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jeweler

Test and grade genome-scale metabolic models (GEMs).

https://github.com/opencobra/jeweler

Science Score: 67.0%

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

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    CITATION.cff file
    Found CITATION.cff file
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    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
    Found .zenodo.json file
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    DOI references
    Found 7 DOI reference(s) in README
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    Academic publication links
    Links to: zenodo.org
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    Scientific vocabulary similarity
    Low similarity (15.9%) to scientific vocabulary

Keywords

cobra gem gsmm memote nextflow nf-core sbml sbml-model
Last synced: 6 months ago · JSON representation ·

Repository

Test and grade genome-scale metabolic models (GEMs).

Basic Info
  • Host: GitHub
  • Owner: opencobra
  • License: apache-2.0
  • Language: Nextflow
  • Default Branch: dev
  • Homepage:
  • Size: 2.16 MB
Statistics
  • Stars: 1
  • Watchers: 5
  • Forks: 0
  • Open Issues: 0
  • Releases: 3
Topics
cobra gem gsmm memote nextflow nf-core sbml sbml-model
Created over 2 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog License Citation

README.md

DOI

Introduction

opencobra/jeweler is a bioinformatics pipeline that tests and grades genome-scale metabolic models (GEMs). It first validates SBML documents that describe metabolic models for constraint-based analysis. Valid documents are then passed on to the genome-scale metabolic model test suite (MEMOTE).

  1. Optionally, attempt to download an SBML document from a given model identifier (COBRApy).
  2. Validate the SBML document for use with constraint-based analysis (COBRApy).
  3. Test the model in the SBML document with the genome-scale metabolic model test suite (MEMOTE).

Usage

[!NOTE] If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

[!IMPORTANT] Currently, only a Docker image and a conda environment definition exist. Thus, only the options -profile docker or -profile conda are guaranteed to succeed.

First, prepare a samplesheet with your input data that looks as follows. Please also take a look at the test samplesheet for inspiration.

samplesheet.csv:

csv id,name,model MODEL1507180060,iJR904, MODEL2109130006,,

If the SBML document exists in an online repository, such as BioModels or BiGG, then the model identifier is enough. Otherwise, you need to reference the model file directly. An entry for the name is entirely optional.

Now, you can run the pipeline using:

bash nextflow run opencobra/jeweler \ -profile <docker/singularity/.../institute> \ --input samplesheet.csv \ --outdir <OUTDIR>

[!WARNING] Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

Credits

opencobra/jeweler was originally written by Moritz E. Beber.

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

Citations

If you use opencobra/jeweler for your analysis, please cite it using the following doi: 10.5281/zenodo.10173259.

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.

Owner

  • Name: openCOBRA
  • Login: opencobra
  • Kind: organization
  • Location: Terra

Community driven constraint-based reconstruction, analysis and modelling of biology

Citation (CITATIONS.md) 

# opencobra/jeweler: Citations

## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)

> Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031.

## [Nextflow](https://pubmed.ncbi.nlm.nih.gov/28398311/)

> Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.

## Pipeline tools

- [COBRApy](https://doi.org/10.1186/1752-0509-7-74)

  > Ebrahim, A., Lerman, J. A., Palsson, B. O., & Hyduke, D. R. (2013). COBRApy: COnstraints-Based Reconstruction and Analysis for Python. BMC Systems Biology, 7(1), 74.

- [MEMOTE](https://doi.org/10.1038/s41587-020-0477-4)

  > Lieven, C., Beber, M. E., Olivier, B. G., Bergmann, F. T., Ataman, M., Babaei, P., Bartell, J. A., Blank, L. M., Chauhan, S., Correia, K., Diener, C., Dräger, A., Ebert, B. E., Edirisinghe, J. N., Faria, J. P., Feist, A. M., Fengos, G., Fleming, R. M. T., García-Jiménez, B., … Zhang, C. (2020). Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing. Nature Biotechnology, 38(4), 504–504.

- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)

  > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.

## Software packaging/containerisation tools

- [Anaconda](https://anaconda.com)

  > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.

- [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)

  > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.

- [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)

  > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.

- [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)

  > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.

- [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)

  > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.

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Dependencies

modules/nf-core/custom/dumpsoftwareversions/meta.yml cpan
modules/nf-core/multiqc/meta.yml cpan
pyproject.toml pypi