Modeling | The LifeLine Group | Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics |
| PAC – Protective Action Criteria | USDOE | Cheminformatics – Property/Activity Prediction |
| PaGE – Patterns from Gene Expression | PaGE development team, University of Pennsylvania | Bioinformatics – Biomolecular Sequences/Structures |
| Pajek | Batagelj et al., University of Ljubljana, Slovenia | Exposure/Risk Analysis – Socioeconomic/LSB Modeling; General Development Tools – Development and Programming |
| PAM – Prediction Analysis for Microarrays | Stanford University | Bioinformatics – Biomolecular Sequences/Structures |
| Pan Asian SNP Database | Pan-Asian SNP Consortium | Bioinformatics – Biomolecular Sequences/Structures; Exposure/Risk Analysis – Biomarkers |
| Pandora (“HPC Agent-Based Modelling framework”) | Barcelona Supercomputing Center | Exposure/Risk Analysis – Socioeconomic/LSB Modeling; General Development Tools – Development and Programming |
| PANTHER – Protein ANalysis THrough Evolutionary Relationships | PANTHER development team (Paul Thomas) | Bioinformatics – Interactions/Biopathways/Bionetworks; Bioinformatics – Data Integration |
| ParaView | ParaView project team | General Development Tools – Data Visualization |
| PATCH – Program to Assist in Tracking Critical Habitat (see HexSim) | USEPA | Exposure/Risk Analysis – Ecological Risks |
| PathArt | Jubilant Biosys | Bioinformatics – Interactions/Biopathways/Bionetworks |
| PathCase Pathways Database System | Case Western Reserve University | Bioinformatics – Interactions/Biopathways/Bionetworks |
| Pathogen Portal | Pathogen Portal Project Team | Exposure/Risk Analysis – Biomarkers |
| Pathophysiology of the Digestive System | Colorado State University | Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics |
| Pathophysiology of the Endocrine System | Colorado State University | Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics |
| PathVisio (“a tool to edit and analyze biological pathways”) | PathVisio development team | Bioinformatics – Interactions/Biopathways/Bionetworks |
| Pathway Commons | Memorial Sloan-Kettering Cancer Center and University of Toronto | Bioinformatics – Interactions/Biopathways/Bionetworks |
| Pathway Database | Protein Lounge | Bioinformatics – Interactions/Biopathways/Bionetworks |
| Pathway Map Creator | Thomson Reuters | Bioinformatics – Interactions/Biopathways/Bionetworks |
| Pathway Processor | Istituto Agrario di San Michele all’Adige, Italy | Bioinformatics – Interactions/Biopathways/Bionetworks |
| Pathway Studio | Pathway Studio | Bioinformatics – Interactions/Biopathways/Bionetworks; Bioinformatics – Biological Dose-Response; Computational Toxicology – Toxicoinformatics |
| Pathway Tools | Pathway Tools development team | Bioinformatics – Interactions/Biopathways/Bionetworks |
| PathwayLab – in silico pathway analysis tool | Innetics | Cheminformatics – Interaction/Reaction Modeling; Bioinformatics – Interactions/Biopathways/Bionetworks |
| PatientsLikeMe (network of patients sharing experiences on diseases) | PatientsLikeMe team | Exposure/Risk Analysis – Human Health Risks |
| PATRIC – Pathosystems Resource Integration Center | PATRIC Project Team | Bioinformatics – Data Integration; Exposure/Risk Analysis – Biomarkers |
| PAYAOLOGUE | SBI and OIST, Japan; PathText | Bioinformatics – Interactions/Biopathways/Bionetworks |
| PCRAMMET | USEPA | Enviroinformatics – Environmental Fate and Transport |
| PCS-ICIS – Permit Compliance System and Integrated Compliance Information System | USEPA | Enviroinformatics – Release Mapping/Modeling |
| PD map – Parkinson’s disease map | LCSB and Hiroaki Kitano team at SBI, Tokyo | Bioinformatics – Interactions/Biopathways/Bionetworks; Computational Toxicology – Toxicoinformatics; Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics; Exposure/Risk Analysis – Biomarkers |
| PDB – Protein Data Bank | RCSB PDB (Rutgers University, UCSD) | Bioinformatics – Biomolecular Sequences/Structures |
| PDP – Pesticide Data Program | USDA ARS | Exposure/Risk Analysis – Microenvironmental/LCA Modeling |
| PEARL – Pesticide Emission Assessment at Regional and Local scales, GeoPEARL | Alterra, PBL and RIVM | Enviroinformatics – Environmental Fate and Transport; Exposure/Risk Analysis – Ecological Risks |
| pepgrep | University of Essex | Bioinformatics – Biomolecular Sequences/Structures |
| Peptide Atlas | PeptideAtlas team, Institute for Systems Biology | Bioinformatics – Biomolecular Sequences/Structures |
| Perl | Perl development team | General Development Tools – Development and Programming |
| PERPEST – Predicts the Ecological Risks of PESTicides in freshwater ecosystems | Alterra and Wageningen UR, The Netherlands | Exposure/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-bank | Marshfield Clinic Research Foundation | Bioinformatics – Biological Dose-Response; Bioinformatics – Data Integration |
| PEST – Parameter ESTimation | PEST development team | Data/Simulation Pattern Analysis – Sensitivity/Uncertainty Analysis |
| PFAAT – Protein Family Alignment Annotation Tool | PFAAT development team | Bioinformatics – Biomolecular Sequences/Structures |
| PFAM – Pesticides in Flooded Application Model | USEPA | Enviroinformatics – 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, US | Bioinformatics – Biomolecular Sequences/Structures |
| PharmGKB – Pharmacogenomics Knowledgebase | US Dept of Health and Human Services | Bioinformatics – Data Integration; Computational Toxicology – Toxicoinformatics |
| Phoenics | CHAM | Exposure/Risk Analysis – Microenvironmental/LCA Modeling |
| PHS – Public Health Statements | ATSDR, CDC | Cheminformatics – Property/Activity Prediction |
| PHYLIP – PHYLogeny Inference Package | University of Washington | Bioinformatics – Interactions/Biopathways/Bionetworks |
| PhyML | S. Guindon, et al., CNRS | Bioinformatics – Biomolecular Sequences/Structures |
| Phyre | Structural Bioinformatics Group, Imperial College, London | Bioinformatics – Biomolecular Sequences/Structures |
| PhysioDesigner | PhysioDesigner development team | Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics; Computational Toxicology – Virtual Cells, Tissues, Organs |
| PHYSPROP – Physical Properties Database | SRC | Cheminformatics – 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 team | Bioinformatics – Biomolecular Sequences/Structures |
| PID – Pathway Interaction Database | NCI (National Cancer Institute), NIH | Bioinformatics – Interactions/Biopathways/Bionetworks |
| PID – Physiological Information Database | USEPA | Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics |
| PIRAT – Pesticide Inert Risk Assessment Tool | USEPA | Exposure/Risk Analysis – Microenvironmental/LCA Modeling; Exposure/Risk Analysis – Cumulative/Aggregate Exposures |
| PK Solutions | Summit Research | Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics |
| PKQuest | David Levitt, University of Minnesota | Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics |
| PK-Sim | Bayer Technology | Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics |
| PLINK (“Whole genome association analysis toolset”) | PLINK development team, CHGR – Massachusetts General Hospital, Boston, MA | Bioinformatics – Biomolecular Sequences/Structures; Exposure/Risk Analysis – Biomarkers |
| Pollen.com (National Allergy Forecast & Information About Allergies) | IMS Health Inc. | Enviroinformatics – Release Mapping/Modeling |
| PollenLibrary | IMS Health Inc. | Enviroinformatics – Release Mapping/Modeling |
| PolyBayes (“automated analysis of single-nucleotide polymorphism (SNP) discovery in redundant DNA sequences”) | Washington University Genome Sequencing Center | Bioinformatics – 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 Project | Enviroinformatics – Spatiotemporal Mapping/Analysis |
| PostgreSQL | PostgreSQL Global Development Group | General Development Tools – Development and Programming |
| PPDB – Pesticide Properties DataBase | University of Hertfordshire | Exposure/Risk Analysis – Ecological Risks |
| PRED-GPCR | University of Athens, Greece | Bioinformatics – Biomolecular Sequences/Structures |
| PredictProtein | ROSTLAB | Bioinformatics – Biomolecular Sequences/Structures |
| Primate Info Net | National Primate Research Center, University of Wisconsin | Computational Toxicology – Virtual Model Organisms |
| PRIMET – Pesticides RIsks in the tropics to Man, Environment and Trade | Alterra and Wageningen UR, The Netherlands | Exposure/Risk Analysis – Ecological Risks |
| PRINTS | Bioinformatics at Manchester, University of Manchester | |
| ProcessIt NMR | Bio-Rad Laboratories | Cheminformatics – Structure Elucidation |
| ProfileAnalysis | Bruker Daltonics | Exposure/Risk Analysis – Biomarkers |
| Progenetix (“genomic copy number aberrations in cancer”) | Baudis Laboratory, University of Zurich | Exposure/Risk Analysis – Biomarkers |
| PROSITE | SIB – Swiss Institute of Bioinformatics | |
| Protective Action Criteria | EMI SIG | Cheminformatics – Property/Activity Prediction |
| PRoTEGE – Prioritization/Ranking of Toxic Exposures with GIS Extension | Computational Chemodynamics Laboratory | Exposure/Risk Analysis – Microenvironmental/LCA Modeling |
| Protein Database | National Center for Biotechnology Information, NLM, NIH | |
| Protein Prospector | UCSF | Bioinformatics – Biomolecular Sequences/Structures |
| Protein Sequence Database | University of Delaware and Georgetown University | |
| ProteinScape | Bruker Daltonics | Exposure/Risk Analysis – Biomarkers |
| ProteoIQ (“qualitative and quantitative suite for proteomics”) | Premier Biosoft | Bioinformatics – Biological Dose-Response; Exposure/Risk Analysis – Biomarkers |
| Proteome Bioknowledge Library | University of Manchester | |
| PRS – Pesticide Reregistration Status | USEPA | Cheminformatics – Property/Activity Prediction |
| PRZM – Pesticide Root Zone Model | USEPA | Enviroinformatics – Environmental Fate and Transport |
| PRZM/EXAMS Shell | USEPA | Enviroinformatics – Environmental Fate and Transport; Exposure/Risk Analysis – Ecological Risks |
| PRZM-GW | USEPA | Enviroinformatics – Environmental Fate and Transport; Exposure/Risk Analysis – Ecological Risks |
| PSAP – Priority Substances Assessment Program | Health Canada | Cheminformatics – Property/Activity Prediction |
| Ps-i | Lustick Consulting | General Development Tools – Development and Programming |
| PSI-BLAST – Protein Similarity Search BLAST | EMBL-EBI | Bioinformatics – Biomolecular Sequences/Structures |
| PubChem | National Center for Biotechnology Information, NLM, NIH | Cheminformatics – Property/Activity Prediction |
| PubMed | National Center for Biotechnology Information, NLM, NIH | Cheminformatics – Property/Activity Prediction; Bioinformatics – Biological Dose-Response; Computational Toxicology – Toxicoinformatics; Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics |
| PubMeth | BioBix, Laboratory for Bioinformatics and Computational Genomics, Ghent University, Belgium | Bioinformatics – Biological Dose-Response; Bioinformatics – Data Integration; Exposure/Risk Analysis – Biomarkers |
| PUMAdb – Princeton University MicroArray database (supersedes SMD) | Princeton University | Bioinformatics – Biological Dose-Response |
| PyDSTool | Robert Clewley, GSU | General Development Tools – Development and Programming |
| PyMOL | PyMOL Team | Cheminformatics – Property/Activity Prediction; Bioinformatics – Biomolecular Sequences/Structures |
| Python | Python Software Foundation | General Development Tools – Development and Programming |
| QGIS (“Create, edit, visualise, analyse and publish geospatial information”) | QGIS development team | Enviroinformatics – Spatiotemporal Mapping/Analysis; General Development Tools – Data Visualization |
| QiKProp | Schrodinger, LLC | Cheminformatics – Property/Activity Prediction |
| QSAR Toolbox | Organisation for Economic Co-operation and Development and European Chemicals Agency | Cheminformatics – Property/Activity Prediction |
| QTDT (Linkage Disequilibrium Analyses for Quantitative and Discrete Traits) | Abecasis Lab, University of Michigan | Bioinformatics – Biomolecular Sequences/Structures; Bioinformatics – Data Integration |
| QTX | QTX development team | Bioinformatics – Biomolecular Sequences/Structures |
| QUAL2E (Enhanced Stream Water Quality model) | Tufts University and USEPA | Enviroinformatics – Environmental Fate and Transport; Exposure/Risk Analysis – Ecological Risks |
| QUAL2K – River and Stream Water Quality Model | USEPA | Enviroinformatics – Environmental Fate and Transport; Exposure/Risk Analysis – Ecological Risks |
| QuEST – Quantitative Enrichment of Sequence Tags | Stanford University | Bioinformatics – Biomolecular Sequences/Structures |
| QUIC – Quick Urban & Industrial Complex | Los Alamos National Laboratory | Enviroinformatics – Environmental Fate and Transport |
| R package | R package development team | General Development Tools – Development and Programming |
| R/maanova | Churchill Group, Jackson Laboratory | Bioinformatics – Biological Dose-Response |
| Raidar | CEMC, Canada | Exposure/Risk Analysis – Microenvironmental/LCA Modeling |
| RAMAS GIS | Applied Biomathematics | Exposure/Risk Analysis – Ecological Risks |
| RAMS – Regional Atmospheric Modeling System | ATMET, LLC | Enviroinformatics – Environmental Fate and Transport |
| Rapid Miner | rapid-i | Data/Simulation Pattern Analysis – Data Mining/Pattern Recognition |
| RasMol (“Molecular Graphics Visualisation Tool”) | RasMOL development team | Cheminformatics – Structure Elucidation |
| Rational Rose | IBM | General Development Tools – Development and Programming |
| RatMine | University of Cambridge, Cambridge, UK | Bioinformatics – 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. Corbeil | Bioinformatics – Biomolecular Sequences/Structures |
| RCRAInfo | USEPA | Enviroinformatics – Release Mapping/Modeling |
| REACH – Registration, Evaluation, Authorisation and Restriction of Chemical substances | European Chemicals Agency | Cheminformatics – Property/Activity Prediction |
| ReachScan | USEPA | Exposure/Risk Analysis – Ecological Risks |
| Reactome | Reactome team | Bioinformatics – 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, NOAA | Enviroinformatics – Spatiotemporal Mapping/Analysis |
| RealTimeDesign Software | Biosearch Technologies | Bioinformatics – Biological Dose-Response |
| Reaxys Chemistry Database | Reaxys | Cheminformatics – Property/Activity Prediction |
| Reaxys system (Search substances, reactions, citations, patents, etc.) | Reaxys development team | Cheminformatics – Property/Activity Prediction; Bioinformatics – Biomolecular Sequences/Structures |
| REBASE – The Restriction Enzyme dataBASE | New England Biolabs, Inc. (Roberts, R.J., Macelis, D.) | Bioinformatics – Biological Dose-Response; Bioinformatics – Data Integration |
| REDUCE | Harmen Bussemaker Laboratory, Columbia University | Bioinformatics – Biomolecular Sequences/Structures; Bioinformatics – Interactions/Biopathways/Bionetworks |
| RefSeq – NCBI Reference Sequence Database | National Center for Biotechnology Information, NLM, NIH | Bioinformatics – Biomolecular Sequences/Structures; Exposure/Risk Analysis – Biomarkers |
| REMSAD – Regional Modeling System for Aerosols and Deposition | ICF Consulting | Enviroinformatics – Environmental Fate and Transport |
| Repast | Argonne National Laboratory | Exposure/Risk Analysis – Socioeconomic/LSB Modeling; General Development Tools – Development and Programming |
| RESRAD – RESidual RADioactive | Argonne National Laboratory | Enviroinformatics – 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”) | USEPA | Enviroinformatics – Spatiotemporal Mapping/Analysis |
| RetroMEX | CompuDrug | Cheminformatics – Interaction/Reaction Modeling |
| RExcel (Excel add-in to use R from Microsoft Excel) | RExcel development team | General Development Tools – Data Visualization |
| RGD – Rat Genome Database | Medical College of Wisconsin | Bioinformatics – Biomolecular Sequences/Structures; Bioinformatics – Interactions/Biopathways/Bionetworks; Bioinformatics – Data Integration; Computational Toxicology – Virtual Model Organisms |
| RIOPA – Relationships of Indoor, Outdoor, and Personal Air | EOHSI and Health Effects Institute | Exposure/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 reports | RIVM | Cheminformatics – Property/Activity Prediction |
| RMAP (next-generation sequencing read mapper) | Cold Spring Harbor Laboratory, NY and USC, CA | Bioinformatics – Biomolecular Sequences/Structures |
| RNA CoMPASS – RNA Comprehensive Multi-Processor Analysis System for Sequencing | Guorong Xu and RNA CoMPASS development team | Bioinformatics – Biomolecular Sequences/Structures |
| RNA World (“collection of links to RNA-related information”) | Leibniz Institute for Age Research, FLI, Germany and RNA World team | Bioinformatics – Biomolecular Sequences/Structures |
| RNAi database | NYU’s Center for Genomics & Systems Biology | Bioinformatics – Biological Dose-Response; Bioinformatics – Data Integration |
| Roadmap Epigenomics Project Data | NIEHS | Bioinformatics – Biological Dose-Response; Bioinformatics – Data Integration |
| RPM-AERO (Modelling platform for studying photochemical gaseous and aerosol phase processes) | Computational Chemodynamics Laboratory | Enviroinformatics – Environmental Fate and Transport |
| RS-HDMR – Random-Sampling High Dimensional Model Representation | Rabitz Laboratory, Princeton University and Computational Chemodynamics Laboratory | Data/Simulation Pattern Analysis – Data Mining/Pattern Recognition; Data/Simulation Pattern Analysis – Sensitivity/Uncertainty Analysis |
| RTECS – Registry of Toxic Effects of Chemical Substances | CDC | Cheminformatics – Property/Activity Prediction |
| Ruby | Ruby development team (Yukihiro “Matz” Matsumoto) | General Development Tools – Development and Programming |
| RUCDR – Rutgers University Cell and DNA Repository | RUCDR Team | Bioinformatics – Biological Dose-Response; Bioinformatics – Data Integration |
| R-UNSAT | USGS | Enviroinformatics – Environmental Fate and Transport; Exposure/Risk Analysis – Ecological Risks |
| SAMBA | Shamir Laboratory, Tel Aviv University | Bioinformatics – Biomolecular Sequences/Structures; Bioinformatics – Interactions/Biopathways/Bionetworks |
| SAMtools – Sequence Alignment/Map | Li et al., Wellcome Trust Sanger Institute, UK and Broad Institute of MIT and Harvard, USA | Bioinformatics – Biomolecular Sequences/Structures |
| SANDY | Gerstein Laboratory, Yale University | Bioinformatics – Biomolecular Sequences/Structures; Bioinformatics – Interactions/Biopathways/Bionetworks |
| SAS – Statistical Analysis System | SAS Institute Inc. | General Development Tools – Development and Programming |
| SAS-EM – SAS Enterprise Miner | SAS Institute Inc. | Data/Simulation Pattern Analysis – Data Mining/Pattern Recognition; General Development Tools – Development and Programming |
| SAS-SDS – SAS Scientific Discovery Solutions | SAS 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, Germany | Bioinformatics – Interactions/Biopathways/Bionetworks |
| SBKB – Structural Biology Knowledgebase | Protein Structure Initiative and Nature Publishing Group | Bioinformatics – Biomolecular Sequences/Structures; Bioinformatics – Data Integration |
| SBML – Systems Biology Markup Language | SBML Team | Computational Toxicology – Virtual Cells, Tissues, Organs |
| SBML Converter | SBML Team | Computational Toxicology – Virtual Cells, Tissues, Organs |
| SBML Test Suite | SBML Team | Computational Toxicology – Virtual Cells, Tissues, Organs |
| SBMLeditor | SBML team | Computational Toxicology – Virtual Cells, Tissues, Organs |
| SBMLToolbox (for MATLAB and Octave) | SBML Team | Computational 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 & Simulation | Bioinformatics – Biological Dose-Response; Computational Toxicology – Toxicoinformatics; Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics |
| SCAMPI (“Prediction of membrane protein topology”) | Stockholm Bioinformatics Center, Stockholm University | Bioinformatics – Biomolecular Sequences/Structures |
| SCAN (“SNP and CNV Annotation Database”) | The University of Chicago | Bioinformatics – 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 Water | USEPA | Enviroinformatics – Environmental Fate and Transport; Exposure/Risk Analysis – Ecological Risks |
| Scilab (“software for numerical computation”) | Scilab Enterprises, former Scilab Consortium and Scilab contributors | General Development Tools – Development and Programming |
| SCiLS (“Statistical analysis of MALDI imaging data”) | SCiLS GmbH and Bruker Daltonics | Exposure/Risk Analysis – Biomarkers |
| SCIPUFF – Second-order Closure Integrated PUFF Model | Titan Products | Enviroinformatics – Environmental Fate and Transport |
| SCoP – Simulation Control Program | Simulation Resources Inc | General Development Tools – Development and Programming |
| SCOP – Structural Classification of Proteins | MRC Laboratory of Molecular Biology | Bioinformatics – Biomolecular Sequences/Structures |
| Scorecard Chemical Profiles | GoodGuide | Cheminformatics – Property/Activity Prediction |
| SDBS – Spectral Database for Organic Compounds | National Institute of Advanced Industrial Science and Technology (AIST), Japan | Cheminformatics – Structure Elucidation |
| SDWIS – Safe Drinking Water Information System | USEPA | Exposure/Risk Analysis – Microenvironmental/LCA Modeling |
| See5/ C5.0 | RuleQuest | Data/Simulation Pattern Analysis – Data Mining/Pattern Recognition |
| SEQUEST | Yates Laboratory, University of Washington | Bioinformatics – Biomolecular Sequences/Structures |
| SERAFM – Spreadsheet-based Ecological Risk Assessment for the Fate of Mercury | USEPA | Exposure/Risk Analysis – Ecological Risks |
| SeSAm – Shell for Simulated Agent Systems | SeSAm development team | General Development Tools – Development and Programming |
| Sets2Networks | SBCNY and Mount Sinai School of Medicine | Bioinformatics – Interactions/Biopathways/Bionetworks |
| SEVENS database (“summarizes GPCR (G-protein coupled receptor) genes that are identified […] from […] eukaryote genomes”) | Computational Biology Research Center, AIST, Japan | Bioinformatics – Biomolecular Sequences/Structures |
| SGD – Saccharomyces Genome Database | Stanford University | Bioinformatics – Biomolecular Sequences/Structures; Bioinformatics – Interactions/Biopathways/Bionetworks; Bioinformatics – Biological Dose-Response; Computational Toxicology – Virtual Model Organisms |
| Shape Signatures | Welsh Laboratory, RWJMS | Bioinformatics – Biomolecular Sequences/Structures |
| SHEDS Multimedia – Stochastic Human Exposure and Dose Simulation model | USEPA | Exposure/Risk Analysis – Cumulative/Aggregate Exposures |
| SHEDS-AIRTOXICS – Stochastic Human Exposure and Dose Simulation for Air Toxics | USEPA | Exposure/Risk Analysis – Cumulative/Aggregate Exposures |
| SHEDS-Pesticides – Stochastic Human Exposure and Dose Simulation Model for Pesticides | USEPA | Exposure/Risk Analysis – Cumulative/Aggregate Exposures |
| SHEDS-PM – Stochastic Human Exposure and Dose Simulation for Particulate Matter | USEPA | Exposure/Risk Analysis – Cumulative/Aggregate Exposures |
| SHEDS-WOOD – Stochastic Human Exposure and Dose Simulation Model for Wood Preservatives | USEPA | Exposure/Risk Analysis – Cumulative/Aggregate Exposures |
| SICER (“clustering approach for identification of enriched domains from histone modification ChIP-Seq data”) | W. Peng lab, George Washington University | Bioinformatics – Biomolecular Sequences/Structures; Exposure/Risk Analysis – Biomarkers |
| SIDS – Screening Information Dataset | UNEP | Enviroinformatics – Release Mapping/Modeling |
| Sigma-Aldrich – Chemical search | Sigma-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 |
| SigmaPlot | Systat Software Inc. | General Development Tools – Data Visualization |
| SigmaStat | Systat 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 |
| SIMCA | Umetrics | General 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 |
| Simcyp | Simcyp Ltd | Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics |
| Simul8 | Simul8 Corp | General Development Tools – Development and Programming |
| Simulink | The 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”) | USEPA | Enviroinformatics – Environmental Fate and Transport; Exposure/Risk Analysis – Ecological Risks |
| Skin Deep Database | Environmental Working Group | Exposure/Risk Analysis – Microenvironmental/LCA Modeling |
| SKY/M-FISH and CGH Database | National Center for Biotechnology Information, NLM, NIH and National Cancer Institute, NIH | Bioinformatics – Data Integration; Exposure/Risk Analysis – Biomarkers |
| SMART-BS-Seq – Specific Methylation Analysis and Report Tool for BS-Seq data | Python Software Foundation | Bioinformatics – Biomolecular Sequences/Structures; Bioinformatics – Biological Dose-Response; Exposure/Risk Analysis – Biomarkers |
| SMBioNet | University of Nice, France | Bioinformatics – Interactions/Biopathways/Bionetworks |
| SMD – Stanford Microarray Database (see PUMAdb) | Stanford University | Bioinformatics – Biological Dose-Response; Exposure/Risk Analysis – Biomarkers |
| SMOKE – Sparse Matrix Operator Kernel Emissions | CMAS Center, UNC-Chapel Hill | Enviroinformatics – Release Mapping/Modeling |
| SMS – Surface Water Modeling System | Coastal and Hydraulics Laboratory | Enviroinformatics – Environmental Fate and Transport |
| SNAP – Screening for Non-Acceptable Polymorphisms | Rost Lab, Columbia University, New York | Bioinformatics – Biomolecular Sequences/Structures; Exposure/Risk Analysis – Biomarkers |
| SNAP – SNP Annotation and Proxy Search | SNAP Development Team | Bioinformatics – Biomolecular Sequences/Structures; Exposure/Risk Analysis – Biomarkers |
| SNIP – S-Space Network Inference Procedure | Rabitz Laboratory, Princeton University | Bioinformatics – Interactions/Biopathways/Bionetworks |
| SNP500Cancer | SAIC-Frederick, NCI-FCRDC, MD | Bioinformatics – Biomolecular Sequences/Structures; Exposure/Risk Analysis – Biomarkers |
| SNPinfo Web Server | NIEHS | Bioinformatics – Biomolecular Sequences/Structures; Exposure/Risk Analysis – Biomarkers |
| SNP-o-matic (analysis of Solexa reads and comparison with reference) | Sanger Institute | Bioinformatics – Biomolecular Sequences/Structures; Exposure/Risk Analysis – Biomarkers |
| SNPTrack | USFDA | Bioinformatics – Biomolecular Sequences/Structures; Exposure/Risk Analysis – Biomarkers |
| SOAP – Short Oligonucleotide Analysis Package | Beijing Genomics Institute | Bioinformatics – Biomolecular Sequences/Structures |
| SOAPdenovo2 (Large-size genome de-novo assembler) | Ruibang Luo, et al., Tai Po Industrial Estate | Bioinformatics – Biomolecular Sequences/Structures |
| SOARS – Spot Oriented Agent Role Simulator | SOARS Project and Deguchi Lab, Tokyo Institute of Technology | Exposure/Risk Analysis – Socioeconomic/LSB Modeling; General Development Tools – Development and Programming |
| SocDynamics.org (Modeling Social Dynamics) | SocDynamics.org development team | Exposure/Risk Analysis – Microenvironmental/LCA Modeling; Exposure/Risk Analysis – Socioeconomic/LSB Modeling |
| Soil Data Mart (see Web Soil Survey) | USDA NRCS | Enviroinformatics – Spatiotemporal Mapping/Analysis |
| SOPRA – Scaffolding algorithm for paired reads via statistical optimization | A. Sengupta lab, Rutgers University | Bioinformatics – Biomolecular Sequences/Structures |
| SOSUI (“predicts a part of the secondary structure of proteins from a given amino acid sequence”) | Tokyo University | Bioinformatics – Biomolecular Sequences/Structures |
| Soundcities | Stanza team | General Development Tools – Data Visualization |
| SPAD – Signaling Pathway Database | Kyushu University | Bioinformatics – Interactions/Biopathways/Bionetworks |
| SPADE – Smart Python multi-Agent Development Environment | SPADE development team | Exposure/Risk Analysis – Socioeconomic/LSB Modeling; General Development Tools – Development and Programming |
| SPARC – SPARC Performs Automated Reasoning in Chemistry | USEPA | Cheminformatics – Property/Activity Prediction |
| SPARK – Simple Platform for Agent-based Representation of Knowledge | SPARK development team | Exposure/Risk Analysis – Socioeconomic/LSB Modeling; General Development Tools – Development and Programming |
| Spark (“engine for large-scale data processing”) | The Apache Software Foundation | General Development Tools – Development and Programming |
| SPARTAN – Surface PARTiculate mAtter Network | SPARTAN Network team | Exposure/Risk Analysis – Microenvironmental/LCA Modeling; Exposure/Risk Analysis – Cumulative/Aggregate Exposures |
| Spartan (molecular modeling package) | WaveFunction | Cheminformatics – Structure Elucidation; Cheminformatics – Property/Activity Prediction; Cheminformatics – Interaction/Reaction Modeling |
| SPEAR – SPEcies At Risk Calculator/ TU – Toxic-Unit Calculator | UFZ Leipzig | Exposure/Risk Analysis – Ecological Risks |
| SpecInfo | John Wiley & Sons, Inc. | Cheminformatics – Structure Elucidation |
| Spectral database | USEPA and US Air Force | Cheminformatics – Structure Elucidation |
| SPELL – Serial Pattern of Expression Levels Locator | Princeton University | Bioinformatics – Biological Dose-Response |
| Spin Trap Database | NIEHS | Cheminformatics – Property/Activity Prediction |
| SPLS – Sparse partial least squares | Keles Research Group, University of Wisconsin | Bioinformatics – Biological Dose-Response; Data/Simulation Pattern Analysis – Data Mining/Pattern Recognition |
| Spotfire Decision Site Software | TIBCO Spotfire | Data/Simulation Pattern Analysis – Data Mining/Pattern Recognition; General Development Tools – Development and Programming |
| Spotfire S-Plus | TIBCO Spotfire | General Development Tools – Development and Programming |
| SpringerProtocols | Springer-Verlag | Bioinformatics – Biomolecular Sequences/Structures; Bioinformatics – Interactions/Biopathways/Bionetworks; Bioinformatics – Biological Dose-Response; Bioinformatics – Data Integration |
| SRD – Source Ranking Database | USEPA | Enviroinformatics – Release Mapping/Modeling |
| SRS – Substance Registry Services | USEPA | Cheminformatics – Property/Activity Prediction |
| SRSM – Stochastic Response Surface Method | Computational Chemodynamics Laboratory | Data/Simulation Pattern Analysis – Sensitivity/Uncertainty Analysis |
| SSEARCH (sequence similarity search) | SSEARCH team | Bioinformatics – Biomolecular Sequences/Structures |
| SSTS – Section Seven Tracking System | USEPA | Enviroinformatics – Release Mapping/Modeling |
| SSURGO – Soil Survey Geographic Database | USDA NRCS | Enviroinformatics – Spatiotemporal Mapping/Analysis |
| StarLogo/ OpenStarLogo | MIT | Exposure/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 Center | Bioinformatics – Interactions/Biopathways/Bionetworks |
| Statistica (with Data and Text Miner) | StatSoft | Data/Simulation Pattern Analysis – Data Mining/Pattern Recognition; General Development Tools – Development and Programming |
| Statistical Abstract | US Census Bureau | Enviroinformatics – Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis – Socioeconomic/LSB Modeling |
| STATSGO/ U.S. General Soil Map | USDA NRCS | Enviroinformatics – Spatiotemporal Mapping/Analysis |
| STELLA | isee systems | General Development Tools – Development and Programming |
| StellaR | StellaR development team | General Development Tools – Development and Programming |
| STEM – Spatiotemporal Epidemiological Modeler | Eclipse | Enviroinformatics – Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis – Human Health Risks |
| StemBase (gene expression data obtained from stem cells) | Canadian Stem Cell Network | Bioinformatics – Biological Dose-Response; Exposure/Risk Analysis – Biomarkers |
| STIR – Screening Tool for Inhalation Risk | USEPA | Exposure/Risk Analysis – Ecological Risks |
| STITCH – Search Tool for Interactions of Chemicals | STITCH development team | Bioinformatics – Interactions/Biopathways/Bionetworks |
| STORET – STOrage and RETrieval | USEPA | Enviroinformatics – Spatiotemporal Mapping/Analysis; Enviroinformatics – Release Mapping/Modeling |
| STRING – Search Tool for the Retrieval of Interacting Genes/Proteins | STRING Team | Bioinformatics – Biomolecular Sequences/Structures |
| Structural Biology Software Database | Theoretical and Computational Biophysics Group, University of Illinois | Bioinformatics – Biomolecular Sequences/Structures |
| Structure-Activity Relationships | USEPA | |
| SubMAP – Subnetwork Mappings in Alignment of Pathways | Bioinformatics Lab, University of Florida | Bioinformatics – Interactions/Biopathways/Bionetworks |
| SUCcESS (Integration of quantitative information from ChIP-chip experiments into motif finding) | Keles Research Group, University of Wisconsin | Bioinformatics – Biomolecular Sequences/Structures; Bioinformatics – Biological Dose-Response; Exposure/Risk Analysis – Biomarkers |
| Sugarscape | Sugarscape development team | Exposure/Risk Analysis – Socioeconomic/LSB Modeling; General Development Tools – Development and Programming |
| Swarm | Swarm Development Group | Exposure/Risk Analysis – Socioeconomic/LSB Modeling; General Development Tools – Development and Programming |
| SWASH – Surface WAter Scenarios Help | Alterra and Wageningen UR, The Netherlands | Exposure/Risk Analysis – Ecological Risks |
| SWCC – Surface Water Concentration Calculator | USEPA | Enviroinformatics – Environmental Fate and Transport |
| SWIMODEL – Swimmer Exposure Assessment Model | USEPA | Exposure/Risk Analysis – Microenvironmental/LCA Modeling |
| SYBYL (“Molecular Modeling from Sequence through Lead Optimization”) | Certara, L.P. and Tripos | Cheminformatics – Structure Elucidation; Cheminformatics – Property/Activity Prediction; Bioinformatics – Biomolecular Sequences/Structures |
| SYSTAT | Systat Software, Inc. | Data/Simulation Pattern Analysis – Data Mining/Pattern Recognition; General Development Tools – Development and Programming |
| SystemsReality | USEPA | Exposure/Risk Analysis – Microenvironmental/LCA Modeling |
| Tableau | Tableau Software | General Development Tools – Data Visualization |
| TANKS | USEPA | Enviroinformatics – Release Mapping/Modeling |
| TargetP | Center for Biological Sequence Analysis, Technical University of Denmark | Bioinformatics – Interactions/Biopathways/Bionetworks |
| Taverna | myGrid, University of Manchester | Bioinformatics – Data Integration |
| Taxonomic Data Center | Biota of North America Program (BONAP) | Enviroinformatics – Spatiotemporal Mapping/Analysis |
| TB Drug Target Database | TB Drug Target Database development team | Exposure/Risk Analysis – Biomarkers |
| T-Coffee | EMBL-EBI | Bioinformatics – Biomolecular Sequences/Structures |
| TDS – Total Diet Study | USFDA | Exposure/Risk Analysis – Microenvironmental/LCA Modeling |
| TEACH – Toxicity and Exposure Assessment for Children’s Health | USEPA | Cheminformatics – Property/Activity Prediction; Exposure/Risk Analysis – Cumulative/Aggregate Exposures |
| TEAM – Total Exposure Assessment Methodology Study | USEPA | Exposure/Risk Analysis – Microenvironmental/LCA Modeling; Exposure/Risk Analysis – Biomarkers |
| TEAM – Trade and Environment Assessment Model | Abt Associates, Inc. and USEPA | |
| Tecplot | Tecplot Inc | General Development Tools – Data Visualization |
| TerraME | TerraME Develppment Team, Federal University of Ouro Preto | General Development Tools – Development and Programming |
| TerrPLANT | USEPA | Enviroinformatics – Environmental Fate and Transport; Exposure/Risk Analysis – Ecological Risks |
| The Interactive Fly | The Interactive Fly development team (Thomas B. Brody) | Computational Toxicology – Virtual Cells, Tissues, Organs |
| The Nanodatabase | The Ecological Council, DTU Environment and Danish Consumer Council, Denmark | Exposure/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”) | USEPA | Exposure/Risk Analysis – Ecological Risks |
| THREADER (Protein Structure Prediction tool) | Bioinformatics Group, University College London | Cheminformatics – Structure Elucidation; Bioinformatics – Biomolecular Sequences/Structures |
| Tier 1 Rice Model (“estimate surface water exposure from the use of pesticides in rice paddies”) | USEPA | Enviroinformatics – Environmental Fate and Transport; Exposure/Risk Analysis – Ecological Risks |
| TIGER – Topologically Integrated Geographic Encoding and Referencing | US Census Bureau | Enviroinformatics – Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis – Socioeconomic/LSB Modeling |
| TileHGMM (Mixture modeling for genome-wide localization of transcription factors) | Keles Research Group, University of Wisconsin | Bioinformatics – Biomolecular Sequences/Structures; Bioinformatics – Biological Dose-Response; Exposure/Risk Analysis – Biomarkers |
| TissueDistributionDBs | German Cancer Research Center, DKFZ, Heidelberg | Bioinformatics – Biological Dose-Response; Computational Toxicology – Virtual Cells, Tissues, Organs |
| Titanium | Appcelerator Inc | General 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 ROOT | TMVA development team | Data/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 Biology | Bioinformatics – Biomolecular Sequences/Structures |
| TOPKAT – TOxicity Prediction by Komputer Assisted Technology | accelrys | Cheminformatics – Property/Activity Prediction |
| TopoToolbox (“MATLAB program for the analysis of digital elevation models”) | TopoToolbox development team | Enviroinformatics – Spatiotemporal Mapping/Analysis |
| TopPred (“Topology prediction of membrane proteins”) | TopPred development team | Bioinformatics – Biomolecular Sequences/Structures |
| TOPS – Topology of Protein Structure | University of Leeds | |
| TopSpin (NMR data analysis and acquisition and processing of NMR spectra) | Bruker Corporation | Cheminformatics – Structure Elucidation; Bioinformatics – Biomolecular Sequences/Structures; Exposure/Risk Analysis – Biomarkers |
| Tox Town | U.S. National Library of Medicine | Computational Toxicology – Toxicoinformatics |
| ToxCast – Toxicity Forecaster | USEPA | Cheminformatics – Property/Activity Prediction; Bioinformatics – Biological Dose-Response; Computational Toxicology – Toxicoinformatics |
| ToxFAQs | ATSDR, CDC | Cheminformatics – Property/Activity Prediction; Computational Toxicology – Toxicoinformatics |
| ToxFX | NIEHS | Bioinformatics – Biological Dose-Response; Computational Toxicology – Toxicoinformatics |
| ToxGuides™ | ATSDR, CDC | Cheminformatics – Property/Activity Prediction; Computational Toxicology – Toxicoinformatics; Exposure/Risk Analysis – Human Health Risks |
| Toxic Substances Portal | ATSDR, CDC | Computational Toxicology – Toxicoinformatics; Exposure/Risk Analysis – Human Health Risks |
| TOXLINE – Toxicology Literature Online | National Library of Medicine | Cheminformatics – Property/Activity Prediction; Computational Toxicology – Toxicoinformatics |
| TOXMAP | Division of Specialized Information Services, US National Library of Medicine | Enviroinformatics – Release Mapping/Modeling; Computational Toxicology – Toxicoinformatics |
| Toxmatch | Joint Research Centre, IHCP | Bioinformatics – Biomolecular Sequences/Structures; Computational Toxicology – Toxicoinformatics |
| ToxNet | National Library of Medicine | Cheminformatics – Property/Activity Prediction; Computational Toxicology – Toxicoinformatics |
| ToxProfiles | ATSDR, CDC | Cheminformatics – Property/Activity Prediction; Computational Toxicology – Toxicoinformatics |
| ToxRefDB – Toxicity Reference Database | USEPA | Cheminformatics – Property/Activity Prediction; Computational Toxicology – Toxicoinformatics |
| ToxRTool – Toxicological data Reliability Assessment Tool | European Commission | Computational Toxicology – Toxicoinformatics |
| TOXSWA – TOXic substances in Surface WAters | TOXSWA team | Enviroinformatics – Environmental Fate and Transport; Exposure/Risk Analysis – Ecological Risks |
| Toxtree (Estimatation of toxic hazard by applying a decision tree approach) | Ideaconsult Ltd | Cheminformatics – Property/Activity Prediction; Computational Toxicology – Toxicoinformatics |
| TRA – Targeted Risk Assessment Tool | ECETOC | Exposure/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) | USEPA | Enviroinformatics – Environmental Fate and Transport; Exposure/Risk Analysis – Microenvironmental/LCA Modeling; Exposure/Risk Analysis – Ecological Risks |
| TransFac | Gene Regulation | Bioinformatics – Biomolecular Sequences/Structures; Bioinformatics – Interactions/Biopathways/Bionetworks |
| TransPath | Gene Regulation | Bioinformatics – Interactions/Biopathways/Bionetworks |
| T-REX – Terrestrial Residue Exposure (“model to calculate the residues on avian and mammalian food items”) | USEPA | Exposure/Risk Analysis – Ecological Risks |
| trex2-agent (“A formal framework for situated agent deliberation and execution”) | trex2-agent development team | General Development Tools – Development and Programming |
| TRI – Toxics Release Inventory | USEPA | Enviroinformatics – Release Mapping/Modeling |
| Trinity RNA-Seq Assembly | Broad Institute, Hebrew University of Jerusalem and Trinity Developers Group | Bioinformatics – Biomolecular Sequences/Structures |
| Trinotate (“Transcriptome Functional Annotation and Analysis”) | Trinotate development team | Bioinformatics – Biomolecular Sequences/Structures; Exposure/Risk Analysis – Biomarkers |
| truPK | Strand Genomics | Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics |
| TSCAInv – TSCA Inventory | USEPA | Cheminformatics – Property/Activity Prediction |
| TSCATS – Toxic Substance Control Act Test Submission Database | SRC Inc | Cheminformatics – Property/Activity Prediction |
| Tute (“web application […] in the cloud and […] analyze and annotate entire human genomes”) | Tute Genomics | Bioinformatics – Biomolecular Sequences/Structures; Bioinformatics – Data Integration; Exposure/Risk Analysis – Biomarkers |
| Tweet Archivist | Tweet Archivist | Data/Simulation Pattern Analysis – Data Mining/Pattern Recognition |
| Twinscan/N-SCAN (“gene-structure prediction”) | Brent Lab, Washington University in St. Louis | Bioinformatics – Biomolecular Sequences/Structures |
| UAM-V – Urban Airshed Model-V | ICF International and USEPA | Enviroinformatics – Environmental Fate and Transport |
| ubertool (“Cloud-based environmental models for evaluating pesticide risks to ecosystems”) | USEPA | Exposure/Risk Analysis – Ecological Risks |
| UCINET (“software package for the analysis of social network data”) | Analytic Technologies. | Exposure/Risk Analysis – Socioeconomic/LSB Modeling |
| UCSC Genome Browser | Genome Bioinformatics Group, UC Santa Cruz | Bioinformatics – Biological Dose-Response |
| Ullmann’s Encyclopedia of Industrial Chemistry | John Wiley & Sons, Inc | Cheminformatics – Property/Activity Prediction |
| UniProtKB – Universal Protein Resource Knowledgebase | UniProt Consortium | |
| UniSTS (“database of sequence tagged sites”) | National Center for Biotechnology Information, NLM, NIH | Bioinformatics – Biomolecular Sequences/Structures |
| United Nations Statistical Yearbook | United Nations | Exposure/Risk Analysis – Microenvironmental/LCA Modeling; Exposure/Risk Analysis – Socioeconomic/LSB Modeling; Exposure/Risk Analysis – Cumulative/Aggregate Exposures |
| Unmix | USEPA | Enviroinformatics – Environmental Fate and Transport |
| Unregulated Contaminant Monitoring data | USEPA | Enviroinformatics – Release Mapping/Modeling; Enviroinformatics – Environmental Fate and Transport; Exposure/Risk Analysis – Human Health Risks |
| UR3M – Unified Radon Relative Risk Model | USEPA | Exposure/Risk Analysis – Human Health Risks |
| US Census Population Database | US Census Bureau | Enviroinformatics – Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis – Socioeconomic/LSB Modeling; Exposure/Risk Analysis – Human Health Risks |
| US Census Survey | US Census Bureau | Exposure/Risk Analysis – Microenvironmental/LCA Modeling; Exposure/Risk Analysis – Socioeconomic/LSB Modeling; Exposure/Risk Analysis – Human Health Risks |
| US Economic Census | US Census Bureau | Enviroinformatics – 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) Tox | USEtox development team | Enviroinformatics – Environmental Fate and Transport; Exposure/Risk Analysis – Microenvironmental/LCA Modeling; Exposure/Risk Analysis – Ecological Risks |
| USGS Pesticide Use Database | US Geological Survey | Enviroinformatics – Release Mapping/Modeling |
| VANTED – Visualization and Analysis of Networks containing Experimental Data | Plant Bioinformatics Group, Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben, Germany | Bioinformatics – Interactions/Biopathways/Bionetworks |
| VCell – The Virtual Cell | Center for Cell Analysis and Modeling (CCAM), University of Connecticut | Computational Toxicology – Virtual Cells, Tissues, Organs |
| VectorBase (“Bioinformatics Resource for Invertebrate Vectors of Human Pathogens”) | VectorBase Project team | Bioinformatics – Data Integration |
| VEGA – Vertebrate Genome Annotation | HAVANA group, Wellcome Trust Sanger Institute, UK | Bioinformatics – Biomolecular Sequences/Structures |
| VEGAS – Versatile Gene-based Association Study | VEGAS development team, Queensland Institute of Medical Research, Australia | Bioinformatics – Biomolecular Sequences/Structures |
| VegScape – Vegetation Condition Explorer | USDA National Agricultural Statistics Service | Enviroinformatics – Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis – Microenvironmental/LCA Modeling; Exposure/Risk Analysis – Cumulative/Aggregate Exposures |
| Velvet (“Sequence assembler for very short reads”) | EMBL-EBI | Bioinformatics – Biomolecular Sequences/Structures |
| v-Embryo – Virtual Embryo Project | USEPA | Computational Toxicology – Toxicoinformatics; Computational Toxicology – Virtual Cells, Tissues, Organs |
| VERDI – Visualization Environment Rich Data Interpretation | Argonne National Laboratory, USEPA, and CMAS Center | Enviroinformatics – Spatiotemporal Mapping/Analysis |
| VIDA (molecular modeling software) | OpenEye Scientific Software Inc. | Cheminformatics – Structure Elucidation |
| ViPR – Virus Pathogen Resource | ViPR Project team | Bioinformatics – Biomolecular Sequences/Structures; Bioinformatics – Data Integration |
| VirtualLeaf (“cell-based computer-modeling framework for plant tissue morphogenesis”) | VirtualLeaf development team | Computational Toxicology – Virtual Cells, Tissues, Organs |
| visANT | Boston University | Bioinformatics – Interactions/Biopathways/Bionetworks |
| Visible Human Project | National Library of Medicine | |
| Visio stencils for UML and SysML | Software Stencils development team (P. Hruby) | General Development Tools – Data Visualization |
| Visual Studio | Microsoft | General Development Tools – Development and Programming |
| VLEACH | Dynamac Corporation and USEPA | Enviroinformatics – Environmental Fate and Transport |
| v-Liver – Virtual Liver Project | USEPA | Computational Toxicology – Toxicoinformatics; Computational Toxicology – Virtual Cells, Tissues, Organs |
| VT-KB – Virtual Tissues Knowledgebase | USEPA | Computational Toxicology – Toxicoinformatics; Computational Toxicology – Virtual Cells, Tissues, Organs |
| WashU Epigenome Browser | Washington University | Bioinformatics – Biological Dose-Response; Bioinformatics – Data Integration |
| WASP – Water Quality Analysis Simulation Program | USEPA | Enviroinformatics – Environmental Fate and Transport; Exposure/Risk Analysis – Ecological Risks |
| Water Quality Standards Database | USEPA | Exposure/Risk Analysis – Ecological Risks |
| WATERS – Watershed Assessment, Tracking & Environmental Results System | USEPA | Exposure/Risk Analysis – Microenvironmental/LCA Modeling; Exposure/Risk Analysis – Ecological Risks |
| Watershed Plan Builder | USEPA | Exposure/Risk Analysis – Ecological Risks |
| WATERSHEDSS – WATER, Soil, and Hydro- Environmental Decision Support System | North Carolina State University and USEPA | Enviroinformatics – Environmental Fate and Transport |
| WCIT – Water Contaminant Information Tool | USEPA | Exposure/Risk Analysis – Ecological Risks |
| Weather Underground (Current and historical weather forecasts and reports from across the world) | The Weather Channel, LLC | Enviroinformatics – Spatiotemporal Mapping/Analysis; Enviroinformatics – Environmental Fate and Transport |
| Web Soil Survey | USDA | Enviroinformatics – Spatiotemporal Mapping/Analysis |
| WebArray | WebArray project team | Bioinformatics – Biological Dose-Response |
| WebGIS (A Geographic Information System Resource) | Lakes Enviornmental Software | Enviroinformatics – Spatiotemporal Mapping/Analysis |
| Web-ICE – Web-based Interspecies Correlation Estimation | USEPA | Exposure/Risk Analysis – Ecological Risks |
| WebMD | WebMD team | |
| Weka | Machine Learning Group, University of Waikato | Data/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 Technology | General Development Tools – Data Visualization |
| WhAEM2000 | USEPA | Enviroinformatics – Environmental Fate and Transport |
| WHATIF – Watershed Health Assessment Tools Investigating Fisheries | Canaan Valley Institute and USEPA | Exposure/Risk Analysis – Ecological Risks |
| WhiteStar data | WhiteStar Corporation | General Development Tools – Data Visualization |
| WHO Global Health Observatory Map Gallery | World Health Organization (WHO) | Enviroinformatics – Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis – Socioeconomic/LSB Modeling |
| Whole Brain Atlas | Johnson and Becker, Harvard Medical School | Computational Toxicology – Virtual Cells, Tissues, Organs |
| WholeCellKB-MG – Mycoplasma genitalium WholeCellKB | Stanford University | Computational Toxicology – Virtual Cells, Tissues, Organs; Computational Toxicology – Virtual Model Organisms |
| WinNonlin | Pharsight | Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics |
| WinNonMix | Pharsight | Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics |
| WinSAAM | University of Pennsylvania | General Development Tools – Development and Programming |
| WISER – Wireless Information System for Emergency Responders | National Library of Medicine | Cheminformatics – Property/Activity Prediction |
| WMS – Watershed Modeling System | Aquaveo | Enviroinformatics – Environmental Fate and Transport |
| Wolfram SystemModeler | Wolfram Research | General 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 Group | Exposure/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 Team | Enviroinformatics – Spatiotemporal Mapping/Analysis; Exposure/Risk Analysis – Socioeconomic/LSB Modeling; General Development Tools – Data Visualization |
| WormAtlas | Albert Einstein College of Medicine | Computational Toxicology – Virtual Cells, Tissues, Organs; Computational Toxicology – Virtual Model Organisms |
| WormBase | WormBase development team | Bioinformatics – Biomolecular Sequences/Structures; Computational Toxicology – Virtual Cells, Tissues, Organs; Computational Toxicology – Virtual Model Organisms |
| WormBook | WormBook development team | Computational Toxicology – Virtual Cells, Tissues, Organs; Computational Toxicology – Virtual Model Organisms |
| WQN – Water Quality Network | US Geological Survey | Enviroinformatics – Spatiotemporal Mapping/Analysis; Enviroinformatics – Release Mapping/Modeling |
| WRDB – Water Resources Database | Georgia Environmental Protection Division and USEPA | Exposure/Risk Analysis – Ecological Risks |
| WRF – The Weather Research & Forecasting Model | WRF Consortium | Enviroinformatics – Environmental Fate and Transport |
| WRF User’s Forum | WRF User’s Forum Team | Enviroinformatics – Environmental Fate and Transport |
| WRF-Chem – WRF weather prediction coupled with chemistry | WRF-Chem development team | Enviroinformatics – Environmental Fate and Transport |
| WWEIA – What We Eat In America, NHANES | USDA ARS and CDC | Exposure/Risk Analysis – Microenvironmental/LCA Modeling; Exposure/Risk Analysis – Socioeconomic/LSB Modeling |
| wwPDB – Worldwide Protein Data Bank | RCSB PDB, USA, PDBe, Europe, PDBj, Japan and BMRB, USA | Bioinformatics – Biomolecular Sequences/Structures |
| X!Tandem | The Global Proteome Machine Organization | Bioinformatics – Biomolecular Sequences/Structures |
| Xenbase (“Xenopus laevis and Xenopus tropicalis biology and genomics resource”) | University of Calgary, Alberta, Canada | Computational Toxicology – Virtual Model Organisms |
| Xpose (for NONMEM) | Xpose development team | Computational Toxicology – Dosimetry, Toxicokinetics, Toxicodynamics |
| X-Tile | Yale University | Bioinformatics – Data Integration; Exposure/Risk Analysis – Biomarkers |
| Yeast GFP Fusion Localization Database | University of California, San Francisco and SGD | Bioinformatics – Data Integration; Computational Toxicology – Virtual Model Organisms |
| YeastMine (“Search and retrieve S. cerevisiae data”) | SGD and Intermine project at Cambridge Systems Biology Centre, UK | Bioinformatics – Bio-Ontologies; Bioinformatics – Interactions/Biopathways/Bionetworks; Bioinformatics – Biological Dose-Response; Computational Toxicology – Virtual Model Organisms |
| YEASTNET (“A consensus reconstruction of yeast metabolism”) | Yeastnet development team | Bioinformatics – Interactions/Biopathways/Bionetworks |
| ZebrafishMine | ZFIN at University of Oregon and InterMine project at Cambridge Systems Biology Centre, UK | Bioinformatics – Bio-Ontologies; Bioinformatics – Biomolecular Sequences/Structures; Computational Toxicology – Virtual Model Organisms |
| ZFIN (Zebrafish Model Organism Database) | ZFIN Database development team | Computational Toxicology – Virtual Cells, Tissues, Organs; Computational Toxicology – Virtual Model Organisms |
| Zinc Library | Auckland Bioengineering Institute, University of Auckland, NZ | Computational Toxicology – Virtual Cells, Tissues, Organs |