ZebrafishBMD: A software program for benchmark dose calculations using toxicity screening data from high-throughput zebrafish assays

The ZebrafishBMD program was written by Dr. Dennis Thomas and Dr. Harish Shankaran in collaboration with Dr. Katrina Waters, at the Pacific Northwest National Laboratory. The program was developed as part of projects funded by the National Institutes of Health and the Environmental Protection Agency.

Main Features

The program calculates BMD10 values for 22 developmental and 2 behavioral endpoints of zebrafish using the methods described in the paper.

Version

The current version (ZebrafishBMD v1.0) is a Windows standalone application that was created using Matlab 2016b.

Software requirements:

Matlab Runtime v. 9.1 (Matlab 2016b) for Windows

Downloading and Running ZebrafishBMD

Download and unzip the following .zip folder files
- ZebrafishBMD_v1.0.zip
- example_data_v1.0.zip
Move the input_data folder from example_data_v1.0 into ZebrafishBMD_v1.0 folder

The input_data folder contains zebrafish developmental and behavioral assay data for 10 chemicals. Details about the assay and computational approach are provided in this paper.
Go to ZebrafishBMD_v1.0 folder on Windows command prompt window
Type ZebrafishBMD.exe and press Enter. A user interface window will open. The text fields are pre-filled, so the users don't have to edit these fields. Simple click on the 'Run' button at each step after the previous step run is completed.
The program will create the following folders to save the run output files:
- morphology_response_data
- morphology_fit_results
- behavior_response_data
- behavior_fit_results

Citing ZebrafishBMD

Please cite

Thomas, D. G., Shankaran, H., Truong, L., Tanguay, R. L., & Waters, K. M. (2018). Time-dependent behavioral 
data from zebrafish reveals novel signatures of chemical toxicity using point of 
departure analysis. Computational Toxicology. https://doi.org/10.1016/j.comtox.2018.11.001

Disclaimer

This material was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor the United States Department of Energy, nor Battelle, nor any of their employees, nor any jurisdiction or organization that has cooperated in the development of these materials, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness or any information, apparatus, product, software, or process disclosed, or represents that its use would not infringe privately owned rights.

Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof, or Battelle Memorial Institute. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof.

	 PACIFIC NORTHWEST NATIONAL LABORATORY
		      operated by
			BATTELLE
			for the
	   UNITED STATES DEPARTMENT OF ENERGY
	    under Contract DE-AC05-76RL01830

pnnl / ZebrafishBMD