Jason R Phillips1, Daniel L Svoboda1, Arpit Tandon1, Shyam Patel1, Alex Sedykh1, Deepak Mav1, Byron Kuo2, Carole L Yauk2, Longlong Yang3, Russell S Thomas4, Jeff S Gift5, J Allen Davis6, Louis Olszyk7, B Alex Merrick8, Richard S Paules8, Fred Parham8, Trey Saddler8, Ruchir R Shah1, Scott S Auerbach8. 1. Sciome LLC, Research Triangle Park, NC, USA. 2. Environmental Health Science and Research Bureau, Environmental and Radiation Health Sciences Directorate, HECSB, Health Canada, Ottawa, ON, Canada. 3. D.S. Technologies, Inc, Research Triangle Park, NC, USA. 4. National Center for Computational Toxicology, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA. 5. National Center for Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA. 6. National Center for Environmental Assessment, U.S. Environmental Protection Agency, Cincinnati, OH, USA. 7. CSRA Inc, Research Triangle Park, NC, USA. 8. National Toxicology Program, NIEHS, Research Triangle Park, NC, USA.
Abstract
SUMMARY: A new version (version 2) of the genomic dose-response analysis software, BMDExpress, has been created. The software addresses the increasing use of transcriptomic dose-response data in toxicology, drug design, risk assessment and translational research. In this new version, we have implemented additional statistical filtering options (e.g. Williams' trend test), curve fitting models, Linux and Macintosh compatibility and support for additional transcriptomic platforms with up-to-date gene annotations. Furthermore, we have implemented extensive data visualizations, on-the-fly data filtering, and a batch-wise analysis workflow. We have also significantly re-engineered the code base to reflect contemporary software engineering practices and streamline future development. The first version of BMDExpress was developed in 2007 to meet an unmet demand for easy-to-use transcriptomic dose-response analysis software. Since its original release, however, transcriptomic platforms, technologies, pathway annotations and quantitative methods for data analysis have undergone a large change necessitating a significant re-development of BMDExpress. To that end, as of 2016, the National Toxicology Program assumed stewardship of BMDExpress. The result is a modernized and updated BMDExpress 2 that addresses the needs of the growing toxicogenomics user community. AVAILABILITY AND IMPLEMENTATION: BMDExpress 2 is available at https://github.com/auerbachs/BMDExpress-2/releases. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Published by Oxford University Press 2018. This work is written by US Government employees and is in the public domain in the US.
SUMMARY: A new version (version 2) of the genomic dose-response analysis software, BMDExpress, has been created. The software addresses the increasing use of transcriptomic dose-response data in toxicology, drug design, risk assessment and translational research. In this new version, we have implemented additional statistical filtering options (e.g. Williams' trend test), curve fitting models, Linux and Macintosh compatibility and support for additional transcriptomic platforms with up-to-date gene annotations. Furthermore, we have implemented extensive data visualizations, on-the-fly data filtering, and a batch-wise analysis workflow. We have also significantly re-engineered the code base to reflect contemporary software engineering practices and streamline future development. The first version of BMDExpress was developed in 2007 to meet an unmet demand for easy-to-use transcriptomic dose-response analysis software. Since its original release, however, transcriptomic platforms, technologies, pathway annotations and quantitative methods for data analysis have undergone a large change necessitating a significant re-development of BMDExpress. To that end, as of 2016, the National Toxicology Program assumed stewardship of BMDExpress. The result is a modernized and updated BMDExpress 2 that addresses the needs of the growing toxicogenomics user community. AVAILABILITY AND IMPLEMENTATION: BMDExpress 2 is available at https://github.com/auerbachs/BMDExpress-2/releases. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Published by Oxford University Press 2018. This work is written by US Government employees and is in the public domain in the US.
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