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 |