R client for the OmniPath web service

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

Functional Associations using Variational Autoencoders

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

`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 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…

A multi-reference network annotation tool to support omics analysis

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

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

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

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.

AnnNet (Annotated Network) is a unified, high-expressivity graph platform designed to bring the convenience of AnnData-style annotated containers to networks, multilayer structures, and hypergraphs.

Simulating and analyzing dynamical network models

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

Supplementary data 1 of the paper Mello et al. 2019 (NatureEcoEvo).

Structure Learning for Hierarchical Networks