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Benchmark Dose Software (BMDS)

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BMDS 2.5 and Related Software/Documentation

BMDS VERSION 2.5 SYSTEM REQUIREMENTS

This BMDS 2.5 final version is being released for use by risk assessors as the official BMDS system. BMDS requires at least 16 Megabytes of RAM and should run in Microsoft Windows 2000, NT, XP, Vista, and 7, however only operation in Windows XP has been fully tested at this time. BMDS Version 2.5 can be installed in any folder that the user has create/read/write privileges.

BMDS also requires the latest version of .NET (4.0 or later). If your machine is set up to allow or be notified of downloads of Microsoft software, then it is likely that that version of the .NET framework is already installed. Otherwise, the latest version of .NET for client desktops can be downloaded from http://www.microsoft.com/net/downloads Exit EPA Disclaimer.

To run the toxicodiffusion model included in Version 2.5, you must install the R statistical software to your computer (go to http://www.r-project.org/ Exit EPA Disclaimer for more information). Although the toxicodiffusion model is designed to run using version 2.6.2 or later of R, issues have been noted with at least one version (version 3.0.2); EPA currently recommends using version 3.1.0 of R.

CHANGES TO BMDS INSTALLATION PROCEDURE

Previous BMDS versions (BMDS 2.1.2 or earlier) 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 2.5 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 (a) user's do not need administrative rights to install BMDS 2.5, (b) BMDS Version 2.5 can be installed in any folder that the user has create/read/write privileges, and (c) users will need to create their own shortcuts to the program (e.g., on their computer's desktop).

If you already have a version of BMDS installed on your computer, read the section CONSIDERATIONS FOR PREVIOUS BMDS INSTALLATIONS & UNINSTALLING. If you're new to BMDS, go to the section INSTALLING BMDS and then read the instructions in the section AFTER INSTALLING BMDS for creating a desktop shortcut.

CONSIDERATIONS FOR PREVIOUS BMDS INSTALLATIONS & UNINSTALLING

It is not necessary to uninstall previous versions of BMDS to install and run BMDS 2.5. However, if you want to uninstall previous versions of BMDS, it is recommended that you retain the directory structure for the folders where your previous model runs reside in order to maintain the functionality of previous sessions.

Installing BMDS 2.5 and Wizard 1.9

To install BMDS:

  1. Click here to save (download) the zip file for BMDS 2.5 and Wizard 1.9 (14.4MB, ZIP file)
  2. Note1: Subsequent to the release of BMDS 2.5, the poly.exe model was updated to fix an error in the restricted linear model when variance is non-constant. After installing BMDS 2.5, click here to download the updated poly.exe model (340KB, ZIP file). You should extract the model from the zip file to your main BMDS250 directory on your computer, replacing the original poly.exe file that was distributed with BMDS 2.5.
    Note2: This BMDS 2.5 zip file does not contain the Wizard Report Template Microsoft Word file that is needed for the Wizard report feature that prepares formatted Word tables of model results. Click here to download the BMDS Wizard Report Template.docx file and save it to your ...\BMDS250\Wizard folder after installing BMDS 2.5.
    Note3: To run the toxicodiffusion model included in Version 2.5, you must install the R statistical software to your computer (go to http://www.r-project.org/ Exit EPA Disclaimer for more information). Although the toxicodiffusion model is designed to run using version 2.6.2 or later of R, issues have been noted with at least one version (version 3.0.2); EPA currently recommends using version 3.1.0 of R.
  3. Locate the BMDS zip file you downloaded. Typical locations for file downloads are the Windows Desktop or the Download directory in My Documents.
  4. In Windows Explorer, double-click the downloaded .zip file. Drag and drop the BMDS250 folder from the .zip file to the directory of your choice on your computer. It is recommended that you place the BMDS250 folder (and its subfolders) in the simplest (shortest) directory for which you have administrative rights (Note: for most EPA users, this will be C:\Users\[EPA user's LAN ID]; for non-EPA users, this could be as simple as C:\). The new Excel-based Wizard templates will work with BMDS 2.5 installed in any directory, however the Wizard folder MUST be installed in the same directory as the BMDS250 executable.

    Please use the "Problem Report" feature listed in the "Help" menu of BMDS 2.5 or contact us using our Help Desk Form Exit EPA Disclaimer if you experience installation problems or have questions.

AFTER INSTALLING BMDS

Please read the Readme 2.5.pdf file in your main BMDS directory for additional information (e.g., regarding verification of the installation and any known bugs in the current version).

You may find it more convenient to run BMDS from a desktop shortcut icon. Here's how to create one:

  1. In Windows Explorer, navigate to the BMDS250 folder.
  2. Right-click the BMDS250.exe file. A context menu appears.
  3. Click Send To. A submenu appears.
  4. Click "Desktop (Create Shortcut)". Windows creates a shortcut to the file on your desktop.

Once in the system, use the Help feature for further assistance. If you have problems or concerns, please use the "Problem Report" feature listed in the "Help" menu of BMDS 2.5 or contact us using our Help Desk Form Exit EPA Disclaimer.

To determine whether BMDS is properly loaded on your computer, choose "File" from the menu at the top of the BMDS program, then "Open," then "Dose Response Session (.ssn)." The Window should open to the BMDS SessionFiles folder. Select and open any .ssn file (e.g., Cancer-BMR10.ssn). When the Session screen appears, click the "Save As" button and resave the session under a different name (e.g., Cancer-BMR10-test.ssn; you can delete this file later). Then click the "Run" button on the resaved Session screen. When the plots and summary report appear, click on "File" at the top of the summary report screen and then "Export to Excel." Pre-selected summary report data should export to several Excel worksheets, with the "Dichotomous Format" or "Continuous Format" worksheet in the initial view. If you are able to complete these steps without extraordinary (i.e., not normal model error messages), BMDS is likely to have been installed properly and completely.

Registering: Registration is not required to download the software. However, if you would like to receive a notification when new releases or important information becomes available, please register on the download page. We also offer the C source code files for the individual models used in the BMDS system to reviewers/programmers that might be interested in performing an in-depth analysis of the model algorithms and features. We welcome, in fact encourage, comments, recommendations, suggested revisions, or corrections, through our Help Desk Form Exit EPA Disclaimer.

Note: To keep your BMDS system current, check the BMDS website (http://www.epa.gov/ncea/bmds) periodically for updates to the software or help manual.

Toxicodiffusion model documentation

To run the Toxicodiffusion model that is in BMDS 2.5 you will need to also install the R statistical software to your computer (http://www.r-project.org/) Exit EPA Disclaimer (Note that you do not need to install R to run any of the other BMDS Models). Although the toxicodiffusion model is designed to run using version 2.6.2 or later of R, issues have been noted with at least one version (version 3.0.2); EPA currently recommends using version 3.1.0 of R.

For a complete description of the beta toxicodiffusion model contained in BMDS 2.5, download the beta toxicodiffusion model documentation file (PDF) (53 pp, 699KB, about PDF).

Ten Berge model documentation

The ten Berge model has been incorporated into the BMDS 2.5 interface. The following ten Berge documentation and reviewer comment files are available for downloading.

  1. Click here to download the ten Berge model documentation file (PDF) (89pp, 756 KB, about PDF)
  2. Click here to download the ten Berge model peer review comments (PDF) (26pp, 94.4 KB, about PDF)

Multitumor model documentation

The multitumor (MS_combo) model has been incorporated into the BMDS 2.5 interface. The following multitumor model technical background document is available for downloading.

  1. Click here to download the multitumor model technical background document (PDF) (2pp, 200 KB, about PDF)
  2. Click here to download EPA technical guidance for choosing the appropriate stage of a multistage model for cancer modeling (PDF) (6pp, 465 KB, about PDF)

Multistage Weibull Time-to-Tumor Software and Documentation

The Multistage Weibull (MSW) Time-to-Tumor model is run from a Windows command prompt window. Users are urged to register so they will be notified of improvements and release of graphical programs for R (expected early in 2009). The following materials are available for downloading:

  1. Click here to download the MSW time-to-tumor model executable, user manual, spreadsheet data template, and sample data and output files (378KB, ZIP file)
  2. Click here to download the MSW time-to-tumor model peer review comments and response (PDF) (also includes review of other models) (16 pp, 212KB, about PDF)
  3. Click here to download the MSW time-to-tumor model technical documentation files (1.32MB, ZIP file)

Obtaining Older Versions of BMDS

To obtain older versions of BMDS send an e-mail to gift.jeff@epa.gov with your request, including the BMS version you would like to receive.

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