systems-biology

There are 26 repositories under systems-biology topic.

opencobra / cobrapy
COBRApy is a package for constraint-based modeling of metabolic networks.
modeling metabolic-models metabolic-network metabolism flux bioinformatics biochemistry computational-biology systems-biology cell-design strain-engineering python cobra sbml sbml-model sbml-simulation
Language:Python 453
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.
differential-equations chemical-reactions reaction-network sde dsl ode gillespie-algorithm biology systems-biology rate-laws sciml scientific-machine-learning systems-biology-simulation julia simulation
Language:Julia 436
awesome-biology
raivivek / awesome-biology
Curated (meta)list of resources for Biology.
biology awesome-list bioinformatics books evolution systems-biology science
334
pyPESTO
ICB-DCM / pyPESTO
python Parameter EStimation TOolbox
parameter-estimation optimization systems-biology python hacktoberfest
Language:Python 206
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
metagenomics computational-biology metabolic-models gut-microbiome snakemake metagenome-assembled-genomes mags metabolism bioinformatics flux-balance-analysis genome-scale-metabolic-model metabolic-modeling microbial-ecology microbiome systems-biology
Language:Python 176
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.
systems-biology modeling biology computational-biology bioinformatics pysb nlp indra sbml
Language:Python 167
pysb / pysb
Python framework for Systems Biology modeling
systems-biology
Language:Python 161
genular / pandora
PANDORA - Predictive Analytics aNd Data Oriented Research Applications :computer:
machine-learning systems-biology data-science data-visualization data-mining pandora bioinformatics biomarkers clinical-data clustering data-integration drug-discovery genomic-data-analysis microbiome predictive-analytics transcriptomics tsne umap unsupervised-machine-learning
Language:Vue 133
pybel / pybel
🌶️ An ecosystem in Python for working with the Biological Expression Language (BEL)
bioinformatics biological-expression-language bioregistry domain-specific-language networks networks-biology pybel systems-biology
Language:Python 131
florianhartig / BayesianTools
General-Purpose MCMC and SMC Samplers and Tools for Bayesian Statistics
bayes cran ecological-models mcmc optimization smc systems-biology
Language:R 115
MaayanLab / biojupies
Automated generation of tailored bioinformatics Jupyter Notebooks via a user interface.
bioinformatics systems-biology jupyter rna-seq pipeline notebook cloud dcppc
Language:HTML 105
SBRG / ssbio
A Python framework for structural systems biology
systems-biology protein-structure structural-biology constraint-based-modeling cobrapy structural-systems-biology
Language:Python 101
SysBioChalmers / RAVEN
The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.
genome-scale-models constraint-based-modeling metabolic-reconstruction gap-filling human-metabolism metabolic-models metabolic-engineering systems-biology sysbio
Language:MATLAB 97
saeyslab / multinichenetr
MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data
cell-cell-communication differential-expression intercellular-communication intercellular-signaling ligand-receptor ligand-receptor-interaction ligand-target scrna-seq single-cell single-cell-rna-seq systems-biology cell-cell-interaction
Language:HTML 96
SysBioChalmers / yeast-GEM
The consensus GEM for Saccharomyces cerevisiae
genome-scale-models yeast systems-biology hacktoberfest saccharomyces-cerevisiae matlab biology reconstruction consensus python metabolic-models standard-gem
Language:MATLAB 91
copasi / COPASI
COPASI is a software application for simulation and analysis of biochemical networks and their dynamics.
copasi simulation modeling systems-biology dynamics chemistry biochemistry kinetics chemical-kinetics
Language:C++ 88
micom-dev / micom
Python package to study microbial communities using metabolic modeling.
microbiota cobrapy modeling metabolic-models flux biochemistry systems-biology microbiome python cobra community hacktoberfest
Language:Python 82
seek4science / seek
For finding, sharing and exchanging Data, Models, Simulations and Processes in Science.
isa science systems-biology synthetic-biology fair data publication opendata datamanagement semantic-web biohackcovid20
Language:Ruby 74
SysBioChalmers / GECKO
Toolbox for including enzyme constraints on a genome-scale model.
proteomics data-integration toolbox matlab kinetics enzyme-constraints systems-biology
Language:MATLAB 64
ecell / ecell4_base
An integrated software environment for multi-algorithm, multi-timescale, multi-spatial-representation simulation of various cellular phenomena
c-plus-plus jupyter-notebook python simulation systems-biology
Language:C++ 62
jpquast / protti
Picotti lab data analysis package.
r proteomics mass-spectrometry data-analysis systems-biology lip-ms omics protein
Language:R 57
Data2Dynamics / d2d
a modeling environment tailored to parameter estimation in dynamical systems
modeling matlab systems-biology computational-biology parameter-estimation model-calibration
Language:MATLAB 56
PEtab
PEtab-dev / PEtab
PEtab - an SBML and TSV based data format for parameter estimation problems in systems biology
systems-biology parameter-estimation sbml-model data-format sbml combine-archive modelling hacktoberfest
56
iVis-at-Bilkent / pathway-mapper
PathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways
systems-biology pathways pathway-analysis cancer-pathways cancer-genomics network-visualization tcga bioinformatics graphviz
Language:TypeScript 55
CellMLToolkit.jl
SciML / CellMLToolkit.jl
CellMLToolkit.jl is a Julia library that connects CellML models to the Scientific Julia ecosystem.
cellml systems-biology differential-equations julia ode physiology scientific-machine-learning sciml
Language:Julia 55
NBISweden / workshop_omics_integration
Workshop in omics integration and systems biology
systems-biology integrative-omics
Language:HTML 54
iVis-at-Bilkent / newt
A web application to visualize and edit pathway models
pathways pathway-analysis network-visualization editor bioinformatics systems-biology biology sbgn web-based-visualization visualization pathway-models newt celldesigner sif layout sbml
Language:JavaScript 52
CRI-iAtlas / shiny-iatlas
An interactive web portal for exploring immuno-oncology data. This repo now superseded by iatlas-app
genomics systems-biology immunology cancer
Language:R 47
augustinas1 / MomentClosure.jl
Tools to generate and study moment equations for any chemical reaction network using various moment closure approximations
systems-biology chemical-reaction-networks stochastic-processes moments moment-closure moment-equations gillespie-algorithm gene-network
Language:Julia 44
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!
metabolic-models constraint-programming bioinformatics flux-balance-analysis sbml systems-biology computational-biology cobra stoichiometric-modeling constraint-based-modeling constraint-based-analysis metabolic-reconstruction constraint-based-reconstruction metabolic-networks flux-variability metabolic-engineering fba fva
Language:Python 43
Armavica / rebop
Fast stochastic simulator for chemical reaction networks
simulation gillespie systems-biology monte-carlo science scientific-computing
Language:Rust 42
GeomScale / dingo
A python library for metabolic networks sampling and analysis
sampling metabolic-network polytope random-walk systems-biology hacktoberfest
Language:Python 42
SystemsBioinformatics / stochpy
StochPy is a versatile stochastic modeling package which is designed for stochastic simulation of molecular control networks
bioinformatics console-application kinetic-modeling python stochastic-simulation-algorithm systems-biology
Language:Python 39
biosustain / shu
Multi-dimensional, trans-omics metabolic maps.
metabolism systems-biology visualization
Language:Rust 38
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.
api library libsbml sbml systems-biology
Language:C++ 38
SciML / SBMLToolkit.jl
SBML differential equation and chemical reaction model (Gillespie simulations) for Julia's SciML ModelingToolkit
chemical-reaction-networks differential-equations gillespie-algorithm julia ode quantitative-systems-pharmacology sbml sciml systems-biology
Language:Julia 37