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COBRApy is a package for constraint-based modeling of metabolic networks.
Created
2012-11-02
2,741 commits to devel branch, last one 23 days ago
Chemical reaction network and systems biology interface for scientific machine learning (SciML). High performance, GPU-parallelized, and O(1) solvers in open source software.
Created
2017-02-06
4,776 commits to master branch, last one a day ago
Curated (meta)list of resources for Biology.
Created
2014-09-19
136 commits to master branch, last one 11 months ago
python Parameter EStimation TOolbox
Created
2018-07-25
1,340 commits to main branch, last one about a month ago
: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
Created
2018-06-14
669 commits to master branch, last one 4 months ago
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, p...
Created
2014-08-11
13,976 commits to master branch, last one about a month ago
Python framework for Systems Biology modeling
Created
2010-10-08
1,391 commits to master branch, last one 2 months ago
PANDORA :computer:
Created
2018-07-03
1,546 commits to master branch, last one about a month ago
🌶️ An ecosystem in Python for working with the Biological Expression Language (BEL)
Created
2016-09-16
2,964 commits to master branch, last one 2 years ago
MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data
Created
2021-02-16
135 commits to main branch, last one about a month ago
General-Purpose MCMC and SMC Samplers and Tools for Bayesian Statistics
Created
2016-12-14
582 commits to master branch, last one 11 months ago
Automated generation of tailored bioinformatics Jupyter Notebooks via a user interface.
Created
2017-10-25
596 commits to master branch, last one about a month ago
The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.
Created
2016-04-05
1,973 commits to main branch, last one 4 hours ago
COPASI is a software application for simulation and analysis of biochemical networks and their dynamics.
Created
2012-06-27
17,223 commits to develop branch, last one 5 months ago
The consensus GEM for Saccharomyces cerevisiae
Created
2016-02-29
1,013 commits to main branch, last one 28 days ago
Python package to study microbial communities using metabolic modeling.
Created
2017-02-14
813 commits to main branch, last one 10 days ago
For finding, sharing and exchanging Data, Models, Simulations and Processes in Science.
Created
2014-06-13
30,017 commits to main branch, last one 5 days ago
Workshop in omics integration and systems biology
Created
2019-02-27
1,261 commits to OMICSINT_H24 branch, last one 2 months ago
Toolbox for including enzyme constraints on a genome-scale model.
Created
2016-06-15
1,168 commits to main branch, last one 2 months ago
An integrated software environment for multi-algorithm, multi-timescale, multi-spatial-representation simulation of various cellular phenomena
Created
2012-10-23
7,017 commits to master branch, last one 3 years ago
CellMLToolkit.jl is a Julia library that connects CellML models to the Scientific Julia ecosystem.
Created
2020-07-27
255 commits to master branch, last one about a month ago
Picotti lab data analysis package.
Created
2020-06-26
934 commits to master branch, last one 2 months ago
PEtab - an SBML and TSV based data format for parameter estimation problems in systems biology
Created
2018-11-27
501 commits to main branch, last one 17 days ago
a modeling environment tailored to parameter estimation in dynamical systems
Created
2016-06-14
3,132 commits to master branch, last one 9 days ago
PathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways
Created
2016-05-27
834 commits to master branch, last one 9 months ago
A web application to visualize and edit pathway models
Created
2017-01-24
1,758 commits to master branch, last one 3 months ago
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, ...
fba
fva
sbml
cobra
bioinformatics
systems-biology
flux-variability
metabolic-models
metabolic-networks
computational-biology
flux-balance-analysis
metabolic-engineering
constraint-programming
stoichiometric-modeling
metabolic-reconstruction
constraint-based-analysis
constraint-based-modeling
constraint-based-reconstruction
Created
2019-11-15
777 commits to master branch, last one 24 days ago
A python library for metabolic networks sampling and analysis
Created
2021-02-21
77 commits to develop branch, last one about a month ago
Tools to generate and study moment equations for any chemical reaction network using various moment closure approximations
Created
2021-02-14
238 commits to main branch, last one 10 months ago
Multi-dimensional, trans-omics metabolic maps.
Created
2022-11-21
229 commits to master branch, last one 9 months ago