https://github.com/colomoto/biolqm
toolkit for the manipulation and analysis of Logical Qualitative Models of biological regulatory networks
Science Score: 36.0%
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
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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✓Committers with academic emails
4 of 14 committers (28.6%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (9.2%) to scientific vocabulary
Keywords from Contributors
Repository
toolkit for the manipulation and analysis of Logical Qualitative Models of biological regulatory networks
Basic Info
- Host: GitHub
- Owner: colomoto
- License: lgpl-3.0
- Language: Java
- Default Branch: main
- Homepage: http://colomoto.org/biolqm
- Size: 1.67 MB
Statistics
- Stars: 19
- Watchers: 11
- Forks: 15
- Open Issues: 12
- Releases: 1
Metadata Files
README.md
BioLQM: Logical Qualitative Models of biological networks
BioLQM is a toolkit for the manipulation and analysis of Logical (Qualitative) Models of biological networks. A model is composed of a list of components, associated to Boolean or multi-valued activity levels and to dynamical rules driving changes in their activity levels.
BioLQM provides a collection of import/export formats, enabling the exchange of models between complementary tools (motivated by the CoLoMoTo discussion group) and the design of complex analysis workflows. It also allows to define model modifications, to represent biological modifications (mutations) or to facilitate further analysis (model reduction, Boolean mapping of multi-valued models). Finally, it provides some analysis tools, focussing on the identification of attractors and on building-blocks for model simulation.
How to use it?
It can be used either as a standalone command-line tool, or as a programming interface: the Java API can be integrated in other software or used through scripts. Documentation and further information are available on https://colomoto.github.io/bioLQM.
- Install instructions: https://colomoto.github.io/bioLQM/doc/starting.html.
Licence and authors
This code is available under LGPL v3+/CeCILL-C.
The code started as a refactoring of GINsim to cleanup its core and enable more code sharing. Discussions among CoLoMoTo participants showed a growing interest for improved interoperability. This motivated the qualitative extension for SBML and this toolkit.
Aurelien Naldi designed and maintains the project, with feedback and contributions from:
Claudine Chaouiya
Denis Thieffry
Duncan Berenguier
Francisco Plana
Gautier Stoll
Julien Dorier
Loïc Pauleve
Pedro Monteiro
Celine Hernandez
Rui Henriques
Martin Boutroux
Owner
- Name: Consortium for Logical Models and Tools
- Login: colomoto
- Kind: organization
- Website: http://www.colomoto.org
- Repositories: 19
- Profile: https://github.com/colomoto
GitHub Events
Total
- Issue comment event: 1
- Push event: 2
- Fork event: 1
Last Year
- Issue comment event: 1
- Push event: 2
- Fork event: 1
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Aurelien Naldi | a****i@g****m | 393 |
| Martin Boutroux | m****x@o****r | 73 |
| Pedro T. Monteiro | p****o@p****g | 21 |
| Laure | l****l@e****r | 10 |
| Pedro Tiago Monteiro | p****m@k****t | 9 |
| bhagavadgitadu22 | 7****2 | 6 |
| Pedro Tiago Monteiro | p****m@i****t | 6 |
| HannesK | h****r@f****e | 6 |
| Pedro T. Monteiro | P****o@i****t | 5 |
| Loïc Paulevé | l****e@e****g | 4 |
| ruihenriques | r****h@g****m | 2 |
| PanchoTonho | f****a@g****m | 2 |
| Celine Hernandez | c****z@e****r | 1 |
| Lucas Baudin | l****n@e****r | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 20
- Total pull requests: 14
- Average time to close issues: 6 months
- Average time to close pull requests: 3 months
- Total issue authors: 8
- Total pull request authors: 6
- Average comments per issue: 1.15
- Average comments per pull request: 0.14
- Merged pull requests: 11
- Bot issues: 0
- Bot pull requests: 1
Past Year
- Issues: 1
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 0
- Average comments per issue: 1.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- aurelien-naldi (11)
- hklarner (2)
- pauleve (2)
- nanls (1)
- eyshin05 (1)
- kthobe (1)
- sthiele (1)
- ozlembahar (1)
Pull Request Authors
- aurelien-naldi (7)
- pauleve (3)
- chernan (1)
- Bobhuck (1)
- dependabot[bot] (1)
- PanchoTonho (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
- Total downloads: unknown
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 1
repo1.maven.org: org.colomoto:bioLQM
simple toolbox for the manipulation of logical models (not edition)
- Homepage: https://github.com/colomoto/bioLQM
- Documentation: https://appdoc.app/artifact/org.colomoto/bioLQM/
- License: GNU Lesser General Public License Version 3 (LGPL v3+)
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Latest release: 0.7.1
published about 6 years ago
Rankings
Dependencies
- org.kohsuke.metainf-services:metainf-services 1.9 provided
- com.github.rjeschke:txtmark 0.13
- de.fosd.typechef:javabdd_repackaged 1.0b2
- net.sf.saxon:Saxon-HE 11.3
- org.antlr:antlr4-runtime 4.10.1
- org.colomoto:MDDlib 0.4.1
- org.json:json 20220320
- org.ow2.sat4j:org.ow2.sat4j.core 2.3.6
- org.sbml.jsbml:jsbml 1.6.1
- org.yaml:snakeyaml 1.30
- org.junit.jupiter:junit-jupiter-api 5.8.2 test
- actions/checkout v3 composite
- actions/setup-java v3 composite
- actions/checkout v3 composite
- actions/setup-java v3 composite