Computational Toxicology-new

 
Toxicoinformatics

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

Tools

ResourceDeveloperProprietary or Public Domain?
ArrayTrack/ebTrackUSFDA and ebCTCpublic domain
BMDExpress ("analyze microarray dose-response data")BMDExpress teampublic domain
BRB-ArrayToolsDr. Richard Simon and BRB-ArrayTools Development Teampublic domain
CheS-Mapper ("Chemical Space Mapping and Visualization in 3D")Albert-Ludwigs-Universität Freiburg, Germany (M. Gutlein et al.)public domain
Decision ForestUSFDApublic domain
DORIAN - DOse-Response Information ANalysis systemComputational Chemodynamics Laboratoryproprietary
Ingenuity Variant AnalysisQiagenproprietary
IPA - Ingenuity Pathway AnalysisQiagen N.V.proprietary
MATLAB Bioinformatics ToolboxThe Mathworks, Inc.proprietary
maxdViewManchester Bioinformaticspublic domain
NONMEMICON Development Solutions and Regents of the University of Californiaproprietary
Pathway StudioPathway Studioproprietary
SBPOP Package ("Support for Model Based Drug Development – From Mechanistic Models to Complex Trial Simulation")SBPOP Package development team at Novartis Pharma AG Modeling & Simulationpublic domain
ToxFXNIEHSpublic domain
TOXMAPDivision of Specialized Information Services, US National Library of Medicinepublic domain
ToxmatchJoint Research Centre, IHCPpublic domain
ToxRTool - Toxicological data Reliability Assessment ToolEuropean Commissionpublic domain
Toxtree (Estimatation of toxic hazard by applying a decision tree approach)Ideaconsult Ltdpublic domain
v-Embryo - Virtual Embryo ProjectUSEPA
v-Liver - Virtual Liver ProjectUSEPA

Databases

ResourceDeveloperProprietary or Public Domain?
ACToR - Aggregated Computational Toxicology ResourceUSEPApublic domain
AOPWiki - Adverse Outcome Pathway WikiAOPWiki team (includes European Commission JRC, USEPA ORD and OECD)public domain
ArrayExpressEMBL-EBIpublic domain
Biomarkers Database (last updated in August 2004)USEPApublic domain
BOSS - Biomarkers of Oxidative Stress StudyNIEHSpublic domain
CEBS - Chemical Effects in Biological SystemsNIEHSpublic domain
Comparative Toxicogenomics DatabaseMount Desert Island Biological Laboratorypublic domain
Comprehensive Cancer InformationNCI (National Cancer Institute), NIHpublic domain
CPCat - Chemical and Product CategoriesUSEPApublic domain
CPDB - Carcinogenic Potency DatabaseCPDB development teampublic domain
DART - Developmental and Reproductive Toxicology DatabaseNLM, NIHpublic domain
DrugMatrixNIEHSpublic domain
EADB - Estrogenic Activity DatabaseUSFDApublic domain
EDKB - Endocrine Disruptor Knowledge BaseUSFDApublic domain
EMAGE - e-Mouse Atlas of Gene ExpressionEMAGE teampublic domain
Environmental Genome Project/ SNPs ProgramNIEHS and University of Washingtonpublic domain
EPR - Environmental Polymorphisms RegistryNIEHSpublic domain
EXTOXNET - EXTension TOXicology NETworkUniversity of California, Davis, Oregon State University, Michigan State University, Cornell University, and University of Idahopublic domain
GAC - Genetic Alterations in CancerNIEHSpublic domain
GeneToxNLMpublic domain
HGMD - Human Gene Mutation Database (integrated with Ingenuity Variant Analysis) BIOBASEproprietary
HSDB - Hazardous Substances Data BankNational Library of Medicinepublic domain
IARC Monographs- ClassificationsIARC, WHOpublic domain
IARC TP53 DatabaseIARC, WHOpublic domain
ICRP - International Commission on Radiological Protection - Database of Dose CoefficientsICRPpublic domain
IRIS - Integrated Risk Information SystemUSEPApublic domain
KEGG MEDICUSKanehisa Laboratories, Japanpublic domain
LTKB - Liver Toxicity Knowledge BaseUSFDApublic domain
MGI - Mouse Genome InformaticsThe Jackson Laboratory, Maine and MGI teampublic domain
National Toxicology Program Technical ReportsNIEHSpublic domain
NCTRlcdb - NCTR Liver Cancer DatabaseUSFDApublic domain
OpenToxOpenTox project teampublic domain
PD map - Parkinson’s disease mapLCSB and Hiroaki Kitano team at SBI, Tokyopublic domain
PharmGKB - Pharmacogenomics KnowledgebaseUS Dept of Health and Human Servicespublic domain
PubMedNational Center for Biotechnology Information, NLM, NIHpublic domain
RIVM e-toxBase ("ecotoxicity data on both terrestrial and aquatic species")RIVM (Netherlands National Institute for Public Health and the Environment)public domain
Tox TownU.S. National Library of Medicinepublic domain
ToxCast - Toxicity ForecasterUSEPApublic domain
ToxFAQsATSDR, CDCpublic domain
ToxGuides™ATSDR, CDCpublic domain
Toxic Substances PortalATSDR, CDCpublic domain
TOXLINE - Toxicology Literature OnlineNational Library of Medicinepublic domain
ToxNetNational Library of Medicinepublic domain
ToxProfilesATSDR, CDCpublic domain
ToxRefDB - Toxicity Reference DatabaseUSEPApublic domain
VT-KB - Virtual Tissues KnowledgebaseUSEPA
Dosimetry, Toxicokinetics, Toxicodynamics

Dosimetry, toxicokinetics, toxicodynamics

Tools

ResourceDeveloperProprietary or Public Domain?
ADAPT ("computational modeling platform [...] for pharmacokinetic and pharmacodynamic applications")Biomedical Simulations Resource, USCpublic domain
ADME Workbench ("pharmacokinetic modeling by integrating [...] absorption, distribution, metabolism and excretion methods")The AEgis Technologies Groupproprietary
ADMET Predictor - Absorption, Distribution, Metabolism, Elimination, Toxicity PredictorSimulations Plus, Inc.proprietary
bear ("data analysis tool for average bioequivalence (ABE) and bioavailability (BA) for useR")bear development teampublic domain
BEs - Biomonitoring EquivalentsSummit Toxicology, LLPpublic domain
BioDMET ("physiologically-based pharmacokinetic (PBPK) modeling and simulation tool")GE and DTRApublic domain
Biokmod ("Mathematica toolbox […] with application for modeling Linear and Nonlinear Biokinetic Systems")Guillermo Sanchezpublic domain
BiokmodWebGuillermo Sanchezpublic domain
BMDS - Benchmark Dose SoftwareUSEPApublic domain
Boomer ("Non-Linear Regression Program")D.W.A. Bournepublic domain
CalcuSynBiosoftproprietary
Cloe PKCyprotex PLCproprietary
Cloe PredictCyprotexproprietary
Cyber PatientMichael B. Bolger, USCpublic domain
DCAL - Dose and Risk Calculation SoftwareOak Ridge National Laboratory and USEPApublic domain
DDI PredictAureus SciencesProprietary
DORIAN - DOse-Response Information ANalysis systemComputational Chemodynamics Laboratoryproprietary
DoseSimSCB Research Group, Colorado State Universitypublic domain
ERDEM - Exposure Related Dose Estimating ModelUSEPApublic domain
GastroPlusSimulations Plus Incproprietary
InDose ("Internal Dosimetry Code Using Biokinetics Models")Soreq - Nuclear Research Center, Israel (I. Silverman)public domain
ISDD - In vitro Sedimentation, Diffusion and Dosimetry modelPNNLproprietary
LUDEP - Lung Dose Evaluation ProgramNational Radiological Protection Board, UKproprietary
MADr-BMD - Model Averaging for Dichotomous Response Benchmark DoseWheeler and Bailerpublic domain
MENTOR-3P - Modeling ENvironment for TOtal Risk studies using Physiologically-based Pharmacokinetic modeling tools for Population assessmentsComputational Chemodynamics Laboratoryproprietary
MIEP - Modeling Immunity to Enteric PathogensCenter for Modeling Immunity to Enteric Pathogens, Virginia Techpublic domain
MPPD - Multiple-Path Particle Dosimetry ModelApplied Research Associatespublic domain
NONMEMICON Development Solutions and Regents of the University of Californiaproprietary
PhysioDesignerPhysioDesigner development teampublic domain
PK SolutionsSummit Researchproprietary
PKQuestDavid Levitt, University of Minnesotapublic domain
PK-SimBayer Technologyproprietary
SBPOP Package ("Support for Model Based Drug Development – From Mechanistic Models to Complex Trial Simulation")SBPOP Package development team at Novartis Pharma AG Modeling & Simulationpublic domain
SimBiology app for MATLAB ("Model, simulate, and analyze biological systems")The MathWorks, Inc.proprietary
SimcypSimcyp Ltdproprietary
truPKStrand Genomicsproprietary
WinNonlinPharsightproprietary
WinNonMixPharsightproprietary
Xpose (for NONMEM)Xpose development teampublic domain

Databases

ResourceDeveloperProprietary or Public Domain?
AOPWiki - Adverse Outcome Pathway WikiAOPWiki team (includes European Commission JRC, USEPA ORD and OECD)public domain
BioCartaBioCarta LLCproprietary
Biomarkers Database (last updated in August 2004)USEPApublic domain
BioNumbers ("The Database of Useful Biological Numbers")Weizmann Institute, Israelpublic domain
BOSS - Biomarkers of Oxidative Stress StudyNIEHSpublic domain
CEBS - Chemical Effects in Biological SystemsNIEHSpublic domain
Comparative Toxicogenomics DatabaseMount Desert Island Biological Laboratorypublic domain
Drug Information PortalNLM, NIHpublic domain
DrugMatrixNIEHSpublic domain
EPA-Expo-Box - EPA’s EXPOsure toolBOX ("A Toolbox for Exposure Assessors")USEPApublic domain
GAC - Genetic Alterations in CancerNIEHSpublic domain
GerES - German Environmental SurveyThe Federal Environment Agency, Germanypublic domain
HGMD - Human Gene Mutation Database (integrated with Ingenuity Variant Analysis) BIOBASEproprietary
ICRP - International Commission on Radiological Protection - Database of Dose CoefficientsICRPpublic domain
IRIS - Integrated Risk Information SystemUSEPApublic domain
IUPHAR-DB - International Union of Basic and Clinical Pharmacology DatabaseIUPHAR-DB development teampublic domain
KEGG MEDICUSKanehisa Laboratories, Japanpublic domain
KUPKB - The Kidney and Urinary Pathway Knowledge BaseINSERM, France and University of Manchester, UKpublic domain
LIVERTOX™NIDDK and NLMpublic domain
MIEP - Modeling Immunity to Enteric PathogensCenter for Modeling Immunity to Enteric Pathogens, Virginia Techpublic domain
NCTRlcdb - NCTR Liver Cancer DatabaseUSFDApublic domain
NHANES - National Health and Nutrition Examination SurveyCDCpublic domain
NHATS - National Human Adipose Tissue SurveyUSEPApublic domain
OncomineLife Technologies Corporationproprietary
P3M - Physiological Parameters for PBPK ModelingThe LifeLine Grouppublic domain
Pathophysiology of the Digestive SystemColorado State Universitypublic domain
Pathophysiology of the Endocrine SystemColorado State Universitypublic domain
PD map - Parkinson’s disease mapLCSB and Hiroaki Kitano team at SBI, Tokyopublic domain
PID - Physiological Information DatabaseUSEPApublic domain
PubMedNational Center for Biotechnology Information, NLM, NIHpublic domain
Virtual Cells, Tissues, Organs

Virtual modeling of cells, tissues and organs

Tools

ResourceDeveloperProprietary or Public Domain?
AmiGO (Gene Ontology database search)AmiGO development teampublic domain
Biocellion ("Computer Simulation of Living Cell Systems")biocellion development teampublic domain
Cell ExplorerCell Explorer teampublic domain
CellDesignerSystems Biology Institute, Japanpublic domain
CellMLAuckland Bioengineering Institute, University of Auckland, NZpublic domain
CellSysInterdisciplinary Centre for Bioinformatics, University of Leipzig, Germanypublic domain
Cmgui - Continuum Mechanics, Image Analysis, Signal Processing and System Identification Graphical User InterfaceAuckland Bioengineering Institute, University of Auckland, NZpublic domain
CompuCell 3DIndiana University and Biocomplexity Institutepublic domain
CVSimCVSim development teampublic domain
E-CellE-Cell Project Teampublic domain
EpiSIM PlatformTIGA Center Heidelberg, Germanypublic domain
FieldMLAuckland Bioengineering Institute, University of Auckland, NZpublic domain
GOFFA - Gene Ontology for Functional AnalysisUSFDApublic domain
GPU Codes for 3D Model of Epidermal DevelopmentUniversity of California, Irvinepublic domain
JigCellVirgina Techpublic domain
LibSBML/ JSBML - Programming library for C++, Java, Python and othersSBML Teampublic domain
MCell - Monte Carlo cellPittsburgh Supercomputing Center and Computational Neurobiology Laboratory, Salk Institutepublic domain
Morpheus ("modeling and simulation environment for the study of multiscale and multicellular systems")Center for Information Services and High Performance Computing, Technische Universität Dresden, Germanypublic domain
NEURON ("for empirically-based simulations of neurons and networks of neurons")NEURON development teampublic domain
OpenCell (for CellML models)Auckland Bioengineering Institute, University of Auckland, NZpublic domain
OpenCMISS/CM - Open Continuum Mechanics, Imaging, Signal processing and System identificationAuckland Bioengineering Institute, University of Auckland, NZpublic domain
OpenWormOpenWorm development teampublic domain
PhysioDesignerPhysioDesigner development teampublic domain
SBML - Systems Biology Markup LanguageSBML Teampublic domain
SBML ConverterSBML Teampublic domain
SBML Test SuiteSBML Teampublic domain
SBMLeditorSBML teampublic domain
SBMLToolbox (for MATLAB and Octave)SBML Teampublic domain
VCell - The Virtual CellCenter for Cell Analysis and Modeling (CCAM), University of Connecticutpublic domain
v-Embryo - Virtual Embryo ProjectUSEPA
VirtualLeaf ("cell-based computer-modeling framework for plant tissue morphogenesis")VirtualLeaf development teampublic domain
v-Liver - Virtual Liver ProjectUSEPA
Zinc LibraryAuckland Bioengineering Institute, University of Auckland, NZpublic domain

Databases

ResourceDeveloperProprietary or Public Domain?
BioModels ("repository of computational models of biological processes")EMBL-EBIpublic domain
The Interactive FlyThe Interactive Fly development team (Thomas B. Brody)public domain
TissueDistributionDBsGerman Cancer Research Center, DKFZ, Heidelbergpublic domain
VT-KB - Virtual Tissues KnowledgebaseUSEPA
Whole Brain AtlasJohnson and Becker, Harvard Medical SchoolPublic Domain
WholeCellKB-MG - Mycoplasma genitalium WholeCellKBStanford Universitypublic domain
WormAtlasAlbert Einstein College of Medicinepublic domain
WormBaseWormBase development teampublic domain
WormBookWormBook development teampublic domain
ZFIN (Zebrafish Model Organism Database)ZFIN Database development teampublic domain
Virtual Model Organisms

Tools

ResourceDeveloperProprietary or Public Domain?
modMine ("data warehouse for the modENCODE project")University of Cambridge, Cambridge, UKpublic domain
OpenWormOpenWorm development teampublic domain

Databases

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