34 results found Sort:

218
474
gpl-2.0
37
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
78
465
other
17
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
47
227
bsd-3-clause
11
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
67
181
bsd-2-clause
24
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
71
171
bsd-2-clause
20
Python framework for Systems Biology modeling
Created 2010-10-08
1,391 commits to master branch, last one 2 months ago
32
131
mit
9
🌶️ 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
29
98
artistic-2.0
21
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
46
97
cc-by-4.0
18
The consensus GEM for Saccharomyces cerevisiae
Created 2016-02-29
1,013 commits to main branch, last one 28 days ago
18
94
apache-2.0
5
Python package to study microbial communities using metabolic modeling.
Created 2017-02-14
813 commits to main branch, last one 10 days ago
52
77
bsd-3-clause
24
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
23
63
gpl-3.0
12
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
4
60
other
4
Picotti lab data analysis package.
Created 2020-06-26
934 commits to master branch, last one 2 months ago
12
60
mit
17
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
28
57
unknown
27
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
27
53
lgpl-3.0
11
A web application to visualize and edit pathway models
Created 2017-01-24
1,758 commits to master branch, last one 3 months ago
7
47
apache-2.0
3
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, ...
Created 2019-11-15
777 commits to master branch, last one 24 days ago
28
45
lgpl-3.0
6
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
1
44
apache-2.0
3
Multi-dimensional, trans-omics metabolic maps.
Created 2022-11-21
229 commits to master branch, last one 9 months ago