Objectives

FastBMD is a computationally efficient implementation of the National Toxicology Program Approach to Genomic Dose-Response Modeling. Key features include a simplified workflow, ability to download results at each step, and interactive exploration of pathway-level BMDs. In addition to model organisms, FastBMD is designed to support non-model organisms by enabling an annotation-free pipeline that includes feature sensitivity-based point-of-departure analysis. The final part of the analysis is designed to allow users to interactively explore BMDs at different levels of organization:

Implementation:

  • Statistical Backend
    Majority of the statistical analyses are based on R (3.4.1) using R packages below:
    "limma", "vsn", "edgeR", "DESeq2", "lattice", "Cairo", "stringr", "RColorBrewer", "data.table","compiler", "genefilter", "preprocessCore", "RJSONIO"
  • Web Framework
    The web application has been developed based on JavaServer Faces (JSF) using libraries below: "PrimeFaces (v6.2)", "jQuery EasyUI", "Sigma.js", "EChart.js", "CanvasXpress"
  • Server Information
    FastBMD is currently hosted on a Google Cloud Engine with 8 CPU cores and 64G memory

Please cite:

Ewald, J., Soufan, O., Xia, J., and Basu, N. (2020) "FastBMD: an online tool for rapid benchmark dose-response analysis of transcriptomics data" Bioinformatics btaa700

ACKNOWLEDGEMENTS

Last updated 2020-09-18