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 |