biological-networks

There are 58 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.

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  • wangboyunze/Network_Enhancement

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  • colomoto/colomoto-docker

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

    Language:Jupyter Notebook2475310

  • dvklopfenstein/ReactomePy

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

    Language:Python21204

  • krishnanlab/PyGenePlexus

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

    Language:Python203863
  • HuMMuS

    cantinilab/HuMMuS

    Molecular interactions inference from single-cell multi-omics data

    Language:Python15343

  • 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

    Language:MATLAB10501

  • basiralab/MGN-Net

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

    Language:Python9315

  • LSI-UniKonstanz/vanted

    Visualisation and Analysis of Networks conTaining Experimental Data

    Language:Java9601

  • krashkov/SteinerNet

    R Package: Steiner tree approach for graph analysis

    Language:R8145

  • mims-harvard/life-tree

    Evolution of protein interactomes across the tree of life

    Language:C++8305

  • Axelwickm/NeuroCorrelation

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

    Language:C++7211

  • seyuboglu/milieu

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

    Language:Jupyter Notebook7002

  • 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

    Language:Java65171

  • sbgn/cd2sbgnml

    Translation between CellDesigner-flavoured SBML and SBGN-ML

    Language:Java6992

  • abduallahmohamed/MCRM

    MCRM: Mother Compact Recurrent Memory

    Language:Python5300

  • arnaudporet/kali

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

    Language:Go5000

  • planetareum/Planetareum

    Step into the future.

    5001

  • Asplund-Samuelsson/POPPY

    Prospecting Optimal Pathways with PYthon: Tools for creating and exploring metabolic reaction networks.

    Language:Python42161
  • keypathwayminer-R

    daisybio/keypathwayminer-R

    R package for de novo pathway enrichment using KeyPathwayMiner

    Language:R4411

  • draeger-lab/SBMLsqueezer

    Context-sensitive creation of kinetic equations in biochemical networks

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  • jsalbert/awesome-biologically-motivated-learning

    Awesome list of research publications and media on biologically-motivated learning algorithms.

    4100

  • kckishan/BioNetEmbedding

    PyTorch Implementation of Biological Network Embedding.

    Language:Jupyter Notebook4200

  • 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 ]

    Language:Jupyter Notebook4211

  • royludo/cd2sbgnml

    Translation between CellDesigner-flavoured SBML and SBGN-ML

    Language:Java46116

  • arnaudporet/pathrider

    Finding paths of interest in networks

    Language:Go3202

  • raminmh/Worm-Blogging

    Here, I include my thoughts about how does the brain of the worm give rise to remarkable behavioral plasticities

    3311

  • alyst/HierarchicalHotNet.jl

    Julia implementation of Hierarchical HotNet method

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  • arnaudporet/kgml2sif

    Converting KGML encoded KEGG pathways to the SIF file format

    Language:Python2002

  • arnaudporet/sbgn2sif

    Converting SBGN encoded pathways to the SIF file format

    Language:Python2002

  • bhklab/CrosstalkNet

    A web resource to analyze bi-partite and non-bipartite biological networks.

    Language:JavaScript2514

  • cannin/sbgn2sif

    Converting SBGN-encoded pathways to the SIF file format

    Language:Python2201

  • MRIO/oliveML

    neuroML models for reconstructed inferior olivary cells.

    Language:MATLAB2322

  • nsarang/motif_bionet

    Identifying frequent patterns in graphs

    Language:C++210

  • 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.

    Language:Python2

  • 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

    Language:C2501