🌶️ An ecosystem in Python for working with the Biological Expression Language (BEL)

R client for the OmniPath web service

COVID-19 Knowledge Graph: a computable, multi-modal, cause-and-effect knowledge model of COVID-19 pathophysiology

Functional Associations using Variational Autoencoders

`ggbipart`, an R package for plotting bipartite networks

📖 Generation and Applications of Knowledge Graphs in Systems and Networks Biology

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

A multi-reference network annotation tool to support omics analysis

A Bio2BEL package for integrating pathway-related information from KEGG in BEL

A series of simulation codes used to emulate quantum-like networks in the simulation of emergent adaptive behavior, such as network synchronization, and relate the nature of the coupled harmonic oscillators with non-local behavior and chimera states in systems of quantum particles. Coding Used is based on mathematical modelling of transport in q…

Generate dynamic structural causal models from biological knowledge graphs encoded in the Biological Expression Language (BEL)

A Bio2BEL package for DrugBank (https://www.drugbank.ca)

Spicing-aware time-course network enricher - exploratory analysis for transcriptomics and/or proteomics time series data

Tools for Generating, Visualising, and Analysing Link Communities in Networks

A machine learning tool to assign edges in protein-protein interaction networks with a function.

A Bio2BEL package for converting the Human Metabolite Database (HMDB) to BEL

Integration of pathway-related information from Reactome in BEL

A web application for visualizing and exploring pathway knowledge in Biological Expression Language (BEL)

Contextualization of protein-protein interaction databases by cell line

Structure Learning for Hierarchical Networks