Data

Tools

Indexes

Applications

Experiments

Open Source Science

COBREXA

COnstraint Based Reconstruction and EXascale Analysis (in Julia)

https://github.com/cobrexa/cobrexa.jl

Science Score: 57.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (16.8%) to scientific vocabulary

Keywords

cobra constraint-based-modeling high-performance-computing hpc julia metabolic-engineering metabolic-models sbml sbml-simulation
Last synced: 6 months ago · JSON representation ·

Repository

COnstraint Based Reconstruction and EXascale Analysis (in Julia)

Basic Info
Statistics
  • Stars: 15
  • Watchers: 4
  • Forks: 1
  • Open Issues: 10
  • Releases: 17
Topics
cobra constraint-based-modeling high-performance-computing hpc julia metabolic-engineering metabolic-models sbml sbml-simulation
Created about 2 years ago · Last pushed 8 months ago
Metadata Files
Readme Contributing License Code of conduct Citation

README.md

COnstraint-Based Reconstruction and EXascale Analysis

| Documentation | Tests | Coverage | Project status | |:---:|:---:|:---:|:---:| | docs-img-stable docs-img-dev | CI | codecov | repostatus-img |

COBREXA.jl provides constraint-based reconstruction and analysis tools for exa-scale metabolic modeling in Julia.

For COBREXA.jl releases before version 2.0 (released in 2023 and earlier), please see the legacy COBREXA repository with version 0.x and 1.x.

Why use COBREXA.jl?

Compared to the other modeling toolkits, COBREXA.jl offers:

  • Almost effortless parallelization to scale-up to HPC environments. This allows the users to quickly run huge analyses.
  • A straightforward way to construct new kinds of constraint systems by re-using and re-combining the existing ones with newly implemented functionality, provided by ConstraintTrees.jl middleware. This vastly simplifies reconstruction of complex systems, such as multi-compartment ("community") growth-balanced models with both per-member and global resource-allocation and metabolite availability constraints.
  • Performance at the level of "raw" user workflow operations, because all analysis code are compiled and optimized by Julia. This reduces the computation time and memory required to analyze very large models.
  • A wide range of pre-implemented HPC-compatible analysis functions, with tested examples available in the documentation.

Getting started

COBREXA.jl documentation is available online (you may also be interested in the development version of the package documentation).

Installation

COBREXA.jl is best installed using Julia's packaging system.

  1. If you do not have Julia installed, download it from the official site.
  2. Start Julia by typing julia into a terminal
  3. Type ] add COBREXA. This will install COBREXA automatically, with all dependencies.
  4. You may want to install additional constraint-solver software compatible with JuMP. Type e.g. ] add HiGHS to install the HiGHS solver.

Guides

To start quickly, follow the examples in the documentation.

We recommend to start with the usual Flux Balance Analysis example.

Testing the installation

If you run a non-standard platform (e.g. a customized operating system), or if you added any modifications to the COBREXA source code, you may want to run the test suite to ensure that everything works as expected:

julia ] test COBREXA

Prebuilt Docker images docker

Docker image is available from the docker hub as cobrexa/cobrexa.jl, and from GitHub container repository. Download and use them as usual with docker:

```sh docker run -ti --rm cobrexa/cobrexa.jl:latest

or alternatively from ghcr.io

docker run -ti --rm ghcr.io/cobrexa/docker/cobrexa.jl:latest ```

In the container, you should get a julia shell with the important packages already installed, and you may immediately import the package with using COBREXA, and start running COBREXA analyses (such as the ones in the documentation examples).

If you require precise reproducibility, use a tag like v1.2.2 instead of latest (all releases since 1.2.2 are tagged this way).

NOTE: Versions of COBREXA before 2.0 are available from the original repository at github.com/LCSB-BioCore/COBREXA.jl.

Acknowledgements

COBREXA.jl is developed at the Luxembourg Centre for Systems Biomedicine of the University of Luxembourg (uni.lu/lcsb), cooperating with the Institute for Quantitative and Theoretical Biology at the Heinrich Heine University in Dsseldorf (qtb.hhu.de).

The development was supported by European Union's Horizon 2020 Programme under PerMedCoE project (permedcoe.eu) agreement no. 951773.

If you use COBREXA.jl and want to refer to it in your work, use the following citation format (also available as BibTeX in cobrexa.bib):

Miroslav Kratochvl, St Elmo Wilken, Oliver Ebenhh, Reinhard Schneider, Venkata P Satagopam, COBREXA 2: tidy and scalable construction of complex metabolic models, Bioinformatics, Volume 41, Issue 2, February 2025, btaf056, https://doi.org/10.1093/bioinformatics/btaf056

COBREXA logoUni.lu logoLCSB logoHHU logoQTB logoPerMedCoE logo

Owner

  • Name: COBREXA
  • Login: COBREXA
  • Kind: organization

Constraint based modeling and exascale analysis

Citation (CITATION.cff) 

cff-version: 1.2.0
message: If you refer to COBREXA.jl in a scientific publication, please use this citation.
authors:
  - family-names: Kratochvíl
    given-names: Miroslav
  - family-names: Wilken
    given-names: St Elmo
  - family-names: Ebenhöh
    given-names: Oliver
  - family-names: Schneider
    given-names: Reinhard
  - family-names: Satagopam
    given-names: Venkata P
title: 'COBREXA 2: tidy and scalable construction of complex metabolic models'
version: 1.0.0
url: https://doi.org/10.1093/bioinformatics/btaf056
doi: 10.1093/bioinformatics/btaf056
date-released: '2025-02-20'
preferred-citation:
  authors:
    - family-names: Kratochvíl
      given-names: Miroslav
    - family-names: Wilken
      given-names: St Elmo
    - family-names: Ebenhöh
      given-names: Oliver
    - family-names: Schneider
      given-names: Reinhard
    - family-names: Satagopam
      given-names: Venkata P
  title: 'COBREXA 2: tidy and scalable construction of complex metabolic models'
  doi: 10.1093/bioinformatics/btaf056
  url: https://doi.org/10.1093/bioinformatics/btaf056
  type: article-journal
  pages: btaf056
  year: '2025'
  conference: {}
  publisher: {}

GitHub Events

Total
  • Create event: 22
  • Commit comment event: 12
  • Issues event: 11
  • Release event: 7
  • Watch event: 5
  • Delete event: 10
  • Issue comment event: 58
  • Push event: 125
  • Pull request review comment event: 15
  • Pull request review event: 20
  • Pull request event: 29
  • Fork event: 2
Last Year
  • Create event: 22
  • Commit comment event: 12
  • Issues event: 11
  • Release event: 7
  • Watch event: 5
  • Delete event: 10
  • Issue comment event: 58
  • Push event: 125
  • Pull request review comment event: 15
  • Pull request review event: 20
  • Pull request event: 29
  • Fork event: 2

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 20
  • Total pull requests: 86
  • Average time to close issues: 21 days
  • Average time to close pull requests: 9 days
  • Total issue authors: 6
  • Total pull request authors: 3
  • Average comments per issue: 3.15
  • Average comments per pull request: 1.64
  • Merged pull requests: 73
  • Bot issues: 0
  • Bot pull requests: 1
Past Year
  • Issues: 11
  • Pull requests: 33
  • Average time to close issues: 2 days
  • Average time to close pull requests: 4 days
  • Issue authors: 4
  • Pull request authors: 2
  • Average comments per issue: 1.27
  • Average comments per pull request: 1.76
  • Merged pull requests: 26
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • exaexa (8)
  • oxinabox (5)
  • HettieC (3)
  • h-escoffier (3)
  • stelmo (2)
  • JuliaTagBot (1)
Pull Request Authors
  • exaexa (115)
  • stelmo (26)
  • github-actions[bot] (3)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • julia 21 total
  • Total dependent packages: 5
  • Total dependent repositories: 1
  • Total versions: 38
juliahub.com: COBREXA

COnstraint Based Reconstruction and EXascale Analysis (in Julia)

  • Versions: 38
  • Dependent Packages: 5
  • Dependent Repositories: 1
  • Downloads: 21 Total
Rankings
Dependent repos count: 7.7%
Dependent packages count: 9.8%
Average: 12.1%
Stargazers count: 15.4%
Forks count: 15.6%
Last synced: 7 months ago