systems-biology

There are 482 repositories under systems-biology topic.

  • opencobra/cobrapy

    COBRApy is a package for constraint-based modeling of metabolic networks.

    Language:Python46737670218

  • SciML/Catalyst.jl

    Chemical reaction network and systems biology interface for scientific machine learning (SciML). High performance, GPU-parallelized, and O(1) solvers in open source software.

    Language:Julia4641738778
  • awesome-biology

    raivivek/awesome-biology

    Curated (meta)list of resources for Biology.

    35021546
  • pyPESTO

    ICB-DCM/pyPESTO

    python Parameter EStimation TOolbox

    Language:Python2211154347

  • franciscozorrilla/metaGEM

    :gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

    Language:Python204512142

  • sorgerlab/indra

    INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.

    Language:Python1772446068

  • pysb/pysb

    Python framework for Systems Biology modeling

    Language:Python1691928071

  • genular/pandora

    PANDORA :computer:

    Language:Vue135112421

  • pybel/pybel

    🌶️ An ecosystem in Python for working with the Biological Expression Language (BEL)

    Language:Python131939432

  • saeyslab/multinichenetr

    MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data

    Language:HTML12339714

  • florianhartig/BayesianTools

    General-Purpose MCMC and SMC Samplers and Tools for Bayesian Statistics

    Language:R1191422529

  • MaayanLab/biojupies

    Automated generation of tailored bioinformatics Jupyter Notebooks via a user interface.

    Language:HTML108910830

  • SBRG/ssbio

    A Python framework for structural systems biology

    Language:Python104174128

  • SysBioChalmers/RAVEN

    The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.

    Language:MATLAB1011313953

  • SysBioChalmers/yeast-GEM

    The consensus GEM for Saccharomyces cerevisiae

    Language:MATLAB961812446

  • copasi/COPASI

    COPASI is a software application for simulation and analysis of biochemical networks and their dynamics.

    Language:C++9521029

  • micom-dev/micom

    Python package to study microbial communities using metabolic modeling.

    Language:Python9454318

  • seek4science/seek

    For finding, sharing and exchanging Data, Models, Simulations and Processes in Science.

    Language:Ruby77241.4k52

  • NBISweden/workshop_omics_integration

    Workshop in omics integration and systems biology

    Language:HTML71393035

  • SysBioChalmers/GECKO

    Toolbox for including enzyme constraints on a genome-scale model.

    Language:MATLAB661113751

  • ecell/ecell4_base

    An integrated software environment for multi-algorithm, multi-timescale, multi-spatial-representation simulation of various cellular phenomena

    Language:C++631223223
  • CellMLToolkit.jl

    SciML/CellMLToolkit.jl

    CellMLToolkit.jl is a Julia library that connects CellML models to the Scientific Julia ecosystem.

    Language:Julia62101816
  • PEtab

    PEtab-dev/PEtab

    PEtab - an SBML and TSV based data format for parameter estimation problems in systems biology

    601723212

  • jpquast/protti

    Picotti lab data analysis package.

    Language:R594554

  • Data2Dynamics/d2d

    a modeling environment tailored to parameter estimation in dynamical systems

    Language:MATLAB572715528

  • iVis-at-Bilkent/pathway-mapper

    PathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways

    Language:TypeScript551226027

  • iVis-at-Bilkent/newt

    A web application to visualize and edit pathway models

    Language:JavaScript531170127

  • CRI-iAtlas/shiny-iatlas

    An interactive web portal for exploring immuno-oncology data. This repo now superseded by iatlas-app

    Language:R481411812

  • Armavica/rebop

    Fast stochastic simulator for chemical reaction networks

    Language:Rust463103
  • CNApy

    cnapy-org/CNApy

    An integrated visual environment for metabolic modeling with common methods such as FBA, FVA and Elementary Flux Modes, and advanced features such as thermodynamic methods, extended Minimal Cut Sets, OptKnock, RobustKnock, OptCouple and more!

    Language:Python4632277

  • GeomScale/dingo

    A python library for metabolic networks sampling and analysis

    Language:Python4563528

  • augustinas1/MomentClosure.jl

    Tools to generate and study moment equations for any chemical reaction network using various moment closure approximations

    Language:Julia446136

  • biosustain/shu

    Multi-dimensional, trans-omics metabolic maps.

    Language:Rust443331
  • libsbml

    sbmlteam/libsbml

    LibSBML is a native library for reading, writing and manipulating files and data streams containing the Systems Biology Markup Language (SBML). It offers language bindings for C, C++, C#, Java, JavaScript, MATLAB, Perl, PHP, Python, R and Ruby.

    Language:C++41916928

  • SciML/SBMLToolkit.jl

    SBML differential equation and chemical reaction model (Gillespie simulations) for Julia's SciML ModelingToolkit

    Language:Julia4192110

  • SystemsBioinformatics/stochpy

    StochPy is a versatile stochastic modeling package which is designed for stochastic simulation of molecular control networks

    Language:Python408411