ddomingof

PubMed2PDF

A Python package to download full article PDFs from OA publications

np-clinical-trials

Source code and data for "Natural products have increased rates of clinical trial success throughout the drug development process"

PTSDDB-Resources

Resources of the PTSD Biomarker Database

rideshare-app

A web application to share rides with your work colleagues

biomedical-entity-linking

ccs-prediction

Evaluating the generalizability of graph neural networks for predicting collision cross section

chemical-roles

Curation of mechanistic relations from roles in ChEBI and MeSH

COSMOS

COVID-19

Supplementary code for the paper: Network Medicine Framework for Identifying Drug Repurposing Opportunities for COVID-19

covid-pathways.github.io

ddomingof

My Profile

predictme

A web application for stratification of Alzheimer's and Parkinson's disease patients

drug2ways

A Python package for drug discovery by analyzing causal paths on multiscale networks

ethnobotany

Source code and data for "Modern drug discovery using ethnobotany: A large-scale cross-cultural analysis of traditional medicine reveals common therapeutic uses"

famplex

Resources for grounding protein families and complexes from text and describing their hierarchical relationships.

GeVa_NeIF

gp-bench

indra

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.

kgem-ensembles-in-drug-discovery

Source code and data repository for "Ensembles of knowledge graph embedding models improve predictions for drug discovery"

MultiGML

MultiGML

nodevectors

Fastest network node embeddings in the west

phd-commits

Functions for scraping git commits from repositories associated with a PhD (or anything else) and plotting them.

plant-chemical-space

Source code and data for "Exploring the known chemical space of the plant kingdom: Insights into taxonomic patterns, knowledge gaps, and bioactive regions"

probability_cheatsheet

A comprehensive 10-page probability cheatsheet that covers a semester's worth of introduction to probability.

pyobo

A programmatic interface for generating and handling OBO in Python.

RPath

Source code and data for "Causal reasoning over knowledge graphs leveraging drug-perturbed and disease-specific transcriptomic signatures for drug discovery"

simdrugs

Python notebooks for analyses and simulating drug response on patient-specific pathway signatures

transcriptomic-target-correlation

On the correspondence between the transcriptomic response of a compound and its targets

weighting-spectral-similarity

Scripts and notebooks from Weighting low-intensity MS/MS ions and m/z frequency for spectral library annotation

zenodo-client