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The Human Toxome Collaboratorium
Provides a familiar virtual desktop. The Human Toxome Collaboratorium is a shared computational environment hosted on third-party cloud services. It was developed in the context of the Human Toxome Project, a consortium that aims to map pathways of toxicity (PoT) and endocrine disruption (ED). This platform includes almost 30 software packages containing a mix of commercial, open source, and internally developed applications used to analyze omics technologies, along with general-purpose utilities and development platforms.
ChemDIS
Provides enrichment analysis tools for identifying chemical-associated Gene Ontology (GO), pathway (KEGG and Reactome) and Disease Ontology (DO and DOlite) based on a hypergeometric distribution. ChemDIS is a chemical-disease inference system based on chemical-protein interactions. By integrating the chemical-protein interactions and protein-disease interactions, the diseases associated with a given chemical can be inferred from the chemical-protein-disease relationship. ChemDIS is expected to be a useful chemical-disease inference system for assessing potential risks associated with environmental chemicals.
PharmIV / Pharmacoepidemiology Instrumental Variable
A formula necessary to calculate power for instrumental variable analysis with a single binary instrument, binary exposure and continuous outcome in the context of pharmacoepidemiology. PharmIV has been shown to be valid by comparison against a simulation study, which concluded that the formula provided near true values across a range of realistic parameters. Users can download the code or perform their analyses online through a web application.
BMDExpress Data Viewer
Obsolete
A web-based application for visualizing and graphing BMDExpress output files. BMDExpress applies BMD modeling to transcriptomic datasets to identify transcriptional BMDs. Through our case studies, we demonstrate that BMDExpress Data Viewer is a useful tool to visualize, explore and analyze BMDExpress output files. Visualizing the data in this manner enables rapid assessment of data quality, model fit, doses of peak activity, most sensitive pathway perturbations and other metrics that will be useful in applying toxicogenomics in risk assessment.
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