Setting Up and Using BMDS Wizard – Tips and Best Practices
Several of the following tips and best practices are drawn from the BMDS Wizard User's Reference Guide, which you can find in the Wizard subdirectory. Check the guide for other tips on working effectively with BMDS Wizard.
- The BMDS Wizard can be run from any directory on your computer. However, due to character length restrictions in BMDS, it is best to keep directory path and file names as short as possible.
- BMDS currently installs the Wizard templates in the following subdirectory (for example): C:\USEPA\BMDS240\BMDS Wizard 1.8\Templates. The BMDS Wizard User Guide recommends creating the directory path C:\USEPA\Wizard\Templates; alternatively, you could create a C:\Wizard\Templates path.
- The Wizard folder holds the user guide, reporting template, and other helper files. The Templates directory holds the Excel templates you will use to create your results files.
- As you use the Wizard, you will want to create new directories to hold your working files, while leaving the templates in the Templates directory. The next section talks about this in more detail.
For more information on this topic, please refer to the BMDS Wizard User's Reference Guide, Section 1.2 “BMDS Wizard Installation.”
- Pick the appropriate template for the dataset you will model. For example, if modeling a continuous dataset, you may wish to start with the file BMDS Wizard-continuous.xlsm, which is configured to model continuous data (i.e., the relevant models are already selected, and the data tab is pre-formatted to handle these types of data).
- Copy this Excel template file and paste it to a new directory where you will keep all BMDS Wizard modeling spreadsheets. If you’re new to BMDS Wizard, we recommend creating a single directory to keep all of your uniquely named Wizard files together with the associated files they create. You will need to specify this directory later when using the Wizard.
For example, if you are modeling arsenic, create the directory C:\Wizard\arsenic to hold your BMDS Wizard files. Depending on the number of studies and endpoints you have to evaluate, you may want to create subdirectories for your Wizard files and BMD outputs. The BMDS Wizard will prompt you to enter the directory where you want to save your output files before running the model.
When you create new directories, remember: Keep the directory path short.
- With the template in the new folder, rename the spreadsheet to contain a unique identifier along with the study name and description of the endpoint being modeled.
- The BMDS Wizard User's Reference Guide recommends creating a new folder or path where BMDS modeling inputs, outputs, and intermediate files will be placed; this would typically be a new path within the folder you created for the Wizard template file. (You can specify this path later from within the Wizard.) You do not need to keep these output files after the run is completed because the worksheet contains all the information needed to reproduce the run.
- Open the Wizard file and ensure macros are enabled in the spreadsheet. For details on how to do this in various versions of Excel, refer to the BMDS Wizard User Guide, Section 1.2.4.
- When you have completed the above steps, you are ready to move to the next exercise. Before you do, be sure to read the “Best Practices” below.
For more information, refer to the BMDS Wizard User's Reference Guide, Section 2.1 “Setting Up a New Run”.
- BMDS Wizard only allows for analysis of continuous and dichotomous data that is summarized by dose group. Individual test subject data must be converted to summary data (means and standard deviations) by the user before entering into Wizard.
- Create a new BMDS Wizard Template for each dataset you model. Don't complete multiple BMDS modeling sessions in the same BMDS Wizard file, as you'll overwrite all previous inputs and outputs and will no longer have a record of what was done and why.
- By default, Microsoft Word reports will be located in the same folder as the BMDS Wizard Excel File. You can specify a different report output directory from within the Wizard.
- BMDS output files and images are embedded in the BMDS Wizard file (on the hidden “Output” worksheet) so you do not need to keep the output files on your hard drive. You can email the BMDS Wizard file to anyone and they can generate the outputs from a BMDS modeling run. For more information, refer to the BMDS Wizard User’s Reference Guide, Section 2.7, “Viewing Imported Results.”
- Although BMDS Wizard will recommend a model, you still need to “Select” a best-fitting model on the Results tab. If you do not select a model, the automated summary reports will state that no model was selected as best-fitting. For more information, refer to the BMDS Wizard User’s Guide, Section 2.8.1, “Selecting a Best-Fitting Model”
- At this time, BMDS continuous models require more than 1 subject per dose.
- Standard errors are not estimated for all parameters.
- To edit plots, you may have to copy them to another application such as Microsoft PowerPoint or open them from within BMDS and use GnuPlot.
- Be very particular about naming your Wizard files and entering in Study information. This will facilitate being able to match files created by BMDS (option, output, and plot files) with the Wizard file used to run BMDS.
- After running the BMDS Wizard on a dataset, a good practice is to save your result, open a new template, and run the same dataset again. Then, compare the results between the two files.