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

PyBEL Logo PyBEL creator, maintainer GitHub logo WikiData logo
Compiler for the Biological Expression Language
Bio2BEL Logo Bio2BEL creator, maintainer GitHub logo
Framework for reproducible data integration in BEL
BEL Commons Logo BEL Commons creator, maintainer GitHub logo
Interactive exploration of networks encoded in the BEL
PyOBO Logo PyOBO creator, maintainer GitHub logo
Harmonization of biological ontologies and controlled vocabularies
GuiltyTargets Logo GuiltyTargets advisor, maintainer GitHub logo
Target prioritization framework using gene expression and network representation learning
PyKEEN Logo PyKEEN maintainer (core team member) GitHub logo
The most expansive knowledge graph embedding framework to date
ComPath Logo ComPath contributor (core team member) GitHub logo
Platform and web application for integrating and curating pathway databases
PathMe Logo PathMe contributor (core team member) GitHub logo
Web application for exploration of pathway databases
Pathway Forte Logo Pathway Forte contributor (core team member) GitHub logo
Benchmarking pathway databases in functional enrichment analysis and prediction methods
RatVec Logo RatVec contributor GitHub logo
Sequence-based representation learning
PS4DR Logo PS4DR advisor GitHub logo
Drug repositioning based on bioactivity pattern matching and GWAS
SeffNet Logo SeffNet advisor, maintainer GitHub logo
Drug repositioning framework based on network representation learning
CLEP Logo CLEP advisor GitHub logo
Patient stratification framework based on network representation learning
BEL2SCM Logo BEL2SCM contributor (core team member) GitHub logo
Generation of structural causal models (SCMs) from BEL graphs
y0 Logo y0 maintainer (core team member) GitHub logo
Representation and manipulating probabilistic expressions
STonKGs Logo STonKGs advisor GitHub logo
Multimodal Transformers for biomedical text and Knowledge Graph data
ChemicalX Logo ChemicalX contributor (core team member) GitHub logo
A deep learning library for drug-drug interaction, polypharmacy side effect, and synergy prediction.
RexMex Logo RexMex contributor GitHub logo
A library implementing a comprehensive collection of metrics for the evaluation of recommender systems.

Databases

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

CONSO Logo CONSO creator, maintainer GitHub logo
Ontology of phenomena related to neurodegeneration
CONIB Logo CONIB creator, maintainer GitHub logo
Curated knowledge graphs describing neurodegeneration in BEL
NeuroMMSig Logo NeuroMMSig contributor GitHub logo
Multimodal Mechanistic Signatures for Neurodegenerative Diseases
Biomappings Logo Biomappings creator, maintainer GitHub logo
Predicted and curated mappings between named biological entities
Bioversions Logo Bioversions creator, maintainer GitHub logo
What's the current version for each biological database?
Bioregistry Logo Bioregistry creator, maintainer GitHub logo
An integrative meta-registry of biological databases, ontologies, and nomenclatures.
Ooh Na Na Logo Ooh Na Na creator, maintainer
Comprehensive metadatabase of identifiers and names for biological entities
Inspector Javert's Xref Database Logo Inspector Javert's Xref Database creator, maintainer
Comprehensive metadatabase of cross-references between databases of biological entities
Chemical Roles Graph Logo Chemical Roles Graph creator, maintainer GitHub logo
Connecting roles in the ChEBI ontology to their targets

Scientific Programming 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: