Computational Toxicology » Environmental Bioinformatics Knowledge Base


  Toxicoinformatics

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

Computational Analysis Tools

Information Portals and Databases

Resource Developer
ACToR – Aggregated Computational Toxicology Resource USEPA
AOPWiki – Adverse Outcome Pathway Wiki AOPWiki team (includes European Commission JRC, USEPA ORD and OECD)
ArrayExpress EMBL-EBI
Biomarkers Database (last updated in August 2004) USEPA
BOSS – Biomarkers of Oxidative Stress Study NIEHS
CEBS – Chemical Effects in Biological Systems NIEHS
Comparative Toxicogenomics Database Mount Desert Island Biological Laboratory
Comprehensive Cancer Information NCI (National Cancer Institute), NIH
CPCat – Chemical and Product Categories USEPA
CPDB – Carcinogenic Potency Database CPDB development team
DART – Developmental and Reproductive Toxicology Database NLM, NIH
DrugMatrix NIEHS
EADB – Estrogenic Activity Database USFDA
EDKB – Endocrine Disruptor Knowledge Base USFDA
EMAGE – e-Mouse Atlas of Gene Expression EMAGE team
Environmental Genome Project/ SNPs Program NIEHS and University of Washington
EPR – Environmental Polymorphisms Registry NIEHS
EXTOXNET – EXTension TOXicology NETwork University of California, Davis, Oregon State University, Michigan State University, Cornell University, and University of Idaho
GAC – Genetic Alterations in Cancer NIEHS
GeneTox NLM
HGMD – Human Gene Mutation Database (integrated with Ingenuity Variant Analysis) BIOBASE
HSDB – Hazardous Substances Data Bank National Library of Medicine
IARC Monographs- Classifications IARC, WHO
IARC TP53 Database IARC, WHO
ICRP – International Commission on Radiological Protection – Database of Dose Coefficients ICRP
IRIS – Integrated Risk Information System USEPA
KEGG MEDICUS Kanehisa Laboratories, Japan
LTKB – Liver Toxicity Knowledge Base USFDA
MGI – Mouse Genome Informatics The Jackson Laboratory, Maine and MGI team
National Toxicology Program Technical Reports NIEHS
NCTRlcdb – NCTR Liver Cancer Database USFDA
OpenTox OpenTox project team
PD map – Parkinson’s disease map LCSB and Hiroaki Kitano team at SBI, Tokyo
PharmGKB – Pharmacogenomics Knowledgebase US Dept of Health and Human Services
PubMed National 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 Town U.S. National Library of Medicine
ToxCast – Toxicity Forecaster USEPA
ToxFAQs ATSDR, CDC
ToxGuides™ ATSDR, CDC
Toxic Substances Portal ATSDR, CDC
TOXLINE – Toxicology Literature Online National Library of Medicine
ToxNet National Library of Medicine
ToxProfiles ATSDR, CDC
ToxRefDB – Toxicity Reference Database USEPA
VT-KB – Virtual Tissues Knowledgebase USEPA

Dosimetry, Toxicokinetics, Toxicodynamics

Dosimetry, toxicokinetics, toxicodynamics

Computational Analysis Tools

Resource Developer
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 Predictor Simulations Plus, Inc.
bear (“data analysis tool for average bioequivalence (ABE) and bioavailability (BA) for useR”) bear development team
BEs – Biomonitoring Equivalents Summit 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
BiokmodWeb Guillermo Sanchez
BMDS – Benchmark Dose Software USEPA
Boomer (“Non-Linear Regression Program”) D.W.A. Bourne
CalcuSyn Biosoft
Cloe PK Cyprotex PLC
Cloe Predict Cyprotex
Cyber Patient Michael B. Bolger, USC
DCAL – Dose and Risk Calculation Software Oak Ridge National Laboratory and USEPA
DDI Predict Aureus Sciences
DORIAN – DOse-Response Information ANalysis system Computational Chemodynamics Laboratory
DoseSim SCB Research Group, Colorado State University
ERDEM – Exposure Related Dose Estimating Model USEPA
GastroPlus Simulations Plus Inc
InDose (“Internal Dosimetry Code Using Biokinetics Models”) Soreq – Nuclear Research Center, Israel (I. Silverman)
ISDD – In vitro Sedimentation, Diffusion and Dosimetry model PNNL
LUDEP – Lung Dose Evaluation Program National Radiological Protection Board, UK
MADr-BMD – Model Averaging for Dichotomous Response Benchmark Dose Wheeler and Bailer
MENTOR-3P – Modeling ENvironment for TOtal Risk studies using Physiologically-based Pharmacokinetic modeling tools for Population assessments Computational Chemodynamics Laboratory
MIEP – Modeling Immunity to Enteric Pathogens Center for Modeling Immunity to Enteric Pathogens, Virginia Tech
MPPD – Multiple-Path Particle Dosimetry Model Applied Research Associates
NONMEM ICON Development Solutions and Regents of the University of California
PhysioDesigner PhysioDesigner development team
PK Solutions Summit Research
PKQuest David Levitt, University of Minnesota
PK-Sim Bayer 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.
Simcyp Simcyp Ltd
truPK Strand Genomics
WinNonlin Pharsight
WinNonMix Pharsight
Xpose (for NONMEM) Xpose development team

Information Portals and Databases

Resource Developer
AOPWiki – Adverse Outcome Pathway Wiki AOPWiki team (includes European Commission JRC, USEPA ORD and OECD)
BioCarta BioCarta LLC
Biomarkers Database (last updated in August 2004) USEPA
BioNumbers (“The Database of Useful Biological Numbers”) Weizmann Institute, Israel
BOSS – Biomarkers of Oxidative Stress Study NIEHS
CEBS – Chemical Effects in Biological Systems NIEHS
Comparative Toxicogenomics Database Mount Desert Island Biological Laboratory
Drug Information Portal NLM, NIH
DrugMatrix NIEHS
EPA-Expo-Box – EPA’s EXPOsure toolBOX (“A Toolbox for Exposure Assessors”) USEPA
GAC – Genetic Alterations in Cancer NIEHS
GerES – German Environmental Survey The Federal Environment Agency, Germany
HGMD – Human Gene Mutation Database (integrated with Ingenuity Variant Analysis) BIOBASE
ICRP – International Commission on Radiological Protection – Database of Dose Coefficients ICRP
IRIS – Integrated Risk Information System USEPA
IUPHAR-DB – International Union of Basic and Clinical Pharmacology Database IUPHAR-DB development team
KEGG MEDICUS Kanehisa Laboratories, Japan
KUPKB – The Kidney and Urinary Pathway Knowledge Base INSERM, France and University of Manchester, UK
LIVERTOX™ NIDDK and NLM
MIEP – Modeling Immunity to Enteric Pathogens Center for Modeling Immunity to Enteric Pathogens, Virginia Tech
NCTRlcdb – NCTR Liver Cancer Database USFDA
NHANES – National Health and Nutrition Examination Survey CDC
NHATS – National Human Adipose Tissue Survey USEPA
Oncomine Life Technologies Corporation
P3M – Physiological Parameters for PBPK Modeling The LifeLine Group
Pathophysiology of the Digestive System Colorado State University
Pathophysiology of the Endocrine System Colorado State University
PD map – Parkinson’s disease map LCSB and Hiroaki Kitano team at SBI, Tokyo
PID – Physiological Information Database USEPA
PubMed National Center for Biotechnology Information, NLM, NIH

Virtual Cells, Tissues, Organs

Virtual modeling of cells, tissues and organs

Computational Analysis Tools

Resource Developer
AmiGO (Gene Ontology database search) AmiGO development team
Biocellion (“Computer Simulation of Living Cell Systems”) biocellion development team
Cell Explorer Cell Explorer team
CellDesigner Systems Biology Institute, Japan
CellML Auckland Bioengineering Institute, University of Auckland, NZ
CellSys Interdisciplinary Centre for Bioinformatics, University of Leipzig, Germany
Cmgui – Continuum Mechanics, Image Analysis, Signal Processing and System Identification Graphical User Interface Auckland Bioengineering Institute, University of Auckland, NZ
CompuCell 3D Indiana University and Biocomplexity Institute
CVSim CVSim development team
E-Cell E-Cell Project Team
EpiSIM Platform TIGA Center Heidelberg, Germany
FieldML Auckland Bioengineering Institute, University of Auckland, NZ
GOFFA – Gene Ontology for Functional Analysis USFDA
GPU Codes for 3D Model of Epidermal Development University of California, Irvine
JigCell Virgina Tech
LibSBML/ JSBML – Programming library for C++, Java, Python and others SBML Team
MCell – Monte Carlo cell Pittsburgh 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 identification Auckland Bioengineering Institute, University of Auckland, NZ
OpenWorm OpenWorm development team
PhysioDesigner PhysioDesigner development team
SBML – Systems Biology Markup Language SBML Team
SBML Converter SBML Team
SBML Test Suite SBML Team
SBMLeditor SBML team
SBMLToolbox (for MATLAB and Octave) SBML Team
VCell – The Virtual Cell Center for Cell Analysis and Modeling (CCAM), University of Connecticut
v-Embryo – Virtual Embryo Project USEPA
VirtualLeaf (“cell-based computer-modeling framework for plant tissue morphogenesis”) VirtualLeaf development team
v-Liver – Virtual Liver Project USEPA
Zinc Library Auckland Bioengineering Institute, University of Auckland, NZ

Information Portals and Databases

Virtual Model Organisms

Computational Analysis Tools

Information Portals and Databases

Resource Developer
Berkeley Drosophila Genome Project Berkeley Drosophila Genome Project Consortium
EMA – e-Mouse Atlas EMA 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 Database HAGR – Human Ageing Genomic Resources
MGI – Mouse Genome Informatics The Jackson Laboratory, Maine and MGI team
modENCODE – Model Organism ENCyclopedia Of DNA Elements modENCODE Project Consortium
Mouse Genome Resequencing Project NIEHS
MouseMine MGI at The Jackson Laboratory and InterMine project at Cambridge Systems Biology Centre, UK
NCBI Model Organisms Guide National Center for Biotechnology Information, NLM, NIH
NIH Model Organisms for Biomedical Research NIH
Primate Info Net National Primate Research Center, University of Wisconsin
RatMine University of Cambridge, Cambridge, UK
RGD – Rat Genome Database Medical College of Wisconsin
SGD – Saccharomyces Genome Database Stanford University
WholeCellKB-MG – Mycoplasma genitalium WholeCellKB Stanford University
WormAtlas Albert Einstein College of Medicine
WormBase WormBase development team
WormBook WormBook development team
Xenbase (“Xenopus laevis and Xenopus tropicalis biology and genomics resource”) University of Calgary, Alberta, Canada
Yeast GFP Fusion Localization Database University of California, San Francisco and SGD
YeastMine (“Search and retrieve S. cerevisiae data”) SGD and Intermine project at Cambridge Systems Biology Centre, UK
ZebrafishMine ZFIN at University of Oregon and InterMine project at Cambridge Systems Biology Centre, UK
ZFIN (Zebrafish Model Organism Database) ZFIN Database development team