Computational Toxicology

 
Toxicoinformatics

Toxicoinformatics of genomic/transcriptomic, epigenomic, proteomic, metabolomic, cytomic, and histomic systems

Computational Analysis Tools

ResourceDeveloper
ArrayTrack/ebTrackUSFDA and ebCTC
BMDExpress ("analyze microarray dose-response data")BMDExpress team
BRB-ArrayToolsDr. Richard Simon and BRB-ArrayTools Development Team
CheS-Mapper ("Chemical Space Mapping and Visualization in 3D")Albert-Ludwigs-Universität Freiburg, Germany (M. Gutlein et al.)
Decision ForestUSFDA
DORIAN - DOse-Response Information ANalysis systemComputational Chemodynamics Laboratory
Ingenuity Variant AnalysisQiagen
IPA - Ingenuity Pathway AnalysisQiagen N.V.
MATLAB Bioinformatics ToolboxThe Mathworks, Inc.
maxdViewManchester Bioinformatics
NONMEMICON Development Solutions and Regents of the University of California
Pathway StudioPathway Studio
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
ToxFXNIEHS
TOXMAPDivision of Specialized Information Services, US National Library of Medicine
ToxmatchJoint Research Centre, IHCP
ToxRTool - Toxicological data Reliability Assessment ToolEuropean Commission
Toxtree (Estimatation of toxic hazard by applying a decision tree approach)Ideaconsult Ltd
v-Embryo - Virtual Embryo ProjectUSEPA
v-Liver - Virtual Liver ProjectUSEPA

Information Portals and Databases

ResourceDeveloper
ACToR - Aggregated Computational Toxicology ResourceUSEPA
AOPWiki - Adverse Outcome Pathway WikiAOPWiki team (includes European Commission JRC, USEPA ORD and OECD)
ArrayExpressEMBL-EBI
Biomarkers Database (last updated in August 2004)USEPA
BOSS - Biomarkers of Oxidative Stress StudyNIEHS
CEBS - Chemical Effects in Biological SystemsNIEHS
Comparative Toxicogenomics DatabaseMount Desert Island Biological Laboratory
Comprehensive Cancer InformationNCI (National Cancer Institute), NIH
CPCat - Chemical and Product CategoriesUSEPA
CPDB - Carcinogenic Potency DatabaseCPDB development team
DART - Developmental and Reproductive Toxicology DatabaseNLM, NIH
DrugMatrixNIEHS
EADB - Estrogenic Activity DatabaseUSFDA
EDKB - Endocrine Disruptor Knowledge BaseUSFDA
EMAGE - e-Mouse Atlas of Gene ExpressionEMAGE team
Environmental Genome Project/ SNPs ProgramNIEHS and University of Washington
EPR - Environmental Polymorphisms RegistryNIEHS
EXTOXNET - EXTension TOXicology NETworkUniversity of California, Davis, Oregon State University, Michigan State University, Cornell University, and University of Idaho
GAC - Genetic Alterations in CancerNIEHS
GeneToxNLM
HGMD - Human Gene Mutation Database (integrated with Ingenuity Variant Analysis) BIOBASE
HSDB - Hazardous Substances Data BankNational Library of Medicine
IARC Monographs- ClassificationsIARC, WHO
IARC TP53 DatabaseIARC, WHO
ICRP - International Commission on Radiological Protection - Database of Dose CoefficientsICRP
IRIS - Integrated Risk Information SystemUSEPA
KEGG MEDICUSKanehisa Laboratories, Japan
LTKB - Liver Toxicity Knowledge BaseUSFDA
MGI - Mouse Genome InformaticsThe Jackson Laboratory, Maine and MGI team
National Toxicology Program Technical ReportsNIEHS
NCTRlcdb - NCTR Liver Cancer DatabaseUSFDA
OpenToxOpenTox project team
PD map - Parkinson’s disease mapLCSB and Hiroaki Kitano team at SBI, Tokyo
PharmGKB - Pharmacogenomics KnowledgebaseUS Dept of Health and Human Services
PubMedNational Center for Biotechnology Information, NLM, NIH
RIVM e-toxBase ("ecotoxicity data on both terrestrial and aquatic species")RIVM (Netherlands National Institute for Public Health and the Environment)
Tox TownU.S. National Library of Medicine
ToxCast - Toxicity ForecasterUSEPA
ToxFAQsATSDR, CDC
ToxGuides™ATSDR, CDC
Toxic Substances PortalATSDR, CDC
TOXLINE - Toxicology Literature OnlineNational Library of Medicine
ToxNetNational Library of Medicine
ToxProfilesATSDR, CDC
ToxRefDB - Toxicity Reference DatabaseUSEPA
VT-KB - Virtual Tissues KnowledgebaseUSEPA
Dosimetry, Toxicokinetics, Toxicodynamics

Dosimetry, toxicokinetics, toxicodynamics

Computational Analysis Tools

ResourceDeveloper
ADAPT ("computational modeling platform [...] for pharmacokinetic and pharmacodynamic applications")Biomedical Simulations Resource, USC
ADME Workbench ("pharmacokinetic modeling by integrating [...] absorption, distribution, metabolism and excretion methods")The AEgis Technologies Group
ADMET Predictor - Absorption, Distribution, Metabolism, Elimination, Toxicity PredictorSimulations Plus, Inc.
bear ("data analysis tool for average bioequivalence (ABE) and bioavailability (BA) for useR")bear development team
BEs - Biomonitoring EquivalentsSummit Toxicology, LLP
BioDMET ("physiologically-based pharmacokinetic (PBPK) modeling and simulation tool")GE and DTRA
Biokmod ("Mathematica toolbox […] with application for modeling Linear and Nonlinear Biokinetic Systems")Guillermo Sanchez
BiokmodWebGuillermo Sanchez
BMDS - Benchmark Dose SoftwareUSEPA
Boomer ("Non-Linear Regression Program")D.W.A. Bourne
CalcuSynBiosoft
Cloe PKCyprotex PLC
Cloe PredictCyprotex
Cyber PatientMichael B. Bolger, USC
DCAL - Dose and Risk Calculation SoftwareOak Ridge National Laboratory and USEPA
DDI PredictAureus Sciences
DORIAN - DOse-Response Information ANalysis systemComputational Chemodynamics Laboratory
DoseSimSCB Research Group, Colorado State University
ERDEM - Exposure Related Dose Estimating ModelUSEPA
GastroPlusSimulations Plus Inc
InDose ("Internal Dosimetry Code Using Biokinetics Models")Soreq - Nuclear Research Center, Israel (I. Silverman)
ISDD - In vitro Sedimentation, Diffusion and Dosimetry modelPNNL
LUDEP - Lung Dose Evaluation ProgramNational Radiological Protection Board, UK
MADr-BMD - Model Averaging for Dichotomous Response Benchmark DoseWheeler and Bailer
MENTOR-3P - Modeling ENvironment for TOtal Risk studies using Physiologically-based Pharmacokinetic modeling tools for Population assessmentsComputational Chemodynamics Laboratory
MIEP - Modeling Immunity to Enteric PathogensCenter for Modeling Immunity to Enteric Pathogens, Virginia Tech
MPPD - Multiple-Path Particle Dosimetry ModelApplied Research Associates
NONMEMICON Development Solutions and Regents of the University of California
PhysioDesignerPhysioDesigner development team
PK SolutionsSummit Research
PKQuestDavid Levitt, University of Minnesota
PK-SimBayer Technology
SBPOP Package ("Support for Model Based Drug Development – From Mechanistic Models to Complex Trial Simulation")SBPOP Package development team at Novartis Pharma AG Modeling & Simulation
SimBiology app for MATLAB ("Model, simulate, and analyze biological systems")The MathWorks, Inc.
SimcypSimcyp Ltd
truPKStrand Genomics
WinNonlinPharsight
WinNonMixPharsight
Xpose (for NONMEM)Xpose development team

Information Portals and Databases

ResourceDeveloper
AOPWiki - Adverse Outcome Pathway WikiAOPWiki team (includes European Commission JRC, USEPA ORD and OECD)
BioCartaBioCarta LLC
Biomarkers Database (last updated in August 2004)USEPA
BioNumbers ("The Database of Useful Biological Numbers")Weizmann Institute, Israel
BOSS - Biomarkers of Oxidative Stress StudyNIEHS
CEBS - Chemical Effects in Biological SystemsNIEHS
Comparative Toxicogenomics DatabaseMount Desert Island Biological Laboratory
Drug Information PortalNLM, NIH
DrugMatrixNIEHS
EPA-Expo-Box - EPA’s EXPOsure toolBOX ("A Toolbox for Exposure Assessors")USEPA
GAC - Genetic Alterations in CancerNIEHS
GerES - German Environmental SurveyThe Federal Environment Agency, Germany
HGMD - Human Gene Mutation Database (integrated with Ingenuity Variant Analysis) BIOBASE
ICRP - International Commission on Radiological Protection - Database of Dose CoefficientsICRP
IRIS - Integrated Risk Information SystemUSEPA
IUPHAR-DB - International Union of Basic and Clinical Pharmacology DatabaseIUPHAR-DB development team
KEGG MEDICUSKanehisa Laboratories, Japan
KUPKB - The Kidney and Urinary Pathway Knowledge BaseINSERM, France and University of Manchester, UK
LIVERTOX™NIDDK and NLM
MIEP - Modeling Immunity to Enteric PathogensCenter for Modeling Immunity to Enteric Pathogens, Virginia Tech
NCTRlcdb - NCTR Liver Cancer DatabaseUSFDA
NHANES - National Health and Nutrition Examination SurveyCDC
NHATS - National Human Adipose Tissue SurveyUSEPA
OncomineLife Technologies Corporation
P3M - Physiological Parameters for PBPK ModelingThe LifeLine Group
Pathophysiology of the Digestive SystemColorado State University
Pathophysiology of the Endocrine SystemColorado State University
PD map - Parkinson’s disease mapLCSB and Hiroaki Kitano team at SBI, Tokyo
PID - Physiological Information DatabaseUSEPA
PubMedNational Center for Biotechnology Information, NLM, NIH
Virtual Cells, Tissues, Organs

Virtual modeling of cells, tissues and organs

Computational Analysis Tools

ResourceDeveloper
AmiGO (Gene Ontology database search)AmiGO development team
Biocellion ("Computer Simulation of Living Cell Systems")biocellion development team
Cell ExplorerCell Explorer team
CellDesignerSystems Biology Institute, Japan
CellMLAuckland Bioengineering Institute, University of Auckland, NZ
CellSysInterdisciplinary Centre for Bioinformatics, University of Leipzig, Germany
Cmgui - Continuum Mechanics, Image Analysis, Signal Processing and System Identification Graphical User InterfaceAuckland Bioengineering Institute, University of Auckland, NZ
CompuCell 3DIndiana University and Biocomplexity Institute
CVSimCVSim development team
E-CellE-Cell Project Team
EpiSIM PlatformTIGA Center Heidelberg, Germany
FieldMLAuckland Bioengineering Institute, University of Auckland, NZ
GOFFA - Gene Ontology for Functional AnalysisUSFDA
GPU Codes for 3D Model of Epidermal DevelopmentUniversity of California, Irvine
JigCellVirgina Tech
LibSBML/ JSBML - Programming library for C++, Java, Python and othersSBML Team
MCell - Monte Carlo cellPittsburgh Supercomputing Center and Computational Neurobiology Laboratory, Salk Institute
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
NEURON ("for empirically-based simulations of neurons and networks of neurons")NEURON development team
OpenCell (for CellML models)Auckland Bioengineering Institute, University of Auckland, NZ
OpenCMISS/CM - Open Continuum Mechanics, Imaging, Signal processing and System identificationAuckland Bioengineering Institute, University of Auckland, NZ
OpenWormOpenWorm development team
PhysioDesignerPhysioDesigner development team
SBML - Systems Biology Markup LanguageSBML Team
SBML ConverterSBML Team
SBML Test SuiteSBML Team
SBMLeditorSBML team
SBMLToolbox (for MATLAB and Octave)SBML Team
VCell - The Virtual CellCenter for Cell Analysis and Modeling (CCAM), University of Connecticut
v-Embryo - Virtual Embryo ProjectUSEPA
VirtualLeaf ("cell-based computer-modeling framework for plant tissue morphogenesis")VirtualLeaf development team
v-Liver - Virtual Liver ProjectUSEPA
Zinc LibraryAuckland Bioengineering Institute, University of Auckland, NZ

Information Portals and Databases

ResourceDeveloper
BioModels ("repository of computational models of biological processes")EMBL-EBI
The Interactive FlyThe Interactive Fly development team (Thomas B. Brody)
TissueDistributionDBsGerman Cancer Research Center, DKFZ, Heidelberg
VT-KB - Virtual Tissues KnowledgebaseUSEPA
Whole Brain AtlasJohnson and Becker, Harvard Medical School
WholeCellKB-MG - Mycoplasma genitalium WholeCellKBStanford University
WormAtlasAlbert Einstein College of Medicine
WormBaseWormBase development team
WormBookWormBook development team
ZFIN (Zebrafish Model Organism Database)ZFIN Database development team
Virtual Model Organisms

Computational Analysis Tools

ResourceDeveloper
modMine ("data warehouse for the modENCODE project")University of Cambridge, Cambridge, UK
OpenWormOpenWorm development team

Information Portals and Databases

ResourceDeveloper
Berkeley Drosophila Genome ProjectBerkeley Drosophila Genome Project Consortium
EMA - e-Mouse AtlasEMA team
FlyBase - "A Database of Drosophila Genes & Genomes"FlyBase development team
FlyMine - "integrated database for Drosophila and Anopheles genomics"University of Cambridge, Cambridge, UK
GenAge DatabaseHAGR - Human Ageing Genomic Resources
MGI - Mouse Genome InformaticsThe Jackson Laboratory, Maine and MGI team
modENCODE - Model Organism ENCyclopedia Of DNA ElementsmodENCODE Project Consortium
Mouse Genome Resequencing ProjectNIEHS
MouseMine MGI at The Jackson Laboratory and InterMine project at Cambridge Systems Biology Centre, UK
NCBI Model Organisms GuideNational Center for Biotechnology Information, NLM, NIH
NIH Model Organisms for Biomedical ResearchNIH
Primate Info NetNational Primate Research Center, University of Wisconsin
RatMineUniversity of Cambridge, Cambridge, UK
RGD - Rat Genome DatabaseMedical College of Wisconsin
SGD - Saccharomyces Genome DatabaseStanford University
WholeCellKB-MG - Mycoplasma genitalium WholeCellKBStanford University
WormAtlasAlbert Einstein College of Medicine
WormBaseWormBase development team
WormBookWormBook development team
Xenbase ("Xenopus laevis and Xenopus tropicalis biology and genomics resource")University of Calgary, Alberta, Canada
Yeast GFP Fusion Localization DatabaseUniversity of California, San Francisco and SGD
YeastMine ("Search and retrieve S. cerevisiae data")SGD and Intermine project at Cambridge Systems Biology Centre, UK
ZebrafishMineZFIN at University of Oregon and InterMine project at Cambridge Systems Biology Centre, UK
ZFIN (Zebrafish Model Organism Database)ZFIN Database development team