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Benchmark Dose Tools

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Benchmark Dose Tools Mailing List Announcements

The following BMDS and CatReg news and announcements were sent to members of the BMDS mailing list and are archived here for historic and reference purposes.

They provide a more detailed complement to the BMDS Release History items with a focus on incremental development.

The announcements have been lightly edited to remove outdated URLs and redundancy. The announcements are organized by year. 

2020

February 5, BMDS-News Announcement #71: Possible issue with Multitumor (MScombo) model and 64-Bit Excel

Some users have experienced failure of the BMDS Multitumor (MScombo) model for runs of multiple datasets.

The failures seem to be related to an incompatibility between MScombo and 64-bit Excel. We are hopeful that this will be fixed in BMDS 3.2, which will also include a beta version of the Agency's Bayesian continuous model averaging (CMA) and is planned for release in March 2020.

In the meantime, if you need to perform perform analyses of multiple datasets with the Multitumor (MScombo) model you can choose from the following options, depending on your circumstances:

  • Use Multitumor (MScombo) in BMDS 2.7.0.4, which should give the same results since it uses the same MScombo executable as BMDS 3.1.2.
  • Use Multitumor (MScombo) in BMDS 3.1.2 on another computer that uses a 32-bit version of Excel, or
  • Use Multitumor (MScombo) in BMDS 3.1.2 on your computer after uninstalling your 64-bit Microsoft Office and installing Office 32-bit by logging into your Microsoft account with your registered email address (according to Microsoft Support, "you would not have to purchase another license and it will not affect your data," but it is always a good idea to back up your data before making any significant changes to the setup of your computer).

As always, thanks you for your valuable feedback. If you have questions or concerns please submit them our BMDS e-Ticket system.

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September 9, BMDS-News Announcement #72: BMDS 3.2 is Available for Download

Version 3.2 of EPA’s risk assessment tool, Benchmark Dose Software (BMDS), is available for download from the BMDS web site.

Enhancements and fixes to the frequentist continuous models – plus the addition of preview versions of Bayesian continuous models – are some of this release’s key features, along with numerous minor improvements to the stability and performance of the BMDS model suite.

The most significant addition to the BMDS model suite are preview versions of Bayesian continuous models. Users can set up individual Bayesian model runs as Normal, Lognormal, or combined Normal and Lognormal. Bayesian models represent the state of the art in dose-response analysis, allowing for more robust handling of problematic datasets. The Bayesian approach allows model developers to consider “prior” or historical information regarding the shape of dose-response curves.

The BMDS Bayesian models come with a caveat: at this time EPA does not offer technical guidance on Bayesian modeling or Bayesian model averaging. Until such guidance is available, EPA risk assessments will continue to rely on existing BMD guidance (U.S. EPA, 2012) for the selection of a single model from the standard (default) suite of non-Bayesian models available in BMDS.

Some of the frequentist continuous model improvements include:
  • Rescaled the v parameter for the Hill model to agree with BMDS 2.7 results.
  • Rescaled model parameters during the optimization process to improve robustness and efficiency of optimization routines.
  • Improved BMDS error handling for cases when some continuous models may not return values for the maximum-likelihood estimation (MLE).
A short rundown of other fixes and enhancements in BMDS 3.2 include:
  • BMDS graphs now extend the plots to zero dose for all models. All plots will begin at dose=0, even if the data has a lowest dose greater than 0.
  • The first five rows of the Analysis Workbook’s Data tab are frozen to keep the Insert New Dataset and Import Dataset buttons visible as new datasets are entered.
  • Improved error messaging for easier bug reporting when models fail while retrieving results from the dynamic link library (DLL).
  • The Results Workbook entry for Litter Specific Covariate (LSC) (under User Input > Model Options) now reports the fixed LSC value in output for nested models.
  • Fixed a bug that caused dichotomous multi-tumor analysis (MS_Combo) to crash 64-bit Excel.
  • Fixed an MS_Combo bug that allowed multiple runs to be set as selected when searching for lowest Akaike Information Criterion (AIC) when no model parameters hit a boundary.
  • When importing BMDS 2.7 .dax files that contain disallowed characters in the column headers, BMDS 3.2 will remove the disallowed characters.

The BMDS Release History page lists all features, enhancements, fixes, and changes introduced for this BMDS 3 release.

And also continue to provide us with your valuable feedback through our BMDS e-Ticket Help system.

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2019

February 28, BMDS-News Announcement #63 - BMDS 3.1 is Now Available!!

The new and improved BMDS 3.1 is now available from the EPA BMDS website. This exciting new version contains many significant improvements based on the insightful comments from BMDS 3.0 users.
  • Now compatible with all 32- and 64-bit versions of Excel released since 2007
  • Enables running BMDS from network drives
  • Improves stability of Multistage model when estimating BMDs for added risk
  • Fixes an issue with AIC derivation for continuous response models
  • Fixes various minor issues with Weibull, nested and continuous models
  • Improves on the organization and readability of modeling results in the Results Workbook

And also continue to provide us with your valuable feedback through our BMDS e-Ticket Help system.

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July 1, BMDS-News Announcement #64: BMDS 3 Tips, Training, and New Releases

BMDS 3 Training

EPA will provide BMDS 3 training at the upcoming December 2019 Society for Risk Analysis (SRA) conference in Arlington, VA. The training will focus on the new BMDS Bayesian model averaging components. Look for a future BMDS News announcement or the SRA 2019 conference web page Exitfor details. Please RSVP to Allen Davis  if you want to attend this training event.

BMDS 3 New Releases

EPA plans on releasing two BMDS 3 updates this year:
  • BMDS 3.1.1 will be released in late July 2019 to fix issues with the Multistage and Exponential model AIC derivations, along with some continuous response model convergence issues that can occur for certain datasets. The release will also contain numerous user interface improvements.
  • BMDS 3.2 will be released in Fall/Winter of 2019 and will contain new features, such as Bayesian model averaging for continuous responses, the NCTR nested dichotomous model for developmental data, and improved Word reporting performance. BMDS 3.2 will also fix a known issue with the AIC derivation for lognormal versions of the Exponential models.

BMDS 3.1 Tips

  • BMDS 2.7's Exponential Model results should be used for the lognormal distribution assumption option. BMDS 3.2 will include a fix for the lognormal Exponential Model AIC derivation issue.   
  • Improving the stability of the BMDS 3.1 multiple model processing feature is a high priority. If you receive the "restart program" message in BMDS 3.1, it is likely due to the inability of one or more models to converge on a solution; in this case, you should try running the models individually. Future versions of BMDS will not require you to restart BMDS if a model fails and will offer increased flexibility for running the individual Multistage and Exponential models.
  • Most importantly, if you are having any issues with BMDS3 please send your feedback via the BMDS e-Ticket Help system. We will respond as quickly as possible.

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August 1, BMDS-News Announcement #65: BMDS 3.1.1 is Here!

BMDS 3.1.1 is now available from the EPA BMDS website and includes a long list of enhancements (thank you all for your suggestions and feedback).  
  • Datasets can be saved for use later in another analysis.
  • BMDS 2.x and saved BMDS 3.x datasets can be imported. 
  • Data points now appear on summary plots for all model types.
  • Confidence interval error bars now appear on plots for all but lognormal models.
  • Convenient checkbox features that allow for selection/deselection of all options.
  • Multitumor model improvements like more user-definable inputs and an improved output format.
  • More interface hover text describing model features and outputs.
  • Faster generation of Result Workbooks.
  • Loading an analysis now loads datasets that were selected when the analysis was run/saved.
  • Improved continuous model convergence.
  • Fixed the parameter count issue for the first-degree multistage model.
  • Fixed a bug related to MS_Combo use of "Test Threshold" from the "Logic" tab.
  • Fixed a bug related to Word report generation from MS_Combo analysis.

Don't delay - download BMDS 3.1.1 now! And also continue to provide us with your valuable feedback through our BMDS e-Ticket Help system.

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August 21, BMDS News Announcement #66: BMDS Training at 2019 SRA Conference, Arlington VA (using new, planned release, BMDS 3.2)

 A full-day workshop on December 12th at the Annual Meeting of the Society for Risk Analysis (SRA) Exitwill provide participants with fundamental knowledge of benchmark dose (BMD) analysis and hands-on experience in support of chemical risk assessment.

The workshop will introduce benchmark dose modeling and analysis, probabilistic dose-response assessment in a Bayesian framework (including distributional BMD estimation), and model-averaging concepts.  In particular, model-averaging approaches will be highlighted given they have recently been suggested as a preferred approach to address modeling uncertainty in dose-response assessments.  Dichotomous model averaging was implemented in EPA's Benchmark Dose Software (BMDS 3.0), which simplified the workflow for modeling by fully implementing all BMDS analyses in Microsoft Excel. 

By the December SRA conference, EPA will have released BMDS 3.2, which will implement Bayesian model averaging methods for continuous data using maximum a posteriori methods in conjunction with model weights based on the Laplace approximation.  The model-averaging approach for continuous data to be implemented in BMDS 3.2 will improve on other model-averaging methods by not only averaging over a model suite, but also across distributional assumptions.  Historically, different organizations have a priori assumed either a normal or lognormal distribution for the continuous endpoint being modeled.  However, this determination has typically been based on assumptions rather than empirical evidence.  Thus, the use of distributional assumptions has also introduced uncertainty into continuous dose-response analyses.  Therefore, the ability of a continuous model-averaging approach to average over models and distributions accounts for both model and distributional uncertainty. 

Additionally, new versions of BMDS will be developed 1) in the R statistical programming language and 2) online in EPA's HAWC Exitinterface.  The R-BMDS version will represent a fully customizable "research" version of BMDS, whereas HAWC-BMDS will be a fully interoperable option for performing dose-response analyses online. 

The SRA training will center on how to use the BMDS 3.2 Excel interface and the theory and application of the new models, particularly the model-averaging methods.  The R- and HAWC-BMDS versions will also be briefly covered.  

Participants will need to attend the workshop with their own laptops; the laptops will need both a recent internet browser (Google Chrome is preferred) and BMDS 3.2  installed.  When available, BMDS 3.2 can be downloaded from the BMDS web site.  The latest version of BMDS is available from the website.

Disclaimer: the views expressed in this abstract are those of the authors and do not necessarily reflect the view or policies of the US EPA.

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September 24, BMDS-News Announcement #67: Registration is Now Open for BMDS Training at 2019 SRA Conference, Arlington VA

Registration is now openExit for the full-day training on Dose-Response Modeling and Risk Assessments -- BMDS 3.2 and Bayesian Model Averaging.  Final decisions on workshop viability will be made by SRA on October 30, 2019.  Please register early; doing so will allow you to register for a discounted price and will ensure that the BMDS workshop is accepted by SRA.  For those interested in attending only the workshop, a registration option for workshops only is available (for no additional cost). 

For more information on the workshop, see BMDS-News Announcement #66.

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September 25, BMDS-News Announcement #68: BMDS 3.1.2 and 3.2 Coming Soon

EPA plans to release two new versions of BMDS over the next few months. Both will be available from the BMDS website.
  • BMDS 3.1.2 will be distributed in October 2019 and will contain model bug fixes that will further enhance BMDS performance and stability.
  • A major release, BMDS 3.2, is planned for December 2019. BMDS 3.2 will contain new Bayesian models and Bayesian model averaging capability for continuous response endpoints. 

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October 18, BMDS-News Announcement #69: Reminder: Early-bird pricing ends October 30 for BMDS Training at 2019 SRA Conference

Early-bird pricing ends October 30 for training provided at the 2019 Society of Risk Analysis (SRA) meeting.Exit The full-day BMDS workshop on December 12th will provide participants with fundamental knowledge of benchmark dose (BMD) analysis and hands-on experience in support of chemical risk assessment.

For more information on the workshop, see BMDS-News Announcement #66.

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November 12, BMDS-News Announcement #70: BMDS 3.1.2 Is Now Available!

BMDS 3.1.2 is now available from the BMDS website and includes the following fixes, changes, and enhancements:
  • Fixed issue with unrestricted frequentist LogProbit model fitting for specific datasets.
  • Fixed issue with Weibull model crashes for specific datasets.
  • Fixed issue with dichotomous model crashes for some combinations of datasets and option sets.
  • Resolved continuous and dichotomous model convergence issues that caused result discrepancies between BMDS 2.7 and 3.1.1 in some cases.
  • Consistent with BMDS 2.x versions, 3.1.2 now defaults to the restricted version of the dichotomous Hill model.
  • The model weight column heading on the main tab of BMDS3.x was changed from "Model Weight" to "Prior Weights", with hover text added to clarify the intent of model weights.

Visit the BMDS website to download BMDS 3.1.2. And also continue to provide us with your valuable feedback through our BMDS e-Ticket Help system.

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2018

September 11, BMDS-News Announcement #59 - 2018 SRA Training - Quantitative Dose-Response Modeling Methods and Tools

Those interested in this course are encouraged to register by October 31, 2018 by visiting the SRA website. While pre-registration is open into November, the course may not be offered if sufficient class size is not reached by October 31.

This will be a two part course. Part I will cover the basics of Bayesian Benchmark Dose Analysis. Part II will focus on performing benchmark dose analyses using the recently released versions of EPA's Categorical Regression (CatReg) and benchmark dose software (BMDS 3.0).

Part I - This half-day workshop will provide participants with fundamental knowledge of benchmark dose (BMD) analysis and hands-on experience in support of chemical risk assessment.

The workshop will introduce benchmark dose modeling and analysis, probabilistic dose-response assessment in a Bayesian framework (including distributional BMD estimation) with hands-on experience on the recently developed web-based Bayesian BMD (BBMD) estimation system and its application to chemical risk assessment. The Bayesian BMD modeling and analysis involves using Markov Chain Monte Carlo (MCMC) algorithm to fit mathematical dose-response models to toxicity data (mainly dichotomous and continuous data) and estimating the distributions of model parameters and quantities of interest (e.g., BMD) by using posterior samples. This important feature makes the Bayesian BMD method particularly useful for probabilistic dose-response assessment, which has been strongly advocated by the WHO/IPCS expert panel.

Another extremely useful feature of this workshop is the introduction on the model averaging techniques for BMD estimation, which has been suggested as a preferred approach to address model uncertainty in dose-response assessment by the European Food Safety Authority (2017).

Additionally, how the distributional estimates of BMD can support the WHO/IPCS probabilistic dose-response assessment framework will be briefly discussed.

This workshop will also provide participants with necessary knowledge for the Part II of the workshop. Participants should bring their own laptop with a recent internet browser installed (the latest version of Google Chrome is preferred).

Part II - This half-day workshop will build on Part I to provide participants with interactive training on the use of the U.S. Environmental Protection Agency's (EPA) Benchmark Dose software (BMDS, version 3.0, released fall 2018) and Categorical Regression software (CatReg, version 3.1, released summer 2017) and their application to risk assessment. 

  • BMDS 3.0 builds upon previous versions of BMDS and the BMDS Wizard by simplifying the workflow for modeling, fully implementing all BMDS analyses in Microsoft Excel. New to BMDS 3.0 are Bayesian model averaging and the ability to assume response lognormality as alternative modeling approaches for analyzing dichotomous and continuous response data, respectively.  The focus of the BMDS training will center on how to use the new interface and the theory and application of the new models, particularly the new model averaging methods. 
  • CatReg is a powerful modeling tool for the analysis of concentration-time-response data and can be used for the meta-analysis of toxicological data.  Categorical regression modeling involves fitting mathematical models to toxicity data that has been assigned ordinal severity categories (i.e., minimal, mild, or marked effects) and can be associated with up to two explanatory variables corresponding to exposure conditions, usually concentration and duration.  The categorization of observed responses allows the expression of dichotomous, continuous, and descriptive data in terms of response severity and supports the analysis of data from single studies or multiple studies.  Additionally, the meta-analytical capability of CatReg allows for the filtering and stratification of data to determine statistically significant different responses between sexes, strains, and/or species.  CatReg training will focus on the theory of categorical regression and the application of the method to animal toxicity data.

Participants are encouraged to bring their own laptops, with CatReg 3.1 and BMDS 3.0 installed, to the workshop. 

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September 30, BMDS-News Announcement #60 - BMDS 3.0 is now available!

Visit the EPA Benchmark Dose website to obtain BMDS 3.0, a major upgrade to the benchmark dose software (BMDS).  BMDS 3.0 is the result of a close collaborative effort between EPA and the National Institute for Occupational Safety and Health (NIOSH) to meet the current dose-response analysis needs of chemical risk assessors and to introduce state-of-the-science dose-response methods, such as Bayesian analysis and Bayesian model averaging. The re-designed Excel-based interface reflects nearly two decades of experience and feedback on the needs of chemical risk assessors with respect to benchmark dose modeling.

Key new components of BMDS 3.0 are new state-of-the-science Bayesian versions of the BMDS dichotomous models and a Bayesian dichotomous model averaging feature. The Bayesian dichotomous models used in BMDS 3.0 are identical to the traditional BMDS frequentist parametric models but incorporate prior information into the analysis that is used in the model fit. All of these Bayesian models are available for use in the new Bayesian model averaging feature of BMDS 3.0.

In addition, all continuous response models have been upgraded in BMDS 3.0 with new features such as Hybrid modeling capability and Lognormal response options, and all models have been recoded to improve performance in terms of stability, accuracy, reliability, and speed.

The new BMDS 3.0 Analysis Workbook is designed to facilitate performing, interpreting and tracking dose-response analyses of multiple dichotomous, combined tumor, nested dichotomous, and continuous response datasets. Depending on the needs of the risk assessment, users can focus a BMDS 3.0 analysis on datasets associated by:
  • study (e.g., for chemicals with a large database of studies)
  • chemical (e.g., for chemicals that are not well-studied)
  • health outcome (e.g., for chemicals with health outcomes that have been assessed in multiple studies and/or by multiple response measures)

A detailed description of the BMDS 3.0 software is contained in the BMDS 3.0 User Guide.

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BMDS-News Announcement #61 - Pre-register Now for 2018 SRA Quantitative Dose-Response Modeling Methods and Tools Training

For the full text, see the September 11, 2018 announcement. 

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BMDS-News Announcement #62: EPA to Release BMDS 3.0.1 With Extended Excel Compatibility

EPA appreciates all of the many positive and constructive comments received since the BMDS 3.0 release earlier this month. In response, EPA is planning to release BMDS 3.0.1 by December 2018.

BMDS 3.0.1 will include the following enhancements, the most prominent of which is a substantial extension of its Excel compatibility:
  • Extended compatibility for use with 64-bit Excel 2016, 32-bit Excel 2013, and 32-bit Excel 2010
  • Extended compatibility for use on network drives
  • Recompiled models for faster run time
  • Interface improvements that further enhance the user-friendly nature of BMDS 3.0
  • Fixes for minor to moderate issues reported for Weibull, Nested Dichotomous, and Continuous Models

As always, EPA greatly appreciates all feedback we receive from our customers. Please continue to provide us with feedback through our online E-Ticket reporting system. Look for BMDS 3.0.1 to be available from EPA?s BMDS website by December 2018.

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2017

June 6, BMDS-News Announcement #54 - EPA CatReg 3.1 - 2017 SRA Training Class

The U.S. Environmental Protection Agency (EPA) would like to announce a full-day training course to be offered at the SRA 2017 annual meeting.

This course will provide participants with interactive training on the use of Categorical Regression software (CatReg) (version 3.1, to be released summer 2017) and its application to risk assessment.

CatReg is a powerful modeling tool for the analysis of concentration-time-response data and can be used for the meta-analysis of toxicological data.

Categorical regression modeling involves fitting mathematical models to toxicity data that has been assigned ordinal severity categories (i.e., minimal, mild, or marked effects) and can be associated with up to two explanatory variables corresponding to exposure conditions, usually concentration and duration.

CatReg calculates the probabilities of observing the different severity categories over the continuum of the explanatory variables describing exposure conditions.

The categorization of observed responses allows the expression of dichotomous, continuous, and descriptive data in terms of response severity and supports the analysis of data from single studies or multiple studies.

CatReg can also estimate the lower confidence limit on the dose (the equivalent of a BMDLHelpBMDLA lower one-sided confidence limit on the BMD.) associated with a given severity probability and exposure duration.

Additionally, CatReg's meta-analytical capability allows for the filtering of data to determine statistically significant different responses between sexes, strains, and/or species.

In the summer of 2017, EPA will release version 3.1 of the CatReg software, with strengthened input file QA protocols to ensure the correct structuring of data for analysis and new plotting functions that allow users to evaluate model fit and performance; this version of the software will be the focus of this training workshop.

Participants need to bring their own laptops, with CatReg installed, to the workshop. The latest version of the software program can be found on the CatReg download page.

June 19, BMDS-News Announcement #55 - CatReg 3.1 for Windows is Now Available

EPA has released an update to its Windows-based version of CatReg for categorical regression analysis.

EPA recommends that new and previous users download the new CatReg version from this BMDS download page rather than rely on the auto update feature in the previous version of CatReg (future updates will be readily available via the new version's enhanced auto-update feature).

CatReg was developed to support risk assessors, toxicologists, and health scientists in conducting exposure-response analyses, most often for controlled animal experiments.

New and improved features in this release of CatReg include:
  • Greatly enhanced input file validation to ensure correctly structured data for analysis.
  • Helpful new output features, including:
    • ​Output (.otx) files now reflect all user-specified model parameters and settings.
    • In addition to the .otx file, CatReg automatically saves the summary output to a .csv file.
    • CatReg 3.1 adds a new bar plot option: Observed and Predicted Probability Versus Dose/Time combination. The stacked bar plot shows the observed probability of each severity level for a given dose/time combination.  
  • New features for saving and loading analysis settings
  • Improved auto-update feature for receiving the latest CatReg enhancements and fixes
  • More explicit error messages that are now saved to the output file
  • Several fixes and enhancements to improve how CatReg works in the Windows operating system 

August 18, BMDS-News Announcement #56 - BMDS 2.7 is Now Available

EPA has released an update to its benchmark dose software (BMDS). EPA recommends that new and previous users download the new BMDS 2.7 version from this BMDS download page rather than rely on the auto update feature in the previous version of BMDS (future updates will be readily available via the new version's enhanced auto-update feature).

BMDS was developed to support risk assessors, toxicologists, and health scientists in conducting dose-response analyses, most often for controlled animal experiments. New and improved features in this release of BMDS 2.7 include:

  • The benchmark dose upper confidence limit (BMDU) result is now included with the BMDL for most BMDS models (primarily continuous and dichotomous).
  • BMDS installation now uses a Windows Installer msi-based file, rather than the zip files of previous releases. The .msi-based release is simpler, more robust, and minimizes problems related to Windows 10’s increased security protocols.
  • The auto-update feature (introduced in BMDS 2.6) works in a wider range of connection scenarios so users can be assured they are running the most recent version.

The Excel-based BMDS Wizard v1.11 is also included as part of the install package. BMDS Wizard remains unchanged except for minor fixes needed for compatibility with BMDS v2.7.

See the BMDS 2.7 readme file for details on this version’s enhancements and fixes.

September 14, BMDS-News Announcement #57 - Register Now for EPA CatReg 3.1 - 2017 SRA Training Class

Registration is now open for the U.S. Environmental Protection Agency full-day training course to be offered at the annual SRA 2017 meeting.

Register prior to 11/8/2017 to receive reduced pricing.

This course will provide participants with interactive training on the use of Categorical Regression software (version 3.1) and its application to risk assessment. 

CatReg is a powerful modeling tool for the analysis of concentration-time-response data and can be used for the meta-analysis of toxicological data. 

Categorical regression modeling involves fitting mathematical models to toxicity data that has been assigned ordinal severity categories (i.e., minimal, mild, or marked effects) and can be associated with up to two explanatory variables corresponding to exposure conditions, usually concentration and duration.  CatReg calculates the probabilities of observing the different severity categories over the continuum of the explanatory variables describing exposure conditions.  The categorization of observed responses allows the expression of dichotomous, continuous, and descriptive data in terms of response severity and supports the analysis of data from single studies or multiple studies. 

CatReg can also estimate the lower confidence limit on the dose (the equivalent of a BMDLHelpBMDLA lower one-sided confidence limit on the BMD.) associated with a given severity probability and exposure duration.

Additionally, the meta-analytical capability of CatReg allows for the filtering of data to determine statistically significant different responses between sexes, strains, and/or species.  CatReg version 3.1  contains strengthened input file QA protocols to ensure the correct structuring of data for analysis and new plotting functions that enable users to evaluate model fit and performance. Version 3.1 will be the focus of this training workshop.

Participants need to bring their own laptops, with CatReg 3.1 installed, to the workshop.  

October 19, BMDS-News Announcement #58 - October Registration - EPA CatReg 3.1 - 2017 SRA Training Class

Those interested in this course are encouraged to register by October 31, 2017, by visiting the SRA website.

While pre-registration is open until 11/8/2017, the course will not be offered if sufficient class size is not reached by October 31.

This course will provide participants with interactive training on the use of EPA's Categorical Regression software (version 3.1) and its application to risk assessment.

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2016

February 24, BMDS - News Announcement #48: Final Report from December, 2015 Model Averaging Workshop

EPA's National Center for Environmental Assessment (NCEA) hosted a public workshop on model averaging methods for dose-response analysis on December 10-11, 2015. The final report from that workshop is now available.

It includes the pre-meeting written responses from discussants, as well as discussant comments during the workshop to the EPA discussion questions and their responses to questions asked by workshop audience participants.

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April 15, BMDS-News Announcement #49: Meeting Notes from December, 2015 Model Averaging Workshop

EPA's National Center for Environmental Assessment (NCEA) hosted a public workshop on model averaging methods for dose-response analysis on December 10-11, 2015.

The official (approved by discussants and cleared by NCEA) version of the meeting notes from that workshop is now available.

It includes the pre-meeting written comments from discussants, as well as discussant responses during the workshop to the EPA discussion questions and questions asked by workshop audience participants.

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June 1, BMDS-News Announcement #50 - Windows CatReg 3.0 is now available!

EPA has released an update to its suite of benchmark dose modeling tools to include a version of the Agency's categorical regression analysis (CatReg) program.

This new CatReg software complements EPA's existing benchmark dose software (BMDS) by greatly enhancing a risk assessor's ability to predict exposures related to various levels (categories) of effect severity and integrate data from separate toxicological studies into a single dose-response-time meta-analysis.

Visit the BMDS CatReg web page to download the CatReg software and user guide, and to read about advantages CatReg offers over other dose-response analysis tools, which include the ability to:
  • Use multiple independent variables to explain the response.
  • Predict exposures related to various levels of effect severity.
  • Combine multiple studies in a single analysis.
  • Test hypotheses related to the importance of covariates and the potential for pooling data.

Feel free to submit your CatReg questions or concerns to our BMDS eTicket help system.

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October 13, BMDS-News Announcement #51 -- CatReg Full-Day Training Course

EPA is offering a new full-day training course in the use of its updated and Windows enhanced categorical regression software, CatReg 3.0.

The objective of this full-day course is to provide participants with interactive training on the use of CatReg 3.0 and its application to risk assessment. 

CatReg is a powerful modeling tool for the analysis of concentration-time-response data and can be used for the meta-analysis of toxicological data. 

Categorical regression modeling involves fitting mathematical models to toxicity data that has been assigned ordinal severity categories (i.e., minimal, mild, or marked effects) and can be associated with up to two explanatory variables corresponding to exposure conditions, usually concentration and duration. 

CatReg calculates the probabilities of observing the different severity categories over the continuum of the explanatory variables describing exposure conditions. 

The categorization of observed responses allows the expression of dichotomous, continuous, and descriptive data in terms of response severity and supports the analysis of data from single studies or multiple studies. 

CatReg can also estimate the lower confidence limit on the dose (the equivalent of a BMDL) associated with a given severity probability and exposure duration.

Additionally, the meta-analytical capability of CatReg allows for the filtering of data in order to determine statistically significant different responses between sexes, strains, and/or species. 

Recently, EPA has released a new graphic-user interface for CatReg (Windows enhanced CatReg 3.0) that will greatly increase the efficiency with which users can perform categorical regression analyses; this version of the software will be the focus of this training workshop. Participants need to bring their own laptops, with CatReg installed, to the workshop.  

Disclaimer:  The views expressed in this abstract are those of the authors and do not necessarily reflect the views or policies of the U.S. EPA.

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October 13, BMDS-News Announcement #52 -- Full-Day CatReg Training Course in San Diego, December 11

The first full-day training course in the use of EPA's Windows enhanced categorical regression software, CatReg 3.0 will be given on December 11, 2016 in San Diego, CA, as part of the Society for Risk Analysis Annual Meeting. 

As described in BMDS-News announcement #51, the objective of this full-day course is to provide participants with interactive training on the use of CatReg 3.0 and its application to risk assessment. 

CatReg is a powerful modeling tool for the analysis of concentration-time-response data and can be used for the meta-analysis of toxicological data. 

Categorical regression modeling involves fitting mathematical models to toxicity data that has been assigned ordinal severity categories (i.e., minimal, mild, or marked effects) and can be associated with up to two explanatory variables corresponding to exposure conditions, usually concentration and duration. 

CatReg calculates the probabilities of observing the different severity categories over the continuum of the explanatory variables describing exposure conditions. 

The categorization of observed responses allows the expression of dichotomous, continuous, and descriptive data in terms of response severity and supports the analysis of data from single studies or multiple studies. 

CatReg can also estimate the lower confidence limit on the dose (the equivalent of a BMDL) associated with a given severity probability and exposure duration.

Additionally, the meta-analytical capability of CatReg allows for the filtering of data in order to determine statistically significant different responses between sexes, strains, and/or species. 

Recently, EPA has released a new graphic-user interface for CatReg (Windows enhanced CatReg 3.0) that will greatly increase the efficiency with which users can perform categorical regression analyses; this version of the software will be the focus of this training workshop. Participants need to bring their own laptops, with CatReg installed, to the workshop.  

Disclaimer:  The views expressed in this abstract are those of the authors and do not necessarily reflect the views or policies of the U.S. EPA.

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October 26, BMDS-News Announcement #53 -- Last Chance to Register for EPA December 11, 2016 Training Class

For those interested in this workshop on Categorical Regression, please register at the SRA site by October 31st to ensure that the course will be offered. The first full-day training course in the use of EPA's Windows enhanced categorical regression software, CatReg 3.0 will be given on December 11, 2016 in San Diego, CA as part of the Society for Risk Analysis Annual Meeting.

The objective of this full-day course is to provide participants with interactive training on the use of CatReg 3.0 and its application to risk assessment. 

CatReg is a powerful modeling tool for the analysis of concentration-time-response data and can be used for the meta-analysis of toxicological data.  

Categorical regression modeling involves fitting mathematical models to toxicity data that has been assigned ordinal severity categories (i.e., minimal, mild, or marked effects) and can be associated with up to two explanatory variables corresponding to exposure conditions, usually concentration and duration. 

CatReg calculates the probabilities of observing the different severity categories over the continuum of the explanatory variables describing exposure conditions.  

The categorization of observed responses allows the expression of dichotomous, continuous, and descriptive data in terms of response severity and supports the analysis of data from single studies or multiple studies. 

CatReg can also estimate the lower confidence limit on the dose (the equivalent of a BMDL) associated with a given severity probability and exposure duration.

Additionally, the meta-analytical capability of CatReg allows for the filtering of data in order to determine statistically significant different responses between sexes, strains, and/or species. 

Recently, EPA has released a new graphic-user interface for CatReg (Windows enhanced CatReg 3.0) that will greatly increase the efficiency with which users can perform categorical regression analyses; this version of the software will be the focus of this training workshop. Participants need to bring their own laptops, with CatReg installed, to the workshop.   

Disclaimer:  The views expressed in this abstract are those of the authors and do not necessarily reflect the views or policies of the U.S. EPA.

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2015

March 2, BMDS - News Announcement #41 - New BMDS 2.6 With Auto-Update and New BMDS Website Quick Start Guide

Visit the BMDS website to download the new BMDS 2.6.

BMDS 2.6 is a significant upgrade that includes improvements to the nested models, parameter standard error reporting, parameter initialization for continuous models, and file and path name handling.

BMDS 2.6 also introduces a new feature: the ability for BMDS to automatically detect and, optionally, install software updates. This feature will ensure BMDS users have access to the latest version of the software with up-to-date fixes and enhancements.

This install package also includes an upgraded version (1.10) of the BMDS Wizard. BMDS Wizard v1.10 incorporates BMDS 2.6 reporting fixes and can also export Microsoft Word-formatted reports that employ the latest EPA-approved reporting format (as of September 2014).

The BMDS 2.6 ReadMe file contains more details on this upgrade’s enhancements and fixes.

Also, the BMDS website now contains a new "Quick Start" to help users become comfortable with the latest BMDS features.

June 23, BMDS-News Announcement #42 - Benchmark Dose Training Page Update

The BMDS training page has been updated to replace out-of-date training videos with new, interactive training materials.  These materials include recorded webinars, exercise files, and PDF versions of the training slides.     

Background: In June of 2014, a series of webinar-based interactive training sessions were given on the use of the U.S. Environmental Protection Agency's (EPA) Benchmark Dose Software (BMDS) and its application to risk assessment. 

BMD modeling involves fitting mathematical models to dose-response, and in some cases dose-time-response, data in order to identify points of departure for use in human health risk assessments, and it addresses many limitations of the traditional No Observed Adverse Effect Level (NOAEL) approach. 

The series of webinars consisted of individual training modules focused on a specific type of date or topic:
  • Introduction to Benchmark Dose Models.
  • Dichotomous Models.
  • Continuous Models.
  • Nested Dichotomous Models.
  • Cancer Models.
  • Time Models (consisting of modeling repeated response data and concentration * time data).

Each training module is provided as a stand-alone unit, so users can focus on only the modeling topics of interest to them and still receive a complete and valuable training experience. 

General topics that will be covered in each training session include:
  • Basic BMD modeling workflows.
  • Selection of appropriate benchmark dose response levels.
  • How to judge model fit.
  • Demonstrations of EPA's BMDS package and the Excel-based BMDS Wizard templates (where appropriate).

All the training sessions are presented as Adobe Connect recordings of the live June 2014 training sessions.  Users have full playback capabilities: users can simply follow the recording in real time, or they can pause, rewind, or fast forward the recordings according to their needs. 

Each training session has a PDF version of the slides that the user can download for reference purposes, as well as any practice files necessary for the exercises in the training session. 

Also provided is a Question and Answer transcript that lists out subject-specific questions posed by users that took the trainings in June 2014, and EPA's responses. 

Lastly, a Slide Errata and Notes PDF file is provided to list out corrections made to the training materials used in the June 3014 training.

In order to make full use of the training materials provided, users must have a number of software packages installed on their workstation.

To participate in the exercises included in the training sessions, users must have the latest version of BMDS installed.
  • EPA users will need to locate the BMDS and Wizard folders in their personal subfolder within the EPA "Users" folder (C:\Users\[LAN ID, e.g., jgift\BMDS260).
  • Non-EPA users can locate their folders in other directories, but the Wizard folder MUST be in the same directory as the BMDS executable. 
  • NOTE:  the June 2014 training used BMDS 2.5, current users may notice a few, small numerical differences between 2.5 and the current BMDS version.

To use the BMDS Wizard templates, Microsoft Excel must be installed on the user's workstation. 

To run the toxicodiffusion model in the Time Models webinar, users must install the 32-bit version of the R statistical software (version 3.1 or later) on their workstation. 

In order to view the PDFs provided on the training page, Adobe Reader must be installed on the user's workstations.

July 14, BMDS-News Announcement #43 - BMDS 2.6.0.1 (with Wizard 1.10) is now available

EPA is now distributing BMDS 2.6.0.1.

If you already have BMDS 2.6, you can obtain this new version of BMDS using the BMDS auto update feature the next time you open BMDS 2.6. If you do not already have BMDS 2.6 you can obtain this new version of BMDS from the BMDS download page.

BMDS 2.6 contains the following fixes and enhancements:
  • Enhanced the Nested models' text results to display the minimum, maximum, and mean of the absolute value of the scaled residuals, as well as the minimum, maximum, and mean of the scaled residuals.
  • Resolved an issue where BMDS 2.6 could not display plots generated by previous BMDS versions.
  • Implemented a fix for an intermittent issue where the BMDS Wizard did not import plots generated by BMDS.
  • Added an Update button to the About BMDS box (accessible from the Help>About menu item). Click the Update button to have BMDS check for and optionally install a BMDS update.
  • Fixes issues associated with specifying parameter values for continuous models.

Refer to the BMDS 2.6.0.1 readme file for more details on using the automatic upgrade facility, verifying the installation, creating a shortcut icon, etc.

August 6, BMDS-News Announcement #44 - Symantec incorrectly tagged BMDS 00poly.exe file as a virus on August 5, 2015

On Wednesday, August 5, 2015, EPA became aware that the Symantec virus protection database had incorrectly identified the 00poly.exe file of BMDS as a virus.

As a result, BMDS users that receive virus protection from Symantec may have had this file deleted from their computer.

EPA has since informed Symantec of this error and Symantec has verified the mistaken identification and removed the 00poly.exe file from their list of viruses. 

For BMDS users that have had their 00poly.exe file removed by their Symantec software, EPA is making available in the near future a "patch" containing a recompiled 00poly.exe file on the BMDS download page. Users can download the patch to reinsert the 00poly.exe file into the BMDS folder on their computer.

BMDS users that have not had their 00poly.exe file removed do not need to take any action, and future downloads of the BMDS software should not trigger a Symantec alert.

We apologize for any inconvenience this may have caused. Please contact us if you have any further questions or concerns.

August 25, BMDS - News Announcement #45 - December 6, 2015 Training Course in use of EPA Categorical Regression Software (CatReg)

The U.S. EPA will provide a full-day training course on the use of the EPA's Categorical Regression software (CatReg) and its application to risk assessment on December 6, 2015 at the 2015 Society for Risk Analysis (SRA) Annual meeting.  

Categorical regression modeling involves fitting mathematical models to toxicity data that has been assigned ordinal severity categories (i.e., minimal, mild, or marked effects) and can be associated with up to two explanatory variables corresponding to exposure conditions, usually concentration and duration. 

CatReg calculates the probabilities of observing the different severity categories over the continuum of the explanatory variables describing exposure conditions.  The categorization of observed responses allows the expression of dichotomous, continuous, and descriptive data in terms of response severity and supports the analysis of data from single studies or multiple studies. 

CatReg can also estimate the lower confidence limit on the dose (the equivalent of a BMDL) associated with a given severity probability and exposure duration.

Additionally, the meta-analytical capability of CatReg allows for the filtering of data in order to determine statistically significant different responses between sexes, strains, and/or species. 

Recently, EPA has released a new graphic-user interface for CatReg that will greatly increase the efficiency with which users can perform categorical regression analyses; this version of the software will be the focus of this training workshop.

October 21, BMDS - News Announcement #46: You can now register for December 6, 2015 SRA Training Course in use of EPA Categorical Regression Software (CatReg)

Registration is now open for the U.S. EPA full-day training course on the use of the EPA's Categorical Regression software (CatReg) and its application to risk assessment. This course will be offered on December 6, 2015 at the 2015 Society for Risk Analysis (SRA) Annual meeting.  

Categorical regression modeling involves fitting mathematical models to toxicity data that has been assigned ordinal severity categories (i.e., minimal, mild, or marked effects) and can be associated with up to two explanatory variables corresponding to exposure conditions, usually concentration and duration. 

CatReg calculates the probabilities of observing the different severity categories over the continuum of the explanatory variables describing exposure conditions.  The categorization of observed responses allows the expression of dichotomous, continuous, and descriptive data in terms of response severity and supports the analysis of data from single studies or multiple studies. 

CatReg can also estimate the lower confidence limit on the dose (the equivalent of a BMDL) associated with a given severity probability and exposure duration.

Additionally, the meta-analytical capability of CatReg allows for the filtering of data in order to determine statistically significant different responses between sexes, strains, and/or species. 

Recently, EPA has released a new graphic-user interface for CatReg that will greatly increase the efficiency with which users can perform categorical regression analyses; this version of the software will be the focus of this training workshop.

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November 10, BMDS - News Announcement #47: Register now for EPA Model Averaging Workshop (December 10-11, 2015)

EPA's National Center for Environmental Assessment (NCEA) is hosting a public workshop on model averaging methods for dose-response analysis. The workshop will be held via webinar in two half-day increments (12:00 PM to 4:00 PM EST) on December 10-11, 2015. 

The purpose of this workshop is to obtain expert peer consultation on model averaging methods for dose-response analysis.

To facilitate the workshop, EPA will provide invited workshop consultants with background and support materials for consideration, including a document describing methods that are consistent with published recommendations and software that illustrates how those existing methods could be implemented.

Workshop consultants will examine EPA's background and support material and provide written comments prior to the workshop. Discussions and conclusions reached during the workshop will form the basis of a workshop report that EPA will consider for the identification of the model averaging method(s) that offer(s) the greatest potential for the development of chemical health assessments.

While the workshop support material and software describe candidate methods for use in evaluating continuous response measures, participants will also be asked to comment on the potential for extension of any preferred method(s) identified to dichotomous response measures.

Dates: The workshop is scheduled for December 10 - 11, 2015. The workshop will consist of two half-day webinar workshop sessions (12:00 PM to 4:00 PM EST) on Model Averaging Methods. The agenda and workshop support material will be posted to the workshop webpage.

Location:This workshop will be held only by webinar. The workshop will be open to attendance by interested public attendees on a first-come, first-served basis up to the limits of available webinar room.

Public Participation: Instructions for workshop registration are described below. Interested parties with expertise in this field of study are invited to provide their perspective by preparing a brief presentation (≤ 5 minutes) for the workshop consultants. Instructions for requesting to make a presentation at the workshop are provided below.

Background: The benchmark dose (BMD) method is a key component of chemical risk assessments performed by EPA, other U.S Federal and State Agencies, and multiple international organizations. The BMD method is used to establish toxicity values such as EPA reference doses and cancer slope factors for chemicals expected to have human health effects.

Existing BMD methods involve the selection of a single dose-response model from among a suite of models with little biological basis, based largely on a comparison of model fits to the data. As such, they have been criticized for not adequately accounting for model uncertainty and biological considerations.

Model averaging is a well-recognized and published scientific approach that can assist in the characterization of model uncertainty, and has the potential for incorporating biological considerations. Bayesian methods can be applied to allow prior information, including biological considerations, to influence model averaging results.

Given these potential benefits, model averaging and several model averaging approaches are being investigated and tested by EPA.

Registration

This workshop will be held only via webinar. The workshop will be open to attendance by interested public attendees on a first-come, first-served basis up to the limits of the webinar room. Registration to attend by webinar will remain open until the conclusion of the workshop.

To register for the workshop, please send your name, title, affiliation, contact information, and if you are interested in making a brief presentation to EPA_MA_Workshop@icfi.com. Registration will remain open, as permitted by webinar capacity, through the duration of the workshop.

If you are requesting to make a brief presentation, you will be sent instructions for the preparation and submission of presentation materials. To promote transparency, if you request to make a presentation, please also disclose:
  • The nature of any financial relationships (e.g., consulting agreements, expert witness support, or research funding) you may have with any organization(s) or entities having an interest in the issues under discussion.
  • The extent to which your comments were reviewed by an interested party prior to submission.

Please direct questions regarding workshop registration or logistics to Susan Blaine at EPA_MA_Workshop@icfi.com or by phone at 703-225-2471. To obtain clarification or provide commentson the workshop support materials, contact Jeff Gift, Ph.D., or by phone at 919-541-4828.

Workshop Support Materials

Support materials for the workshop will be available from the workshop webpage. Support materials will include a workshop support document, workshop discussion questions, software for implementation of model averaging methods described in the support document, and datasets used for the application of tests described in the support document.

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2014

February 14, BMDS - News Announcement #34 - BMDS Wizard 1.8 - New Installation Instructions

Users have experienced problems running certain BMDS models with the BMDS Wizard that are caused predominantly by having too many or unusual characters in the directory structure where Wizard output files are stored.

These problems are generally fixed by renaming the Wizard folder that is currently named "BMDS Wizard 1.8" in the BMDS 2.4 release to something shorter that does not contain the "1.8" text (e.g., "Wizard").

We apologize for any troubles or confusion this may have caused.

February 14, BMDS - News Announcement #35 - EPA-specific BMDS Installation Instructions for Windows 7 Upgrade

For EPA users only, the following installation steps are recommended to optimize the use of BMDS and the BMDS Wizard under the new EPA Windows 7 upgrade.
  1. Download the BMDS 2.4 installation .zip package and unzip it to a local (not network) directory on your computer that contains as few characters as possible, no unusual characters and for which you have read and write authorization. In our experience, the subfolder within C:\Users associated with your EPA user ID works well for this purpose.
  2. Rename the Wizard folder that is currently named "BMDS Wizard 1.8" in the BMDS 2.4 release to something shorter that does not contain the "1.8" text (e.g., "Wizard").
  3. For faster processing time, run BMDS and the BMDS Wizard from their local C:\ location and save their output to a local C:\ directory that contains as few characters as possible, no unusual characters and for which you have read and write authorization. (NOTE: Your output files will not be backed up using this approach.)
  4. To ensure that your output files are saved in a location that is backed up, run the BMDS or Wizard from either a local or network location, but save their output to a "mapped" network directory that contains as few characters as possible, no unusual characters and for which you have read and write authorization (e.g., "Z:\BMDS" or "Z:\Wizard"). (NOTE: This approach will result in slower processing times) CRITICAL NOTE: The Wizard and BMDS will not work properly with a network directory that is not "mapped" to a single letter drive name. Refer to the Readme file that is distributed with BMDS for instructions on how to map a network drive.

May 23, BMDS - News Announcement #36 - Comprehensive Webinar Training on Benchmark Dose Modeling - CLU-In Webinar Series

Benchmark Dose Modeling - CLU-In Webinar Series

The objective of this webinar series is to provide webinar-based, interactive training on the use of the U.S. Environmental Protection Agency's (EPA) Benchmark Dose Software (BMDS) and its application to risk assessment.

Use of BMD methods addresses many of the limitations of the traditional No Observed Adverse Effect Level (NOAEL) approach. BMD modeling involves fitting mathematical models to dose-response, and in some cases dose-time-response, data in order to identify points of departure for use in human health risk assessments.

This series of webinars will consist of individual training modules focusing on a specific type of data or topic.

Session 1 (June 3, 2014: 1:00 PM - 4:30 PM, EDT)

  • Introduction - this training module will introduce users to the basic science and theory of BMD modeling and the advantages it holds over the NOAEL approach.
  • Dichotomous Models - these models describe the dose-response relationship for effects that are measured as incidence.

Session 2A (June 4, 2014: 9:00 AM - 11:30 AM, EDT)

Continuous Models - models for describing the dose-response characteristics of effects measured on a continuous scale (e.g., body weight).

Session 2B (June 4, 2014: 1:00 PM - 3:30 PM, EDT)

Nested Dichotomous Models - these models are modified dichotomous models that can describe the inter-litter effects often observed in developmental toxicity studies.

Session 3A (June 5, 2014: 9:00 AM - 11:30 AM, EDT)

Cancer Modeling - this module will cover the modeling of cancer data, including modeling individual tumors, modeling multiple tumors within a single bioassay, and modeling tumors when survival rates are observed to differ across exposures.

Session 3B (June 5, 2014: 1:00 PM - 3:00 PM, EDT)

Modeling Time - these models can characterize the dose-time-response relationship when animals are exposed for varying durations of time or responses are measured at multiple time points.

Each training webinar will be presented as a standalone unit, so users can attend only the webinars of interest of them and still receive a complete and valuable training experience.

General topics that will be covered in each webinar include:
  • Basic BMD modeling workflows.
  • Selection of appropriate benchmark response levels.
  • Judging model fit.
  • Demonstrations of EPA's BMDS package and the Excel-based BMDS Wizard templates (where appropriate).

Although it is not necessary for participants to attend every webinar, it is highly recommended that all attend the Introduction module, especially if they have no previous BMD experience.

If users wish, they can familiarize themselves with basic concepts through the online tutorial and training materials provided on the EPA BMDS website.

Participants will need to have version of BMDS 2.5 installed (with necessary administrative rights).

Additionally, to use the BMDS Wizard templates, Microsoft Excel must be installed on the user's computers.

For participants of the Modeling Time webinar, the R statistical package (preferably version 3.1.0) must also be installed on their computers.

May 29, BMDS - News Announcement #37 - BMDS 2.5 with Wizard 1.9 now available for download

EPA is now distributing BMDS 2.5, with an upgraded version (1.9) of the Excel-based BMDS Wizard. The BMDS Wizard has been upgraded to include a new template that allows users to run the MS_Combo model once all tumors have been run using the cancer template.

Additionally, an issue with the cancer slope factor not exporting correctly has been resolved.

A number of fixes have also been made to BMDS:
  • The “View Plot” functionality has been improved to make it easier to generate and edit a plot from a previously created .plt file.
  • The multistage, multistage cancer, and MS_Combo models now provide accurate results when non-integer input data are used and beta parameters are specified by the user.
  • The power model now honors the direction of adversity specified by the user.

June 5, BMDS - News Announcement #38 - Wizard Report Template

The Wizard Report Template Microsoft Word file (BMDS Wizard Report Template.docx) that is needed for the Wizard report feature that prepares formatted Word tables of model results was inadvertently not shipped with BMDS 2.5.

If you have not deleted BMDS 2.4 from your computer, you can copy the report from the ...\BMDS240\Wizard folder and paste it into your ...\BMDS250\Wizard folder.

Otherwise, you will be able to obtain the Wizard Report Template file from the BMDS website download page sometime next week.

July 2, BMDS - News Announcement #39 - New Version of Polynomial Model Now Available

EPA is distributing a new version of the BMDS continuous polynomial model that fixes an issue that resulted in incorrect parameter estimates for the first degree (linear) polynomial model when the beta1 (slope) parameter is restricted and variance is modeled as non-constant.

Visit the EPA BMDS download page for instructions on how to download and install the new poly.exe model.

October 27, BMDS - News Announcement #40 - BMDS Training, SRA 2014 Annual Meeting, Denver, CO (December 11)

The following BMDS training course will be offered on December 11, 2014 following the 2014 Society for Risk Analysis (SRA) meeting in Denver, CO. 

The objective of this full-day course is to provide participants with interactive training on the use of the U.S. Environmental Protection Agency's (EPA) Benchmark Dose Software (BMDS) and its application to risk assessment.

Benchmark dose (BMD) modeling involves fitting mathematical models to dose-response data in order to identify points of departure for use in human health risk assessments.

BMD modeling addresses many of the limitations of the traditional No Observed Adverse Effect Level (NOAEL) approach.

In this interactive training workshop, EPA instructors will present:
  • The basic theory of BMD modeling (including selection of a benchmark response level, model fitting and comparison).
  • A demonstration of EPA's BMDS 2.6.
  • Individual and group modeling exercises.

Instructors will focus on the use of the Excel-based BMDS Wizard templates that are provided with BMDS 2.6, including the newly developed MS_Combo Wizard template.

The BMDS Wizard streamlines BMD analyses by allowing users to build BMDS inputs, run models, and import results in Excel. In addition to importing all results, the BMDS Wizard is capable of recommending best-fitting models using customizable decision criteria.

It is recommended that users familiarize themselves with basic BMD concepts through the online tutorial and training materials provided on the EPA BMDS website.

Participants need to bring their own laptops, with BMDS 2.6 installed, to the workshop. To use the BMDS Wizard templates, Microsoft Excel must also be installed on the users' laptops.

Disclaimer: The views expressed in this abstract are those of the authors and do not necessarily reflect the views or policies of the U.S. EPA.

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2013

March 5, BMDS - News Announcement #26 - April 11, 2013 Advanced BMDS Workshop

EPA is announcing an all-day training workshop titled "Benchmark Dose Modeling Software - Advanced Topics" at the Toxicology and Risk Assessment Conference in Cincinnati, OH on April, 11 2013.

Description: The objectives of this full-day course are to provide participants with training on how to use EPA's Benchmark Dose Modeling Software (BMDS) and other software programs, such as EPA's CatReg and ICF's BMDS Wizard, to facilitate advanced BMD analyses in risk assessments.

This course will demonstrate how to use the following advanced BMD models, and will provide fundamental understanding of the approach and model-framework used for the models:
  • The EPA BMDS MS_Combo model for assessing the risk of developing any number of independent tumors in a single bioassay.
  • The EPA Multistate Weibull Time-to-Tumor (MSW) model for cancer analyses when survival rates are observed to differ due to exposure.
  • The EPA BMDS Toxicodiffusion model for analyzing repeated response data common to many neurotoxicity test guidelines.
  • The EPA BMDS Ten Berge model for analyzing concentration x time relationships.
  • The EPA Categorical Regression (CatReg) model for analyzing data for multiple endpoints from multiple bioassays and multiple species simultaneously.
  • The ICF Wizard Excel program for organizing BMDS session and reporting session results.

Organization: This interactive workshop will consist of model-specific instructor presentations, and group class modeling exercises. Questions and critical discussions of presentation materials and class activities are highly encouraged.

Requirements: Participants are expected to have a general understanding of basic benchmark dose methods, either through work-related experience, or previous completion of at least the introductory portion of training courses.

Participants need to bring their own laptops to the workshop with BMDS 2.4, and the Multistage Weibull (MSW) executable installed (with necessary administrative rights).

Specific installation instructions for the software programs can be found on the website and in documentation that can be downloaded from the website.

Participants will not be required to use CatReg at the course, but may want to download the CatReg software to become familiar with it.

March 7, BMDS - News Announcement #27 - EPA planning April/May advanced BMDS training workshop to replace cancelled TRAC workshop

The 2013 TRAC conference and associated BMD advanced training workshop have been cancelled.

To replace the TRAC training, EPA is planning to hold an April/May "Benchmark Dose Modeling Software - Advanced Topics" single-day workshop in Research Triangle Park, NC. There would be no charge for this workshop but, due to space limitations, in-person attendance will be limited.

However, the workshop will be made available to all as a concurrent webinar, which will also be recorded and made available via the BMDS website.

As a member of the BMDS-News list, you will receive a BMDS-News Announcement when plans for this workshop/webinar (described below) are finalized.

Description: The objectives of this full-day course are to provide participants with training on how to use EPA's Benchmark Dose Modeling Software (BMDS) and other software programs, such as EPA's CatReg and ICF's BMDS Wizard, to facilitate advanced BMD analyses in risk assessments.

This course will demonstrate how to use the following advanced BMD models, and will provide fundamental understanding of the approach and model-framework used for the models:
  • The EPA BMDS MS_Combo model for assessing the risk of developing any number of independent tumors in a single bioassay.
  • The EPA Multistate Weibull Time-to-Tumor (MSW) model for cancer analyses when survival rates are observed to differ due to exposure.
  • The EPA BMDS Toxicodiffusion model for analyzing repeated response data common to many neurotoxicity test guidelines.
  • The EPA BMDS Ten Berge model for analyzing concentration x time relationships.
  • The EPA Categorical Regression (CatReg) model for analyzing data for multiple endpoints from multiple bioassays and multiple species simultaneously.
  • The ICF Wizard Excel program for organizing BMDS session and reporting session results.

Organization: This interactive workshop will consist of model-specific instructor presentations, and group class modeling exercises. Questions and critical discussions of presentation materials and class activities are highly encouraged.

Requirements: Participants are expected to have a general understanding of basic benchmark dose methods, either through work-related experience, or previous completion of at least the introductory portion of training courses.

Participants need to bring their own laptops to the workshop with BMDS 2.4, and the Multistage Weibull (MSW) executable installed (with necessary administrative rights).

Specific installation instructions for the software programs can be found on the website and in documentation that can be downloaded from the website.

Participants will not be required to use CatReg at the course, but may want to download the CatReg software to become familiar with it.

April 17, BMDS - News Announcement #28 - June 25th advanced BMDS training workshop at EPA's RTP, NC facility and via webinar

EPA is announcing an all-day training workshop titled "Benchmark Dose Modeling - Advanced Topics" to be held at the Research Triangle Park EPA Campus on June 25th, 2013, and concurrently as a webinar through Adobe Connect.

Benchmark Dose Modeling - Advanced Topics: The objectives of this full-day course are to provide participants with training on how to use EPA's Benchmark Dose Modeling Software (BMDS) and other software programs to facilitate advanced BMD analyses in risk assessments.

Specifically, this course will demonstrate how to use the following advanced BMD models, and will provide fundamental understanding of the approach and model-framework used for the models:
  • The MS_Combo model for assessing the risk of developing any number of independent tumors in a single bioassay.
  • The Multistate Weibull Time-to-Tumor (MSW) model for cancer analyses when survival rates are observed to differ due to exposure.
  • The Toxicodiffusion model for analyzing repeated response data common to many neurotoxicity test guidelines.
  • Categorical Regression (CatReg) modeling for analyzing data for multiple endpoints from multiple bioassays and multiple species simultaneously.

Organization: This interactive workshop will consist of instructor presentations, and individual class modeling exercises. Questions and critical discussions of presentation materials and class activities are highly encouraged.

This course will be given as both an in-person and web-based workshop. In-person attendance is limited to 40 people (with preference given to local EPA and RTP employees).

Webinar attendance is limited to 50 people. Additional information on visiting EPA's campus and using Adobe Connect will be sent in a future announcement.

Prerequisites: Participants are expected to have a general understanding of basic benchmark dose methods, either through work-related experience, or previous completion of at least the introductory portion of online training courses.

Software Requirements: Participants need to bring their own laptops to the workshop with BMDS 2.4, the Multistage Weibull executable, CatReg 2.1, and the R statistical package installed (with necessary administrative rights).

April 20, BMDS - News Announcement #29: Online webinar portion of June 25th advanced training workshop is now full for non-EPA personnel

Registration for the online webinar portion of the June 25th all-day training workshop titled "Benchmark Dose Modeling - Advanced Topics" is now full for all non-EPA personnel.

Spots are still open for EPA personnel to register for the webinar and in-person portions of the workshop and for non-EPA personnel in the RTP area to register for the in-person portion of the workshop.

To register for this course, please contact Allen Davis at (919) 541-3789 or davis.allen@epa.gov and indicate whether you are interested in attending in-person or via webinar.

April 29, BMDS - News Announcement #30 - Release of BMDS 2.4

EPA is now distributing BMDS 2.4, which adds new topics to the BMDS Help file such as "BMDS Best Practices" and fixes issues related to data entry and running the MS_Combo and ten Berge models. Also, this version of BMDS provides preformatted BMDS Wizard templates.

The BMDS Wizard is an Excel-based tool that streamlines data entry and option file creation, and implements logic to compare and analyze modeling results.

TO DOWNLOAD BMDS 2.4 go to the BMDS website.

If you have already installed earlier versions of BMDS, just overwrite those files with the files contained in the BMDS 2.4 zip file.

June 17, BMDS - News Announcement #31 - New Installation Instructions for BMDS 2.4

The instructions on the BMDS website for installation of BMDS 2.4 after it has been downloaded from the website are being revised to read as follows:
  • In Windows Explorer, double-click the downloaded .zip file.
  • Drag and drop the BMDS240 folder from the .zip file to the C:\USEPA folder of your computer (if you do not have a C:\USEPA folder you will need to create it). BMDS 2.4 needs to be installed in this location to function properly with the new Wizard Excel-based software.

Please use the "Problem Report" feature listed in the "Help" menu of BMDS 2.4 or contact us using our Help Desk Form if you experience installation problems or have questions.

NOTE: Previous installation instructions suggested that EPA users could install BMDS 2.4 to their network "My Downloads" directory. Installation in this location currently causes a problem within the plot functionality of BMDS 2.4. We are working to correct this problem, but at this time BMDS 2.4 will only work from a local directory (e.g., the C:\USEPA directory as described above).

August 21, BMDS - News Announcement #32 - New Version 1.8 of BMDS Wizard Released with BMDS 2.4

EPA is now re-distributing BMDS 2.4, with an updated version (1.8) of the Excel-based BMDS Wizard. Version 1.8 of the Wizard has been modified so that it will:
  • Run correctly regardless of where BMDS is installed on a user's computer.
  • Provide the user with the appropriate Multistage of Polynomial model choices given the number of dose groups in a dataset.
Also, the BMDS website has also been updated with:
  • New instructions regarding how to download the source code for the software.
  • Information regarding the current versions of the individual model executable files.

October 22, BMDS - News Announcement #33 - Basic and Advanced Training Courses Offered at 2013 SRA Meeting

EPA is announcing two all-day training workshops to be held at the 2013 Society for Risk Analysis Conference in Baltimore Maryland. A course on "Benchmark Dose Modeling - Basic Methodologies" will be offered on Sunday, December 8, 2013. A course on "Benchmark Dose Modeling - Advanced Topics" will be offered on Thursday, December 12, 2013. 

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2012

January 3, BMDS - News Announcement #17 - release of BMDS 2.2 build 67 with minor interface changes

EPA is now distributing BMDS Version 2.2 (Build 67), which fixes a problem with the exponential model plot file functionality in Windows 7 and corrects a minor problem with the BMDS session interface. While in a session, right clicking on a Data File, then clicking on "New Data File", will open a new data file. In the previous build (build 66), this produced an error message.

TO DOWNLOAD BMDS 2.2 BUILD 67 go to the BMDS website.

If you have already installed Build 66 of BMDS Version 2.2, just overwrite those files with the files contained in the (Build 67) zip file.

You do not need to uninstall previous BMDS versions (e.g., Version 2.1.2) before installing BMDS 2.2. However, you may want to do so to avoid any confusion with pre-existing shortcuts or other files.

To uninstall BMDS 2.1.2 or earlier versions:
  1. Go to the Add/Remove Programs control panel (windows XP or earlier) or the Programs and Features control panel (Windows Vista, Windows 7).
  2. Select the BMDS program in the list.
  3. Select Uninstall. All data files will remain in place and will not be removed.

April 3, BMDS - News Announcement #18 - Two Half-Day BMD Training Courses will be offered on May 3, 2012 at TRAC Conference, West Chester, Ohio

Two half-day BMD training courses will be offered on May 3, 2012 at the Toxicology and Risk Assessment Conference (TRAC) at the Wingate by Wyndham hotel in West Chester Ohio.

The morning course will cover "Benchmark Dose Modeling: Theory and Application of Basic Modeling Methodologies in Risk Assessment" and the afternoon course will cover "Benchmark Dose Modeling: Advanced Methodologies and Tools for Performing More Complex Dose-Response Analyses." To register, visit the conference website.

Participants do NOT need to bring laptops to the workshop. Abstracts for the two workshops are shown below.

AM Course (W-5)

Benchmark Dose Modeling: Theory and Application of Basic Modeling Methodologies in Risk Assessment

The objectives of this course are to provide participants with an introduction to the evaluation of dose-response data in accordance with EPA’s Benchmark Dose (BMD) guidelines and how to use the Agency’s Benchmark Dose Software (BMDS) to facilitate BMD analyses in risk assessments.

Specific topics covered will include:
  • A general overview of the BMD process
  • Determination of data adequacy
  • Model fitting
  • Model comparison
  • Selection and choice of a benchmark response level.

This course will cover all the BMD models available in the current version of BMDS – including the recently added dichotomous hill and exponential models. In addition, key concepts will also be presented using new features in BMDS version 2.2.

By the end of the course, users will know:
  • When to apply BMD modeling, how to apply BMD modeling to a dataset, and how to decide which BMD should be selected.
  • What a BMD is, and the advantages and disadvantages of using a BMD instead of using LOAEL and/or NOAEL.
  • How to select a data-set to be modeled, define a benchmark response, and use the BMDS modeling software to calculate a BMD/BMDL.
  • Understand how BMD values are calculated and various approaches to better approximate equivalent dose in humans using alternative dose metrics.
PM Course (W-8)

Benchmark Dose Modeling: Advanced Methodologies and Tools for Performing More Complex Dose-Response Analyses

This half-day course focuses on how to use advanced benchmark dose modeling applications and an overview of Excel-based tools which organize BMD modeling results and other information used in a chemical dose-response assessment.

Participants are expected to have a general understanding of benchmark dose modeling, or, have taken the course offered in the AM (W-5), “Benchmark Dose Modeling: Theory and Application of Basic Modeling Methodologies in Risk Assessment”.

This course will provide an overview of modeling continuous and dichotomous datasets using Excel-based software packages called the BMDS Wizard and DRAGON, both of which will be provided to those registered for the course.

The BMDS Wizard allows users to build BMDS input from Excel, run BMDS, and import results into an Excel file.

In addition to importing all results, it is capable of recommending best-fitting models using customizable decision criteria.

It will also demonstrate how to use an additional Excel software package titled the Dose Response Analysis Generator and Organizational Network (DRAGON). The DRAGON is designed to store key dose-response information (BMD, NOAEL, LOAEL, etc.) from multiple studies in one Excel-based database.

This course will demonstrate how to use the software, including how to enter information, perform batch BMD modeling for multiple endpoints, calculate standard dosimetric conversions, and generate result reports and documentation.

In addition, this course will demonstrate how to use the following advanced BMD models, and provide fundamental understanding of the approach and modelframework used for the following models: 
  • The MS_Combo model for assessing the risk of developing any number of independent, multiple tumors observed in a single bioassay.
  • The Multistage Weibull Time-to-Tumor Model (MSW) for cancer analyses when survival rates are observed to differ due to exposure.
  • The Toxicodiffusion Model for analyzing repeated response data common to many neurotoxicity test guidelines.
  • Categorical Regression Modeling (CatReg) for modeling data from multiple bioassays or for multiple species simultaneously.

June 22, BMDS - News Announcement #19 - EPA Distributes Final Version of Benchmark Dose Technical Guidance

EPA has published the final version of the Benchmark Dose Technical Guidance for the purpose of updating risk assessment methodologies. This document provides guidance to risk assessors who intend to use the benchmark dose (BMD) method for developing dose response values and determining a point of departure for toxicological studies.

September 5, BMDS - News Announcement #20 - BMDS Training Workshops at SRA 2012 Covering Basic and Advanced Use of BMDS

EPA will offer benchmark dose (BMD) training courses at the Society for Risk Analysis (SRA) meeting in San Francisco, CA. The BMD workshops will be given on Sunday, December 9. Register by November 9 to receive the "Early Fee" discount.

Attendees can register for the full course (WK1) titled "Benchmark Dose (BMD) Modeling – An Introductory Modeling Method and Use of EPA’s Benchmark Dose Software" or the morning (WK1A) or afternoon (WK1B) workshops.

These workshops will provide participants with interactive training on the use of the U.S. EPA’s Benchmark Dose Software (BMDS) and its application to risk assessment.

The morning session will include instructor presentations covering the basic science and theory of BMD modeling, and is intended for those with no prior experience in BMD modeling.

The afternoon session will expand upon the morning session and will consist of a demonstration of the latest version of EPA’s BMDS through individual and group class modeling exercises. Questions and critical discussions of presentation material and class activities are highly encouraged.

Registration for the morning and afternoon sessions is independent of one another, participants are encouraged to attend whichever sessions suit their needs, although it is highly recommended that students only attending the afternoon session be reasonably proficient in the science and theory of BMD modeling.

Participants planning to attend the afternoon session need to bring their own laptops to the workshop with a recent version of BMDS (either version 2.2 or 2.3) installed (BMDS 2.3 will be available in September, 2012).

To ensure students receive the maximum benefit from participating in the workshop, it is recommended that they examine the online training and tutorial materials prior to the workshop.

September 20, BMDS - News Announcement #21 - Release of BMDS 2.3

The new BMDS Version 2.3 (Build 68) fixes several interface problems reported to the BMDS development team since the Version 2.2 release in late 2011.

Most notably, BMDS 2.3 fixes a problem reported by users of Microsoft Office in Windows 7, in which clipboard errors would occasionally crash both BMDS and Microsoft Office.

In addition, BMDS 2.3 now includes more flexible data input error-trapping functionality, enabling users to store comments, documentation, notations, etc. on dataset spreadsheets without triggering data validation errors. This change in functionality enables researchers to document their datasets as necessary within the BMDS environment.

BMDS 2.3 contains no changes any of the BMDS dose-response models.

TO DOWNLOAD BMDS 2.3 go to the BMDS website.

If you have already installed BMDS Version 2.2, just overwrite those files with the files contained in the BMDS 2.3 zip file.

September 24, BMDS - News Announcement #22 - Bug in BMDS 2.3 (build 68)

There is a bug in BMDS 2.3 (build 68) that causes an error message for reasonably formatted dichotomous datasets that contain three columns of data. We apologize for this inconvenience and will distribute a new build of BMDS 2.3 as soon as possible.

In the meantime, as a "work around," users can add an extra column of "fake" data to your dataset and it should run properly.

September 25, BMDS - News Announcement #23 - BMDS 2.3 (build 68) - Two Bugs, Two Temporary Work Arounds

This message is to distribute "work arounds" for two bugs that have been identified in BMDS 2.3 (build 68).

Bug #1 - An error message appears for reasonably formatted dichotomous datasets that contain three columns of data.

Workaround: add an extra column of "fake" data to your dataset and it should run properly.

Bug #2 - An incorrect warning message indicating that the "number of parameters is greater than the number of observations" appears in the model options screen for the Multistage and Polynomial models when there is no column in the dataset that is labeled as "Dose."

Workaround: Label the dose column in the dataset as "Dose" (right-click on the header name to change it). We apologize for these inconveniences and will be releasing a new version of BMDS to fix these issues as soon as possible.

October 4, BMDS - News Announcement #24 - Release of BMDS 2.3.1 and 2012 SRA Training

EPA is now distributing BMDS 2.3.1, which simplifies how data validation errors for certain models are reported to the user and fixes interface issues reported in BMDS 2.3. BMDS 2.3.1 contains no changes any of the BMDS dose-response models.

TO DOWNLOAD BMDS 2.3.1 go to the BMDS website.

If you have already installed BMDS Version 2.3, just overwrite those files with the files contained in the BMDS 2.3.1 zip file or extract the BMDS 2.3.1 zip file to a new (e.g., BMDS231) folder.

**2012 Society for Risk Analysis (SRA) BMD training** - This year's SRA BMD training will be given in San Francisco, CA on Sunday, December 9, prior to the 2012 SRA meeting. Participants planning to attend the afternoon session should bring their own laptops to the workshop with BMDS 2.3.1 installed (with necessary administrative rights).

October 12, BMDS - News Announcement #25 - "% Positive" problem in BMDS 2.3.1

There is a problem with the "% Positive" dichotomous model option screen feature in BMDS 2.3 and 2.3.1. This will be fixed in a future version. For now, all dichotomous responses should be entered as "Incidence" in BMDS 2.3 and 2.3.1.

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2011

July 28, BMDS - News Announcement #14 - BMDS Training Workshop at the SRA 2011 Annual Meeting

EPA is announcing an all-day training workshop titled "Benchmark Dose Modeling (BMD) Analysis – an Introduction to BMD Methods and Application of EPA’s Benchmark Dose Software " at the Society for Risk Analysis' 2011 Annual Meeting in Charleston, SC.  

This workshop will provide participants with interactive training on the use of the U.S. EPA’s Benchmark Dose Software (BMDS) and its application to risk assessment.

The course will provide an overview of the BMD process, including:
  • Determination of data adequacy.
  • Model fitting and comparison.
  • Selection of a benchmark response level.

This workshop will cover all BMD models available in BMDS 2.2 —including the new MS-COMBO model, which calculates multi-tumor composite risk values. Instruction will also be given in regard to new features that have been implemented in version 2.2.  

This interactive training workshop will consist of morning and afternoon sessions.

The morning session will include instructor presentations covering the basic science and theory of BMD modeling, and is intended for those with no prior experience in BMD modeling.

The afternoon session will expand upon the morning session and will consist of a demonstration of EPA’s BMDS 2.2 through individual and group class modeling exercises. Questions and critical discussions of presentation material and class activities are highly encouraged.  

Registration for the morning and afternoon sessions is independent of one another, participants are encouraged to attend whichever sessions suit their needs, although it is highly recommended that students only attending the afternoon session be reasonably proficient in the science and theory of BMD modeling.  

Participants planning to attend the afternoon session need to bring their own laptops to the workshop with BMDS 2.2 installed (BMDS 2.2 will be available by September 1, 2011).

To ensure students receive the maximum benefit from participating in the workshop, it is recommended that they examine the online training and tutorial materials prior to the workshop.

September 19, BMDS - News Announcement #15 - Release of BMDS 2.2 with MultiTumor Analysis, Dichotomous Data Trend Tests, and improved option file, session, and datafile operability!

EPA is now distributing Version 2.2 (Build 66) of the Benchmark Dose Software (BMDS). Key enhancements in BMDS 2.2 (Build 66) include:
  • The ability to perform a combined analysis of multiple independent tumor types by the multistate-cancer model in order to estimate BMDs and BMDLs for the combined incidence of the tumors in question (i.e., BMDs and BMDLs for the likelihood of getting one or more of those tumors).
  • The ability to perform a trend test on dichotomous data sets using the Cochran-Armitage trend test described by Haseman (1984). This is the first in a series of trend test to be added to BMDS (future versions will also include trend test for continuous and nested data).
  • Modification of the dichotomous Hill model regarding parameter initialization to improve convergence features of this model.
  • Variable name changes (e.g., for dose, sample size, response, mean, or standard deviation variables) in one option file in a session can now be automatically transferred to all other option files in that session. Thus, users can change variable name assignments once in a session, without having to make those changes separately in every option file, increasing the utility and efficiency of session batch modeling.
  • Newly created dichotomous, continuous or nested model data files will start with default column headers, in a particular order, as appropriate for the type of data (e.g., Dose, N, and Effect for dichotomous datasets; Dose, N, Mean, and Std for summarized continuous datasets). The user may change those default headers, but will be warned that doing so may affect the running of BMDS-supplied sessions that look for those default names.
CHANGES TO BMDS INSTALLATION PROCEDURE

Previous BMDS versions used a SETUP.EXE file to create the BMDS directory, add icons to the Programs menu, provide an entry in the Add/Remove Programs control panel, and so on.

However, BMDS 2.2 is being distributed as a compressed ZIP file and does not employ any automated install programs or wizards.

The implications of this change are that:
  • Users do not need administrative rights to install BMDS 2.2.
  • BMDS Version 2.2 can be installed in any folder that the user has create/read/write privileges.
  • Users will need to create their own shortcuts to the program (e.g., on their computer's desktop). 
CONSIDERATIONS FOR PREVIOUS BMDS INSTALLATIONS & UNINSTALLING

You do not need to uninstall previous BMDS software before installing BMDS 2.2. However, you may want to do so to avoid any confusion with pre-existing shortcuts or other files.

To uninstall BMDS 2.1.2 or earlier versions:
  1. Go to the Add/Remove Programs control panel (windows XP or earlier) or the Programs and Features control panel (Windows Vista, Windows 7).
  2. Select the BMDS program in the list.
  3. Select Uninstall. All data files will remain in place and will not be removed.

October 13, BMDS - News Announcement #16 - Register by November 4 for BMDS Training Workshop at the SRA 2011 to Receive Discounted "Early Fee"

Register by November 4 to receive the "Early Fee" discount for the EPA all-day training workshop titled "Benchmark Dose Modeling (BMD) Analysis – an Introduction to BMD Methods and Application of EPA’s Benchmark Dose Software."

The BMD workshop will be given on Sunday, December 4 at the Society for Risk Analysis' 2011 Annual Meeting in Charleston, SC.

This workshop will provide participants with interactive training on the use of the U.S. EPA’s Benchmark Dose Software (BMDS) and its application to risk assessment.

The course will provide an overview of the BMD process, including determination of data adequacy, model fitting and comparison, and selection of a benchmark response level.

This workshop will cover all BMD models available in BMDS 2.2 —including the new MS-COMBO model, which calculates multi-tumor composite risk values. Instruction will also be given in regard to new features that have been implemented in version 2.2.

This interactive training workshop will consist of morning and afternoon sessions.

The morning session will include instructor presentations covering the basic science and theory of BMD modeling, and is intended for those with no prior experience in BMD modeling.

The afternoon session will expand upon the morning session and will consist of a demonstration of EPA’s BMDS 2.2 through individual and group class modeling exercises. Questions and critical discussions of presentation material and class activities are highly encouraged.

Registration for the morning and afternoon sessions is independent of one another, participants are encouraged to attend whichever sessions suit their needs, although it is highly recommended that students only attending the afternoon session be reasonably proficient in the science and theory of BMD modeling.

Participants planning to attend the afternoon session need to bring their own laptops to the workshop with BMDS 2.2 installed (BMDS 2.2 will be available by September 1, 2011).

To ensure students receive the maximum benefit from participating in the workshop, it is recommended that they examine the online training and tutorial materials prior to the workshop.

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2010

June 16, BMDS - News Announcement #12 - Release of BMDS 2.1.2

EPA is now distributing the final release of Version 2.1.2 (Build 60) of the Benchmark Dose Software (BMDS). Key enhancements in BMDS 2.1.2 (Build 60) include:
  • Users can now use spaces in directory path and names associated with BMDS files, including data files.
  • The maximum number of characters allowed in directory path + file name has been increased to 255.
  • GnuPlot features have been added for enhanced plot viewing and editing.
  • Help file has been updated, and now includes a section describing the use of session and option file templates that are currently distributed with BMDS.
  • Polynomial and multistage models will now run, with warning messages, when the number of observations is less than the number of parameters being estimated.
  • Users can now specify the lower bound on the Weibull power parameter to be something other than 0 or 1.
  • The Toxicodiffusion model has been fixed so that it will run with all recent versions of R.

For details on these changes, go to the BMDS 2.1.2 Help menu option in the installed software. Also, the Readme.rtf file distributed with BMDS describes the improvements made in version 2.1.2 (Build 60), installation requirements, and known problems.

November 12, BMDS - News Announcement #13 - BMDS Training Workshop at the SRA 2010 Annual Meeting

EPA is announcing an all-day training workshop titled "Benchmark Dose Modeling and Its Use in Risk Assessment - Application of EPA's Benchmark Dose Software (BMDS), Version 2.1.2" at the Society for Risk Analysis' 2010 Annual Meeting in Salt Lake City.

The course will provide an overview of the BMD process, including determination of data adequacy, model fitting and comparison, and selection of a benchmark response level.

This workshop will cover all the BMD models available in the current version of BMDS as well as the new MS-COMBO model, which calculates multi-tumor composite risk values.

Instruction will also be given in regard to additional changes that have been implemented in version 2.1.2, including model input (expanded file lengths and use of spaces in file names) and output (plot editing and improved Excel export) features.

This interactive training workshop in the use of BMDS will consist of a mix of instructor presentations and individual and group class activities. Attendees will work on examples from chemical assessments and learn how to use BMDS to prepare summary reports for insertion in their assessments. Questions and critical discussions of presentation material and class activities are highly encouraged.

Participants need to bring their own laptops to the workshop with the latest version of BMDS 2.1.2 installed (with necessary administrative rights).

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2009

July 31, BMDS - News Announcement #9 - Final release of BMDS 2.1 and Training opportunity

The final release of Version 2.1 (Build 52) of BMDS can now be downloaded from the BMDS website.

BMDS 2.1 (Build 52) contains user interface enhancements as well as several additions/enhancements to the suite of models available for modeling dose-response data, including new features for the continuous exponential models and a new interface for the ten Berge concentration-time model.

For details on the changes to the user interface, go to the BMDS 2.1 Help menu option in the installed software. The Readme.rtf file distributed with BMDS also describes improvements made in version 2.1 (Build 52), installation requirements, and known problems.

In addition, the BMDS website contains information on the upcoming day long hands-on training opportunity at the December, 2009 Society for Risk Analysis (SRA) conference (Baltimore, Maryland).

July 31, BMDS - News Announcement #9b - Some important notes about BMDS installation

Those installing BMDS on computers that are login/password secured, you should be aware of the following details:

  1. Make sure that the BMDS software is installed under the USER'S administrative rights so the user will have access to all areas the program needs to access. Note: You will know that the software is installed correctly if it "passes" the test that is initiated when the program first starts and if you are able to save option files from within the batch "session" feature.
  2. If you do not have a recent version of Windows on your computer, the installation procedure may require you to install the latest version of the .Net software (i.e., 3.5 SP 1) before you install BMDS 2.1. This download and install takes some time (i.e., several minutes), so be patient, but once it is done (you have to reboot), the BMDS installation goes quickly and smoothly. Also, if you have earlier versions of BMDS installed such as BMDS 2.1 beta, you should uninstall it before installing the new BMDS 2.1 version.

November 2, BMDS - News Announcement #10 - December 5, 2009 SRA Workshop for BMDS 2.1.1 - Preregister by November 6 and Save

EPA will be conducting the following full day BMDS workshop on December 6 in conjunction with the December 6-9, 2009 Society for Risk Analysis (SRA) conference.

Introduction to the Benchmark Dose Methodology and Interactive Application of EPA’s Benchmark Dose Software (BMDS), Version 2.1.1
SRA 2009 Annual Meeting (Baltimore MD, Dec 5, 2009)

This daylong course is designed to provide participants with an interactive training workshop on the use of the U.S. EPA’s Benchmark Dose Software, BMDS 2.1.1 and its application to risk assessment.

The course will provide instruction in changes that have been implemented in version 2.1.1, including a new user interface that allows:
  • Multiple run processing.
  • The ability to save model option choices.
  • Summary sheets for side-by-side comparison of model results.
  • Enhanced export to spreadsheet functionality.

The course will provide an overview of the BMD process, including determination of data adequacy, model fitting, model comparison, selection of a benchmark response level, and modeling linear verses nonlinear responses.

Attendees will also work on examples from chemical assessments and learn how to take advantage of the new features offered by version 2.1.1 of BMDS to prepare summary reports for insertion in their assessments.

This workshop will cover all the BMD models available in the current version of BMDS—including the recently added dichotomous hill, background dose, and continuous exponential models.

This course is an interactive training workshop in the features of BMDS 2.1.1 and it is therefore recommended that prior to this training students who are not familiar with BMD modeling take the online BMD training course in order to ensure that they receive the maximum benefit from participating in the workshop.

Participants need to bring their own laptops to the workshop with the latest version of BMDS 2.1.1 installed (with necessary administrative rights).

November 2, Correction: BMDS - News Announcement #10 - December 6, 2009 SRA Workshop for BMDS 2.1.1 - Preregister by November 6 and Save

The BMDS course at SRA will be offered on Sunday, December 6, not December 5.

November 9, BMDS - News Announcement #11 - release of BMDS 2.1.1 with new Export to Excel feature, sample sessions and ten Berge model update!

EPA is now distributing Version 2.1.1 (Build 55) of the Benchmark Dose Software (BMDS).

BMDS 2.1.1 (Build 55) contains a flexible new feature that allows users to export select BMDS summary report data and plots to Excel.

It also contains a comprehensive set of sample session and model option files to assist users in running batch operations, and several improvements to the ten Berge model that were not available in version 2.1.

The Readme.rtf file distributed with BMDS provides details on the improvements made in Version 2.1.1 (Build 55), installation requirements, and known problems.

IF YOU ALREADY HAVE BMDS 2.1 (BUILD 52) INSTALLED, you need only download and unzip a SMALL PATCH FILE, which should allow you to upgrade BMDS without the need for assistance from your local IT/computer support department.

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2008

July 10, BMDS - News Announcement #6 - BMDS 2.0 has arrived!!

BMDS 2.0 is now available from the BMDS website.

After installing this new version of BMDS, you will find it much easier to perform BMD analyses of multiple endpoints using multiple models. You will be able to prepare reports comparing modeling results in a fraction of the time and in most cases you will be able to easily cut and paste those reports into other (e.g., word processor) applications.

BMDS 2.0 uses the same underlying source code for the models in BMDS 1.4.1 software, with minor corrections and some important additions. It contains a new set of quantal models with an alternative background parameter (i.e., background additive to dose) and asymptote parameter (i.e., Hill model for evaluation of saturable dichotomous effects), as well as a suite of beta Exponential models (for increased flexibility in the evaluation of continuous responses).

BMDS 2.0 replaces BMDS 1.4.1c as the official and principal supported version of BMDS software. For details on its new features and modeling options, go to the BMDS 2.0 Help menu in the installed software.

Along with the release of BMDS 2.0, EPA has developed a new e-Ticket support system for the reporting of BMDS problems or questions. The e-Ticket form can be accessed through a new Help option within BMDS 2.0, or by going directly to the e-Ticket website.

October 1, BMDS - News Announcement #7 - New Training Opportunities, BMDS 2.1 beta interface and Time-dependent
Models Released for Public Comment

EPA is making BMDS 2.1 Beta available at this time for public review.

This version of BMDS uses the same underlying source code for the models already included in BMDS 2.0, with minor corrections and some important additions.

The most significant addition is the incorporation of a beta (external peer review) version of a new time-dependent toxicodiffusion model described by Zhu et al. (2005). The BMDS toxicodiffusion model was developed to characterize toxic effects that evolve along critical time points, such as those observed in a neurotoxicity functional observation battery (FOB).

BMDS 2.1 Beta also incorporates graphical plots for the continuous exponential models and allows for the use of individual animal continuous response data.

Details of the new model and interface enhancements in BMDS 2.1 Beta can be obtained in the Help menu option of the installed software.

In addition, EPA is distributing an external review (beta) version of a concentrationtime (CxT) model originally programmed by Wil ten Berge. The EPA ten Berge model implements an approach to evaluating the CxT relationships for effects associated with chemical exposures. The EPA's version 1.0 implementation of this model is being distributed along with associated documentation and comments on the model received from external peer reviewers. EPA plans to respond to external review comments and incorporate the ten Berge model into a future version of BMDS.

Finally, EPA has updated the website to offer new online and hands-on training opportunities. The online training tutorial has been updated for the 2.x versions of BMDS and a new web page has been added that details upcoming training opportunities.

October 3, BMDS - News Announcement #8 - Website Address

The link that appeared in BMDS-News Announcement #7 does not work. Please go to WWW.EPA.GOV/NCEA/BMDS to access BMDS information and download BMDS models.

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2007

March 12, BMDS - News Announcement #1 - Version 1.4.1 Release

A new version of EPA's benchmark dose software, BMDS 1.4.1, is now available.

BMDS 1.4.1 contains several improvements over version 1.3.2, including improved compatibility with the latest Windows operating systems, a new Multistage-cancer model, greater speed and reliability, and an improved output format for all models.

September 3, BMDS - News Announcement #2 - Version 1.4.1b Release

BMDS Version 1.4.1b is now available. This version contains an updated BMDS help file. It can be downloaded from the BMDS website. Installation of this new version over the version that currently exists on your computer will not delete any existing BMDS datasets or output files.    

LOOK FOR NEW BMDS VERSION 2.0 BETA AND NEW BMDS TRAINING MATERIALS LATER THIS MONTH. Sometime in September, 2007 EPA NCEA will make available BMDS 2.0 beta, which will offer several new dichotomous models and an expanded interface with many new features that facilitate running and comparing multiple model and dataset combinations.

Also, a complete set of upgraded and voice narrated BMDS training materials will be available in the month of September.

You will receive an announcement similar to this one when these new materials and upgrades are available, or you can visit the EPA BMDS website to periodically check for new downloads and news items.

September 28, BMDS - News Announcement #3 - Version 2.0 Beta Release

BMDS Version 2.0 beta is now available.

Today, NCEA's BMDS website has been updated to add the new, beta-test BMDS 2.0. BMDS 2.0 employs a new, markedly improved user interface and has enhanced batch processing capabilities with many new features that facilitate running and comparing multiple model and dataset combinations.

BMDS 2.0 includes the same models available in BMDS 1.4.1, and adds new models including a Hill model, useful for the evaluation of saturable dichotomous responses, and new versions of the familiar quantal models which implement alternative background terms (background additive to dose).

October 10, BMDS - News Announcement #4 - Build 19 of BMDS 2.0 beta Release

BMDS 2.0 Beta – Build 19 released on 10/10/2007 replaces the first BMDS 2.0 Beta release of 9/28/2007 (Build 13). The new Build 19 has important changes and enhancements as a result of additional testing and user exposure and should be downloaded and used instead of Build 13.

Enhancements include the ability to better run a number of the BMD models and also added flexibility and fixes for user interface features. Changes include the designation of the new Dichotomous models as Alternate Dichotomous to better reflect their production status.

Please refer to the readme.txt file included with the software installation for more details on BMDS 2.0 Beta.

NOTE: BMDS 2.0 build 19 is still a beta test version, provided only for your examination and testing - until you receive an announcement that BMDS 2.0 has been finalized BMDS 1.4.1b should be used for definitive risk assessment calculations.

November 16, BMDS - News Announcement #5 - Version 1.4.1c Release

BMDS version 1.4.1c is now available from the BMDS website.

This version updates dichotomous models that were already included on BMDS version 1.4.1b. The updates primarily improve the handling of parameter specifications, particularly in situations where the user may wish to specify the background parameter to be zero.

Reminder: EPA is seeking comments over the next two months on BMDS 2.0 Beta (Build 19) released on 10/10/2007 and available from the BMDS website.

BMDS 2.0 includes the same models available in BMDS 1.4.1 and adds:
  • Batch processing features that facilitate running and comparing multiple model and dataset combinations.
  • New dichotomous Hill model.
  • New versions of the familiar quantal models that implement alternative background terms (background additive to dose).

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