Training & Resources

On this page:

• Training
• Working with BMDS Online
• References
  • Technical Guidance
  • Models Included in Current and Previous BMDS Versions
  • History and Peer Reviews
  • Recent BMDS References in the Scientific Literature
• Externally Produced Benchmark Dose Applications

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Training

• A series of BMDS training videos on benchmark dose modeling concepts, the application's numerous modeling choices, and the BMDS Online application. 

Working with BMDS Online

• Step-by-step guide to modeling dichotomous data in BMDS Online.
• Frequent Questions on BMDS Online/Desktop/pybmds and BMDS 3.3.
• What's new and updated in BMDS Online.
• Citing BMDS Results for published research.
• BMDS Glossary - Exhaustive list of technical terms used in the BMDS documentation and BMD Technical Guidance. Another good source of dose-response terminology is the Integrated Risk Information System (IRIS) Glossary.

References

Technical Guidance

• Benchmark Dose Technical Guidance (U.S. EPA, 2012) - Basis for BMDS's approach and methods.
• Choosing Appropriate Stage of a Multistage Model for Cancer Modeling (BMDS Technical Guidance) (U.S. EPA, 2014)

Models Included in Current and Previous BMDS Versions

• A list of all benchmark dose models that have been included in BMDS releases; most models are accessible from BMDS Online/Desktop/pybmds.
• Models no longer included in BMDS but that are available for individual download or in BMDS 2.7:
  • Repeated Response Measures / ToxicoDiffusion
  • ten Berge Concentration x Time (superseded by CatReg 3.0)
  • Multistage Weibull (MSW) Time-to-Tumor

History and Peer Reviews

• BMDS Application History & Peer Reviews - Timeline of BMDS from its inception to its latest release.
• A report from a 2015 public workshop on model averaging methods for dose-response analysis; the report summarizes the workshop, and includes discussion questions and responses.

Recent BMDS References in the Scientific Literature

Recent citations in the scientific literature, from 2022 to the present, to BMDS 3.x and BMDS Online. 

Externally Produced Benchmark Dose Applications

The following externally produced benchmark dose applications can be used in addition to BMDS.

• The PROAST software developed by the Netherlands' National Institute for Public Health and the Environment (RIVM) requires R or S-plus to run, but has some advantages over BMDS, including the ability to include covariates in an analysis. The U.S. EPA and RIVM are working together to achieve consistency between the BMDS and PROAST software packages.
• The Health Assessment Workspace Collaborative (HAWC) is an online application designed to store, display, and synthesize multiple data sources for the purpose of supporting the development of human health and environmental assessments of pollutants. HAWC documents the overall workflow of developing an assessment, from literature search and systematic review, to data extraction (human epidemiology, animal bioassay, and in vitro assay), dose-response analysis, and finally evidence synthesis and visualization.
• BMDExpress provides a workflow to transform toxicogenomic data into benchmark doses for aggregated collections of genes. BMDExpress is the product of an ongoing collaboration between the National Institute of Environmental Health (NIEHS) Division of the National Toxicology Program (NTP), Health Canada, US EPA, and Sciome LLC, with Sciome primarily responsible for designing and implementing the resulting software.
• ToxicR is an R package that utilizes the core functionality of the US EPA's Benchmark Dose Software and the NTP's BMDExpress, which was developed in unison with researchers from the NIEHS. ToxicR is fully interactive and can be used to create custom analysis pipelines within the R programming environment.