OntoMerger is an ontology alignment library for deduplicating knowledge graph nodes that represent the same domain.

The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks

Explore biomolecular pathways in Reactome from the command-line or a Python script

A network based gene classification library to generate genome wide predictions about genes that are functionally similar to the input gene list.

Molecular interactions inference from single-cell multi-omics data

This repository includes Matlab codes/routines that were used in our manuscript entitled "Importance sampling for a robust and efficient multilevel Monte Carlo estimator for stochastic reaction networks" that can be found in this preprint: https://arxiv.org/abs/1911.06286

R Package: Steiner tree approach for graph analysis

Evolution of protein interactomes across the tree of life

MGN-Net: A novel Graph Neural Network for integrating heterogenous graph population derived from multiple sources.

Visualisation and Analysis of Networks conTaining Experimental Data

Mutual Interactors: A graph-based machine learning model with applications in molecular phenotype prediction

PathwayMatcher is a free, open-source software to search for pathways related to a list of proteins in Reactome. This repository is the development repository. For the latest version see: https://github.com/PathwayAnalysisPlatform/PathwayMatcher

Translation between CellDesigner-flavoured SBML and SBGN-ML

3D Spiking neural network simulation exploring Spike Timing Dependent Plasticity (STDP)

MCRM: Mother Compact Recurrent Memory

In silico therapeutic target discovery using network attractors: avoiding pathological phenotypes

Step into the future.

R package for de novo pathway enrichment using KeyPathwayMiner

Translation between CellDesigner-flavoured SBML and SBGN-ML