Software

Data science and software engineering at RS focuses primarily on development of our proprietary Facets™ Prioritization Engine. However, we are excited to share select capabilities and collaborate on software projects that we believe might be of benefit to the broader bioinformatics and biopharma ecosystem.  A complete list of RS open-source projects is available at related-sciences on GitHub.

Clinical Advancement Forecasting (Preprint Publication, Data, and Codebase)
A proof of concept on how to identify preclinical drugs worth pursuing using some of the Related Sciences methods and only one public resource (Open Targets) with all code and data made public. The paper explores how to quantify how much decision-making can be improved using machine learning as compared to heuristic scores or genetic evidence alone, by combining many sources of evidence. https://www.medrxiv.org/content/10.1101/2024.08.02.24311422v2.full.pdf
nxontology
Representing ontologies and computing similarity between terms in Python. Based on the NetworkX library with read support for OBO, OWL, and JSON formats. The networkx-data companion project provides popular biomedical ontologies pre-loaded into NXOntology format including MeSH and PubChem Classifications.
ensembl-genes
Extracting the Ensembl genes catalog to simple tables, with support for human, mouse, and rat genomes. Working towards a collaborative and open framework for easy access to Ensembl gene metadata.
articat
Keeping data artifacts organized and documented, a minimal metadata catalog for data written in Python and connected to Google Cloud Datastore.
gce-github-runner
Enabling big computation via GitHub Actions by providing a GitHub self-hosted runner for Google Compute Engine.