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COBRApy is a package for constraint-based modeling of metabolic networks.
Created
2012-11-02
2,731 commits to devel branch, last one about a month 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
3,584 commits to master branch, last one 6 days ago
Curated (meta)list of resources for Biology.
Created
2014-09-19
136 commits to master branch, last one 4 months ago
python Parameter EStimation TOolbox
Created
2018-07-25
1,285 commits to main branch, last one 18 hours 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
665 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
13,904 commits to master branch, last one 16 days ago
Python framework for Systems Biology modeling
Created
2010-10-08
1,372 commits to master branch, last one 3 months ago
PANDORA - Predictive Analytics aNd Data Oriented Research Applications :computer:
Created
2018-07-03
1,361 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
General-Purpose MCMC and SMC Samplers and Tools for Bayesian Statistics
Created
2016-12-14
582 commits to master branch, last one 4 months ago
Automated generation of tailored bioinformatics Jupyter Notebooks via a user interface.
Created
2017-10-25
594 commits to master branch, last one 2 years ago
The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.
Created
2016-04-05
1,951 commits to main branch, last one 4 days ago
MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data
Created
2021-02-16
129 commits to main branch, last one 9 days ago
The consensus GEM for Saccharomyces cerevisiae
Created
2016-02-29
1,002 commits to main branch, last one 23 days ago
COPASI is a software application for simulation and analysis of biochemical networks and their dynamics.
Created
2012-06-27
17,193 commits to develop branch, last one 24 days ago
Python package to study microbial communities using metabolic modeling.
Created
2017-02-14
783 commits to main branch, last one a day ago
For finding, sharing and exchanging Data, Models, Simulations and Processes in Science.
Created
2014-06-13
29,239 commits to main branch, last one 9 days ago
Toolbox for including enzyme constraints on a genome-scale model.
Created
2016-06-15
1,160 commits to main branch, last one 4 days 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
a modeling environment tailored to parameter estimation in dynamical systems
Created
2016-06-14
3,080 commits to master branch, last one 17 days ago
Picotti lab data analysis package.
Created
2020-06-26
867 commits to master branch, last one 2 days ago
PathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways
Created
2016-05-27
834 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
482 commits to main branch, last one 10 days ago
CellMLToolkit.jl is a Julia library that connects CellML models to the Scientific Julia ecosystem.
Created
2020-07-27
239 commits to master branch, last one 25 days ago
Workshop in omics integration and systems biology
Created
2019-02-27
782 commits to main branch, last one 2 months ago
A web application to visualize and edit pathway models
Created
2017-01-24
1,396 commits to master branch, last one 3 months 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 3 months ago
A python library for metabolic networks sampling and analysis
Created
2021-02-21
71 commits to develop branch, last one 8 days ago
SBML differential equation and chemical reaction model (Gillespie simulations) for Julia's SciML ModelingToolkit
Created
2021-06-16
458 commits to main branch, last one about a month ago
Multi-dimensional, trans-omics metabolic maps.
Created
2022-11-21
229 commits to master branch, last one 2 months ago