dfba
dfba: Software for efficient simulation of dynamic flux-balance analysis models in Python - Published in JOSS (2020)
Science Score: 89.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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✓DOI references
Found 1 DOI reference(s) in JOSS metadata -
○Academic links in README
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✓Committers with academic emails
1 of 5 committers (20.0%) from academic institutions -
○Institutional organization owner
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✓JOSS paper metadata
Published in Journal of Open Source Software
Keywords
Repository
Basic Info
- Host: gitlab.com
- Owner: davidtourigny
- License: gpl-3.0+
- Default Branch: main
Statistics
- Stars: 8
- Forks: 4
- Open Issues: 16
- Releases: 0
Topics
JOSS Publication
dfba: Software for efficient simulation of dynamic flux-balance analysis models in Python
Authors
Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032 USA
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kongens Lyngby, Denmark
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kongens Lyngby, Denmark
Editor
Marcos Vital
Tags
Mathematical optimization Linear programming Numerical simulation Multi-scale metabolic modeling C++Committers
Last synced: 4 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| davidtourigny | d****y@g****m | 174 |
| carrascomj | c****j@g****m | 86 |
| Midnighter | m****r@p****t | 65 |
| Moritz E. Beber | m****b@b****k | 35 |
| yannikschaelte | y****e@g****m | 3 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 4 months ago
Packages
- Total packages: 2
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Total downloads:
- pypi 25 last-month
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Total dependent packages: 0
(may contain duplicates) -
Total dependent repositories: 5
(may contain duplicates) - Total versions: 8
- Total maintainers: 2
pypi.org: dfba
Object-oriented software for dynamic flux-balance simulations.
- Homepage: https://gitlab.com/davidtourigny/dynamic-fba
- Documentation: https://dfba.readthedocs.io/
- License: GNU GPL v3+
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Latest release: 0.1.8
published over 5 years ago
Rankings
Maintainers (2)
conda-forge.org: dfba
This project provides an object-oriented software package for dynamic flux-balance analysis (DFBA) simulations using implementations of the direct method or Algorithm 1 described in the paper Harwood et al., 2016. The main algorithms for solving embedded LP problems are written in C++ and use the GNU Linear Programming Kit (GLPK) and the Suite of Nonlinear and Differential/Algebraic Equation Solvers (SUNDIALS) CVODE or IDA. Extension modules to cobrapy are provided for easy generation and simulation of DFBA models.
- Homepage: https://dynamic-fba.readthedocs.io
- License: GPL-3.0-or-later
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Latest release: 0.1.8
published almost 5 years ago
Rankings
Dependencies
- ipykernel *
- nbsphinx >=0.5.0
- pygments >=2.4.1
- sphinx-autoapi >=1.2.1
- sphinx-copybutton >=0.2.6
- sphinx-material *