networks-biology

🌶️ 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

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

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

Curation of Neurodegeneration in Biological Expression Language (CONIB)

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

Simulating and analyzing dynamical network models

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

Integration of pathway-related information from Reactome in BEL

Structure Learning for Hierarchical Networks

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

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

Modeling heme pathogenicity and pathway dysregulation in the context of hemolytic disorders

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

An environment for curating, validating, and exploring knowledge assemblies encoded in BEL

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

Bio-ModelChecker: Using Bounded Constraint Satisfaction to Seamlessly Integrate Observed Behavior with Prior Knowledge of Biological Networks

Contextualization of protein-protein interaction databases by cell line

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. A full showcase of this project is discussed in the following videos:https://www.youtube.com/watch?time_continue=115&v=WX3Ds_xCOaE

A Shiny Application for Visualization and Analysis of Networks

Phenotype-driven module identification based on multi-level networks

A Bio2BEL package for converting the Gene Ontology (GO) to BEL

Dynamical analysis of minimnal networks based on approximate majority algorithm (AM)

LaTeX source for "Bio2BEL: Integration of Structured Knowledge with Biological Expression Language"

Streaming over networks