Topic: systems-biology Goto Github

👇 Here are 441 public repositories matching this topic...

amberbiology / py4lifesci
systems-biology,Code repository for the book "Python for the Life Sciences" by Lancaster & Webster
Organization: amberbiology
Home Page: http://pythonforthelifesciences.com/
life-sciences python bioinformatics systems-biology computational-biology next-generation-sequencing book

armavica / rebop
systems-biology,Fast stochastic simulator for chemical reaction networks
User: armavica
Home Page: https://armavica.github.io/rebop/
simulation gillespie systems-biology monte-carlo science scientific-computing

augustinas1 / momentclosure.jl
systems-biology,Tools to generate and study moment equations for any chemical reaction network using various moment closure approximations
User: augustinas1
Home Page: https://augustinas1.github.io/MomentClosure.jl/dev/
systems-biology chemical-reaction-networks stochastic-processes moments moment-closure moment-equations gillespie-algorithm gene-network

biomass-dev / biomass
systems-biology,A Python Framework for Modeling and Analysis of Signaling Systems
Organization: biomass-dev
Home Page: http://biomass-core.rtfd.io
python systems-biology computational-biology simulation kinetic-modeling parameter-estimation ode biochemical-networks dynamical-systems ordinary-differential-equations

biosustain / shu
systems-biology,Multi-dimensional, trans-omics metabolic maps.
Organization: biosustain
Home Page: https://biosustain.github.io/shu
metabolism systems-biology visualization

cnapy-org / cnapy
systems-biology,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!
Organization: cnapy-org
Home Page: https://cnapy-org.github.io/CNApy-guide/
metabolic-models constraint-programming bioinformatics flux-balance-analysis sbml systems-biology computational-biology cobra stoichiometric-modeling constraint-based-modeling

copasi / copasi
systems-biology,COPASI is a software application for simulation and analysis of biochemical networks and their dynamics.
Organization: copasi
Home Page: https://copasi.org
copasi simulation modeling systems-biology dynamics chemistry biochemistry kinetics chemical-kinetics

cri-iatlas / shiny-iatlas
systems-biology,An interactive web portal for exploring immuno-oncology data. This repo now superseded by iatlas-app
Organization: cri-iatlas
Home Page: https://www.cri-iatlas.org
genomics systems-biology immunology cancer

cthoyt / doctoral-thesis
systems-biology,📖 Generation and Applications of Knowledge Graphs in Systems and Networks Biology
User: cthoyt
Home Page: https://github.com/cthoyt/doctoral-thesis/raw/master/main.pdf
biological-expression-language knowledge-graphs knowledge-graph-embeddings data-integration curation simulation biocuration networks-biology systems-biology computational-biology

darrenjw / smfsb
systems-biology,Documentation, models and code relating to the 3rd edition of the textbook Stochastic Modelling for Systems Biology
User: darrenjw
Home Page: https://darrenjw.github.io/work/smfsb/3e/
sbml systems-biology inference gillespie-algorithm mcmc

data2dynamics / d2d
systems-biology,a modeling environment tailored to parameter estimation in dynamical systems
Organization: data2dynamics
Home Page: https://github.com/Data2Dynamics/d2d
modeling matlab systems-biology computational-biology parameter-estimation model-calibration

drug2ways / drug2ways
systems-biology,A Python package for drug discovery by analyzing causal paths on multiscale networks
Organization: drug2ways
Home Page: https://drug2ways.readthedocs.io/en/latest/
networks-biology systems-biology drug-discovery causal-networks bioinformatics software

ecell / ecell4_base
systems-biology,An integrated software environment for multi-algorithm, multi-timescale, multi-spatial-representation simulation of various cellular phenomena
Organization: ecell
Home Page: https://ecell4.e-cell.org/
jupyter-notebook python systems-biology c-plus-plus simulation

florianhartig / bayesiantools
systems-biology,General-Purpose MCMC and SMC Samplers and Tools for Bayesian Statistics
User: florianhartig
Home Page: https://cran.r-project.org/web/packages/BayesianTools/index.html
cran mcmc smc bayes ecological-models systems-biology optimization

franciscozorrilla / metagem
systems-biology,: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
User: franciscozorrilla
Home Page: https://franciscozorrilla.github.io/metaGEM/
metagenomics computational-biology metabolic-models gut-microbiome snakemake metagenome-assembled-genomes mags metabolism bioinformatics flux-balance-analysis

genular / pandora
systems-biology,PANDORA - Predictive Analytics aNd Data Oriented Research Applications :computer:
Organization: genular
Home Page: https://genular.org
machine-learning systems-biology data-science data-visualization data-mining pandora bioinformatics biomarkers clinical-data clustering

geomscale / dingo
systems-biology,A python library for metabolic networks sampling and analysis
Organization: geomscale
sampling metabolic-network polytope random-walk systems-biology hacktoberfest

icb-dcm / pesto
systems-biology,PESTO: Parameter EStimation TOolbox, Bioinformatics, btx676, 2017.
Organization: icb-dcm
Home Page: https://doi.org/10.1093/bioinformatics/btx676
parameter-estimation optimization matlab uncertainty-quantification profile-likelihood systems-biology

icb-dcm / pypesto
systems-biology,python Parameter EStimation TOolbox
Organization: icb-dcm
Home Page: https://pypesto.readthedocs.io
parameter-estimation optimization systems-biology python hacktoberfest

ivis-at-bilkent / newt
systems-biology,A web application to visualize and edit pathway models
Organization: ivis-at-bilkent
Home Page: http://newteditor.org
pathways pathway-analysis network-visualization editor bioinformatics systems-biology biology sbgn web-based-visualization visualization

ivis-at-bilkent / pathway-mapper
systems-biology,PathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways
Organization: ivis-at-bilkent
Home Page: https://www.pathwaymapper.org/
systems-biology pathways pathway-analysis cancer-pathways cancer-genomics network-visualization tcga bioinformatics graphviz

ivis-at-bilkent / sbgnviz.js
systems-biology,A web based visualization tool for process description maps in SBGN
Organization: ivis-at-bilkent
Home Page: http://www.cs.bilkent.edu.tr/~ivis/SBGNViz_sample_app/
systems-biology pathways sbgn bioinformatics network-visualization

jpquast / protti
systems-biology,Picotti lab data analysis package.
User: jpquast
Home Page: https://jpquast.github.io/protti/
r proteomics mass-spectrometry data-analysis systems-biology lip-ms omics protein

klamt-lab / straindesign
systems-biology,StrainDesign is a python package for the computational design of metabolic networks and based on COBRApy
Organization: klamt-lab
bioinformatics cobrapy computational-biology mcs milp python strain-engineering systems-biology strain-design flux-space

lcsb-biocore / sbml.jl
systems-biology,Julia interface to the Systems Biology Markup Language (SBML) library
Organization: lcsb-biocore
Home Page: https://lcsb-biocore.github.io/SBML.jl/stable
sbml systems-biology cobra modeling libsbml

lolab-msm / pyvipr
systems-biology,Jupyter widget for the dynamic and static visualizations of systems biology models written in PySB, BNGL, and SBML
Organization: lolab-msm
jupyter-widget pysb systems-biology cytoscapejs visualization network-visualization networkx sbml bionetgen sbgn

maayanlab / biojupies
systems-biology,Automated generation of tailored bioinformatics Jupyter Notebooks via a user interface.
Organization: maayanlab
Home Page: http://biojupies.cloud
bioinformatics systems-biology jupyter rna-seq pipeline notebook cloud dcppc

micom-dev / micom
systems-biology,Python package to study microbial communities using metabolic modeling.
Organization: micom-dev
Home Page: https://micom-dev.github.io/micom
microbiota cobrapy modeling metabolic-models flux biochemistry systems-biology microbiome python cobra

nbisweden / workshop_omics_integration
systems-biology,Workshop in omics integration and systems biology
Organization: nbisweden
Home Page: https://uppsala.instructure.com/courses/52162
systems-biology integrative-omics

opencobra / cobrapy
systems-biology,COBRApy is a package for constraint-based modeling of metabolic networks.
Organization: opencobra
Home Page: http://opencobra.github.io/cobrapy/
modeling metabolic-models metabolic-network metabolism flux bioinformatics biochemistry computational-biology systems-biology cell-design

petab-dev / petab
systems-biology,PEtab - an SBML and TSV based data format for parameter estimation problems in systems biology
Organization: petab-dev
Home Page: https://petab.readthedocs.io
systems-biology parameter-estimation sbml-model data-format sbml combine-archive modelling hacktoberfest

pybel / pybel
systems-biology,🌶️ An ecosystem in Python for working with the Biological Expression Language (BEL)
Organization: pybel
Home Page: http://pybel.readthedocs.io
systems-biology networks biological-expression-language bioinformatics domain-specific-language networks-biology pybel bioregistry

pysb / pysb
systems-biology,Python framework for Systems Biology modeling
Organization: pysb
systems-biology

raivivek / awesome-biology
systems-biology,Curated (meta)list of resources for Biology.
User: raivivek
biology awesome-list bioinformatics books evolution systems-biology science

saeyslab / multinichenetr
systems-biology,MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data
Organization: saeyslab
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

sbmlteam / jsbml
systems-biology,JSBML is a community-driven project to create a free, open-source, pure Java™ library for reading, writing, and manipulating SBML files (the Systems Biology Markup Language) and data streams. It is an alternative to the mixed Java/native code-based interface provided in libSBML.
Organization: sbmlteam
Home Page: https://sbml.org/software/jsbml/
sbml systems-biology java library parser-library modeling api

sbmlteam / libsbml
systems-biology,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.
Organization: sbmlteam
Home Page: https://sbml.org/software/libsbml
api library libsbml sbml systems-biology

sbrg / cobrame
systems-biology,A COBRApy extension for genome-scale models of metabolism and expression (ME-models)
Organization: sbrg
cobra python metabolic-models systems-biology cobrapy gene-expression metabolism computational-biology

sbrg / ssbio
systems-biology,A Python framework for structural systems biology
Organization: sbrg
Home Page: http://ssbio.readthedocs.io/en/latest/
systems-biology protein-structure structural-biology constraint-based-modeling cobrapy structural-systems-biology

sciml / catalyst.jl
systems-biology,Chemical reaction network and systems biology interface for scientific machine learning (SciML). High performance, GPU-parallelized, and O(1) solvers in open source software.
Organization: sciml
Home Page: https://docs.sciml.ai/Catalyst/stable/
differential-equations chemical-reactions reaction-network sde dsl ode gillespie-algorithm biology systems-biology rate-laws

sciml / cellmltoolkit.jl
systems-biology,CellMLToolkit.jl is a Julia library that connects CellML models to the Scientific Julia ecosystem.
Organization: sciml
Home Page: https://docs.sciml.ai/CellMLToolkit/stable/
cellml systems-biology differential-equations julia ode physiology scientific-machine-learning sciml

sciml / sbmltoolkit.jl
systems-biology,SBML differential equation and chemical reaction model (Gillespie simulations) for Julia's SciML ModelingToolkit
Organization: sciml
Home Page: https://docs.sciml.ai/SBMLToolkit/stable/
sbml sciml chemical-reaction-networks gillespie-algorithm ode differential-equations systems-biology quantitative-systems-pharmacology julia

seek4science / seek
systems-biology,For finding, sharing and exchanging Data, Models, Simulations and Processes in Science.
Organization: seek4science
Home Page: http://www.seek4science.org
isa science systems-biology synthetic-biology fair data publication opendata datamanagement semantic-web

sorgerlab / indra
systems-biology,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.
Organization: sorgerlab
Home Page: http://indra.bio
systems-biology modeling biology computational-biology bioinformatics pysb nlp indra sbml

stasaki / decode
systems-biology,A prediction model for differential gene expression (DE) based on genome-wide regulatory interactions
User: stasaki
Home Page: https://stasaki.github.io/DEcode/
transcriptomics computational-biology bioinformatics systems-biology deep-neural-networks

sysbiochalmers / gecko
systems-biology,Toolbox for including enzyme constraints on a genome-scale model.
Organization: sysbiochalmers
Home Page: http://sysbiochalmers.github.io/GECKO/
proteomics data-integration toolbox matlab kinetics enzyme-constraints systems-biology

sysbiochalmers / hgtphylodetect
systems-biology,HGTphyloDetect is a versatile toolbox to identify horizontal gene transfer (HGT) events combined with phylogenetic analysis.
Organization: sysbiochalmers
horizontal-gene-transfer phylogenetics systems-biology high-throughput-pipeline evolutionary-biology sequence-analysis

sysbiochalmers / raven
systems-biology,The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.
Organization: sysbiochalmers
Home Page: http://sysbiochalmers.github.io/RAVEN/
genome-scale-models constraint-based-modeling metabolic-reconstruction gap-filling human-metabolism metabolic-models metabolic-engineering systems-biology sysbio

sysbiochalmers / yeast-gem
systems-biology,The consensus GEM for Saccharomyces cerevisiae
Organization: sysbiochalmers
Home Page: http://sysbiochalmers.github.io/yeast-GEM/
genome-scale-models yeast systems-biology hacktoberfest saccharomyces-cerevisiae matlab biology reconstruction consensus python

systemsbioinformatics / stochpy
systems-biology,StochPy is a versatile stochastic modeling package which is designed for stochastic simulation of molecular control networks
Organization: systemsbioinformatics
Home Page: http://stochpy.sourceforge.net/
stochastic-simulation-algorithm kinetic-modeling systems-biology python bioinformatics console-application