I’ve created many open-source projects as well as made significant contributions to others:

PyBEL Logo PyBEL maintainer
Compiler for the Biological Expression Language
Bio2BEL Logo Bio2BEL maintainer
Framework for reproducible data integration in BEL
BEL Commons Logo BEL Commons maintainer
Interactive exploration of networks encoded in the BEL
PyOBO Logo PyOBO maintainer
Harmonization of biological ontologies and controlled vocabularies
GuiltyTargets Logo GuiltyTargets maintainer
Target prioritization framework using gene expression and network representation learning
PyKEEN Logo PyKEEN maintainer (core team member)
The most expansive knowledge graph embedding framework to date
ComPath Logo ComPath contributor (core team member)
Platform and web application for integrating and curating pathway databases
PathMe Logo PathMe contributor (core team member)
Web application for exploration of pathway databases
RatVec Logo RatVec contributor
Sequence-based representation learning
PS4DR Logo PS4DR advisor
Drug repositioning based on bioactivity pattern matching and GWAS
SeffNet Logo SeffNet advisor
Drug repositioning framework based on network representation learning
CLEPP Logo CLEPP advisor
Patient stratification framework based on network representation learning

Databases

I’ve created many databases myself through curation, automated assembly, and also by coordinating others.

CONSO Logo CONSO maintainer
Ontology of phenomena related to neurodegeneration
CONIB Logo CONIB maintainer
Curated knowledge graphs describing neurodegeneration in BEL
Ooh Na Na maintainer
Comprehensive metadatabase of identifiers and names for biological entities
Inspector Javert's Xref Database maintainer
Comprehensive metadatabase of cross-references between databases of biological entities
Chemical Roles Graph Logo Chemical Roles Graph maintainer
Connecting roles in the ChEBI ontology to their targets

Training

I care very deeply about reproducibility, especially in scientific software development. However, this is not one of the core values taught by most PIs, nor are the core skills part of either scientific or informatics curricula. I’m generating some resources to help fill that gap: