biological-networks
There are 62 repositories under biological-networks topic.
AstraZeneca/onto_merger
OntoMerger is an ontology alignment library for deduplicating knowledge graph nodes that represent the same domain.
colomoto/colomoto-docker
The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks
cantinilab/HuMMuS
Molecular interactions inference from single-cell multi-omics data
dvklopfenstein/ReactomePy
Explore biomolecular pathways in Reactome from the command-line or a Python script
krishnanlab/PyGenePlexus
A network based gene classification library to generate genome wide predictions about genes that are functionally similar to the input gene list.
basiralab/MGN-Net
MGN-Net: A novel Graph Neural Network for integrating heterogenous graph population derived from multiple sources.
hammouc/Multilevel-Monte-Carlo-with-Importance-Sampling-for-SRNs
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
LSI-UniKonstanz/vanted
Visualisation and Analysis of Networks conTaining Experimental Data
krashkov/SteinerNet
R Package: Steiner tree approach for graph analysis
mims-harvard/life-tree
Evolution of protein interactomes across the tree of life
Axelwickm/NeuroCorrelation
3D Spiking neural network simulation exploring Spike Timing Dependent Plasticity (STDP)
seyuboglu/milieu
Mutual Interactors: A graph-based machine learning model with applications in molecular phenotype prediction
PathwayAnalysisPlatform/PathwayMatcher_Dev
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
sbgn/cd2sbgnml
Translation between CellDesigner-flavoured SBML and SBGN-ML
abduallahmohamed/MCRM
MCRM: Mother Compact Recurrent Memory
arnaudporet/kali
In silico therapeutic target discovery using network attractors: avoiding pathological phenotypes
jsalbert/awesome-biologically-motivated-learning
Awesome list of research publications and media on biologically-motivated learning algorithms.
kckishan/BioNetEmbedding
PyTorch Implementation of Biological Network Embedding.
planetareum/Planetareum
Step into the future.
Asplund-Samuelsson/POPPY
Prospecting Optimal Pathways with PYthon: Tools for creating and exploring metabolic reaction networks.
daisybio/keypathwayminer-R
R package for de novo pathway enrichment using KeyPathwayMiner
draeger-lab/SBMLsqueezer
Context-sensitive creation of kinetic equations in biochemical networks
ladyson1806/SerohijosLab-piQTL
GitHub Repository associated with the piQTL project (Mapping effects of genome-wide genetic variation to protein-protein interactions reveals molecular mechanisms of complex traits) [ Serohijos & Michnick Lab, Université de Montréal ]
raminmh/Worm-Blogging
Here, I include my thoughts about how does the brain of the worm give rise to remarkable behavioral plasticities
royludo/cd2sbgnml
Translation between CellDesigner-flavoured SBML and SBGN-ML
arnaudporet/pathrider
Finding paths of interest in networks
alyst/HierarchicalHotNet.jl
Julia implementation of Hierarchical HotNet method
arnaudporet/kgml2sif
Converting KGML encoded KEGG pathways to the SIF file format
arnaudporet/sbgn2sif
Converting SBGN encoded pathways to the SIF file format
bhklab/CrosstalkNet
A web resource to analyze bi-partite and non-bipartite biological networks.
cannin/sbgn2sif
Converting SBGN-encoded pathways to the SIF file format
MRIO/oliveML
neuroML models for reconstructed inferior olivary cells.
nsarang/motif_bionet
Identifying frequent patterns in graphs
pooryaparvizi/BioNE
The BioNE is a new pipeline that integrates embedding results from different graph embedding methods, providing a more comprehensive knowledge of the network and therefore better performance on prediction tasks.
ptgm/bioNuSMV
bioNuSMV is a fork and extension of https://github.com/hklarner/NuSMV-a, which adds a handful of features to ease the use of model checking by biological modelers, in particular, in the context of the verification of qualitative regulatory networks