biological-networks

There are 2 repositories under biological-networks topic.

onto_merger
AstraZeneca / onto_merger
OntoMerger is an ontology alignment library for deduplicating knowledge graph nodes that represent the same domain.
algorithm alignment biological-networks biology graph kg knowledge knowledge-graph mapping ontology ontology-alignment
Language:HTML 95
wangboyunze / Network_Enhancement
network-analysis biological-networks matlab
Language:MATLAB 29
colomoto / colomoto-docker
The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks
biological-networks docker jupyter-notebook model-analysis systems-biology
Language:Jupyter Notebook 25
HuMMuS
cantinilab / HuMMuS
Molecular interactions inference from single-cell multi-omics data
biological-networks epigenomics multi-omics multilayer-networks single-cell transcriptomics
Language:R 22
dvklopfenstein / ReactomePy
Explore biomolecular pathways in Reactome from the command-line or a Python script
reactome reactome-pathway biological-networks molecular-biology pathway-enrichment-analysis pathway-analysis biotechnology biotech bioinformatics bioinformatics-pipeline bioinformatics-analysis bioinformatics-scripts bioinformatics-tool pathway-models protein-protein-interaction
Language:Python 22
krishnanlab / PyGenePlexus
A network based gene classification library to generate genome wide predictions about genes that are functionally similar to the input gene list.
biological-networks gene-classification machine-learning
Language:Python 20
basiralab / MGN-Net
MGN-Net: A novel Graph Neural Network for integrating heterogenous graph population derived from multiple sources.
graph-normalizer biological-networks multiview-networks multigraph graph-integration data-fusion data-integration brain-networks brain-connectivity connectomes network-neuroscience graph-neural-networks
Language:Python 11
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
multilevel-models multilevel multilevel-monte-carlo importance-sampling biological-networks biological-simulations matlab stochastic-simulation-algorithm stochastic-reaction-networks stochastic-biological-systems monte-carlo-methods numerical-analysis numerical-simulations stochastic-process
Language:MATLAB 11
krashkov / SteinerNet
R Package: Steiner tree approach for graph analysis
biological-networks cran graph-algorithms r-language r-package steiner-heuristic steiner-tree steiner-tree-problem
Language:R 9
LSI-UniKonstanz / vanted
Visualisation and Analysis of Networks conTaining Experimental Data
biological-networks graph-drawing
Language:Java 9
mims-harvard / life-tree
Evolution of protein interactomes across the tree of life
network-science biological-networks protein-interaction evolution network-analysis network-resilience
Language:C++ 8
Axelwickm / NeuroCorrelation
3D Spiking neural network simulation exploring Spike Timing Dependent Plasticity (STDP)
biological-networks biological-simulation biological-simulations biology neural-network neuron-simulator opengl simulation spiking-neural-network
Language:C++ 7
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
development proteoforms pathways biological-networks reactome pathway-analysis
Language:Java 7
seyuboglu / milieu
Mutual Interactors: A graph-based machine learning model with applications in molecular phenotype prediction
machine-learning network-analysis biological-networks drug-discovery disease-proteins protein-function
Language:Jupyter Notebook 7
cbrinkrolf / VANESA
Modeling and simulation of biological networks using automatic transformation to Petri nets (HFPN / xHPN)
biological-networks modeling-and-simulation petri-nets systems-biology
Language:Java 6
sbgn / cd2sbgnml
Translation between CellDesigner-flavoured SBML and SBGN-ML
bioinformatics biological-networks sbgn sbgn-ml sbml systems-biology
Language:Java 6
abduallahmohamed / MCRM
MCRM: Mother Compact Recurrent Memory
deep-learning recurrent-neural-networks lstm lstm-neural-networks temporal-models rnn biological-networks
Language:Python 5
arnaudporet / kali
In silico therapeutic target discovery using network attractors: avoiding pathological phenotypes
therapeutic-targets in-silico biological-networks boolean-networks regulatory-networks drug-discovery computational-biology biological-simulation biological-modeling
Language:Go 5
jsalbert / awesome-biologically-motivated-learning
Awesome list of research publications and media on biologically-motivated learning algorithms.
biological-networks biologically-motivated-algorithms feedback-alignment credit-assignment awesome-list deep-learning biologically-plausible-learning
5
kckishan / BioNetEmbedding
PyTorch Implementation of Biological Network Embedding.
biological-networks deep-learning embeddings pytorch
Language:Jupyter Notebook 5
planetareum / Planetareum
Step into the future.
ar augmented-reality virtual-reality virtualization plants permaculture geolocation geographical-information-system blockchain coding-challenge design-systems systems-engineering systems-biology decentralized payment-gateway biological-networks
5
Asplund-Samuelsson / POPPY
Prospecting Optimal Pathways with PYthon: Tools for creating and exploring metabolic reaction networks.
computational-biology bioinformatics pathway-enumeration biological-networks thermodynamics
Language:Python 4
keypathwayminer-R
daisybio / keypathwayminer-R
R package for de novo pathway enrichment using KeyPathwayMiner
standalone pathway-enrichment-analysis interaction-network omics gene-expression-profiles de-novo-pahtway-enrichment singelcell biological-networks multiomics r r-package systems-biology
Language:R 4
draeger-lab / SBMLsqueezer
Context-sensitive creation of kinetic equations in biochemical networks
biological-networks information-extraction mathematical-modelling metabolic-engineering regulatory-network computational-biology systems-biology andreas-zell biochemical-networks andreas-dr-ger kinetic-equations sbo bmc-systems-biology plug equation reactions celldesigner reaction sbml
Language:HTML 4
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 ]
bioinformatics biological-networks gwas omics-data-integration population-genetics protein-protein-interaction-network qtl-mapping systems-biology yeast gene-interaction-network
Language:Jupyter Notebook 4
raminmh / Worm-Blogging
Here, I include my thoughts about how does the brain of the worm give rise to remarkable behavioral plasticities
celegans biological-networks computational-neuroscience complex-neural-networks dynamic-systems modeling simulation
4
royludo / cd2sbgnml
Translation between CellDesigner-flavoured SBML and SBGN-ML
bioinformatics systems-biology sbml sbgn sbgnml biological-networks
Language:Java 4
arnaudporet / pathrider
Finding paths of interest in networks
pathfinding networks network-analysis graphs paths shortest-paths upstream-paths downstream-paths biological-networks computational-biology regulatory-networks signaling-networks signaling-pathways pathways pathway-analysis pathway-tools graph-analysis
Language:Go 3
alyst / HierarchicalHotNet.jl
Julia implementation of Hierarchical HotNet method
random-walk hierarchical-clustering weighted-graphs biological-networks julia-package hierarchical-hotnet
Language:Julia 2
arnaudporet / kgml2sif
Converting KGML encoded KEGG pathways to the SIF file format
kegg kegg-pathway-database kegg-pathways kgml sif sif-file-format kgml-file-format biological-networks signaling-pathways converter kgml2sif kgml-to-sif kgml-files pathways
Language:Python 2
arnaudporet / sbgn2sif
Converting SBGN encoded pathways to the SIF file format
reactome reactome-pathways sbgn sbgn-ml sif sif-file-format sbgn-file-format biological-networks signaling-pathways converter sbgn2sif sbgn-to-sif sbgnml pathways
Language:Python 2
cannin / sbgn2sif
Converting SBGN-encoded pathways to the SIF file format
sif sbgn sbgnml biological-networks sbgn-to-sif pathways reactome kegg sbgn2sif
Language:Python 2
nsarang / motif_bionet
Identifying frequent patterns in graphs
motif-discovery graph-algorithms biological-networks d3-visualization graphs disjoint-motifs
Language:C++ 2
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.
biological-networks network-embedding graph-embedding
Language:Python 2
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
biological-networks formal-verification model-checking
Language:C 2
sysbiolab / PathwaySpace
PathwaySpace is an R package that creates landscape images from graphs containing vertices (nodes), edges (lines), and a signal associated with the vertices.
bioinformatics biological-networks graph r
Language:R 2