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Compi Hub: A Public Repository for Sharing and Discovering Compi Pipelines

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Practical Applications of Computational Biology & Bioinformatics, 14th International Conference (PACBB 2020) (PACBB 2020)

Part of the book series: Advances in Intelligent Systems and Computing ((AISC,volume 1240))

Abstract

Sharing the source code necessary to perform and reproduce any type of data analysis in computational biology and bioinformatics is becoming more and more important nowadays. This includes the publication of complete executable workflows and pipelines in a form that allows to reproduce the original results easily or to re-use them to analyze new datasets. Recently, we have developed Compi, an application framework to develop end-user, pipeline-based applications focused on automatic user interface generation and application packaging, including also the most common features of workflow management systems. Here we introduce Compi Hub, a public repository of Compi pipelines that allows the community to explore them interactively. Within this work, we aim to demonstrate how to use it efficiently in order to release Compi pipelines, giving also some recommendations of good practices illustrated with our own pipelines.

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Notes

  1. 1.

    https://www.sing-group.org/compi/.

  2. 2.

    https://www.go-fair.org/go-fair-initiative/.

  3. 3.

    https://github.com/pditommaso/awesome-pipeline.

  4. 4.

    https://github.com/snakemake-workflows/docs.

  5. 5.

    https://www.encodeproject.org/pipelines/.

  6. 6.

    https://toolshed.g2.bx.psu.edu/.

  7. 7.

    https://nf-co.re/.

  8. 8.

    https://www.sing-group.org/compihub/.

  9. 9.

    https://www.sing-group.org/compi/docs.

  10. 10.

    https://nf-co.re/pipelines.

  11. 11.

    https://github.com/nf-core.

  12. 12.

    https://www.sing-group.org/compihub/explore/5d5bb64f6d9e31002f3ce30a.

  13. 13.

    https://github.com/pegi3s/pss-fs.

  14. 14.

    https://hub.docker.com/r/pegi3s/pss-fs.

  15. 15.

    https://www.sing-group.org/compi/docs/custom_runners.html.

  16. 16.

    https://www.sing-group.org/compihub/explore/5d807e5590f1ec002fc6dd83.

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Acknowledgments

The SING group thanks the CITI (Centro de Investigación, Transferencia e Innovación) from the University of Vigo for hosting its IT infrastructure. This work was partially supported by the Consellería de Educación, Universidades e Formación Profesional (Xunta de Galicia) under the scope of the strategic funding ED431C2018/55-GRC Competitive Reference Group and by the Ministerio de Economía, Industria y Competitividad, Gobierno de España under the scope of the PolyDeep project (DPI2017-87494-R). A. Nogueira-Rodríguez is supported by a pre-doctoral fellowship from Xunta de Galicia (ED481A-2019/299).

Author information

Authors and Affiliations

  1. Department of Computer Science, University of Vigo, ESEI, Campus As Lagoas, 32004, Ourense, Spain

    Alba Nogueira-Rodríguez, Hugo López-Fernández, Osvaldo Graña-Castro, Miguel Reboiro-Jato & Daniel Glez-Peña

  2. The Biomedical Research Centre (CINBIO), Campus Universitario Lagoas-Marcosende, 36310, Vigo, Spain

    Alba Nogueira-Rodríguez, Hugo López-Fernández, Miguel Reboiro-Jato & Daniel Glez-Peña

  3. SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain

    Hugo López-Fernández, Miguel Reboiro-Jato & Daniel Glez-Peña

  4. Bioinformatics Unit, Structural Biology Programme, Spanish National Cancer Research Centre (CNIO), C/ Melchor Fernández Almagro, 3, 28029, Madrid, Spain

    Osvaldo Graña-Castro

Authors
  1. Alba Nogueira-Rodríguez
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  2. Hugo López-Fernández
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  3. Osvaldo Graña-Castro
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  4. Miguel Reboiro-Jato
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  5. Daniel Glez-Peña
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Corresponding author

Correspondence to Hugo López-Fernández .

Editor information

Editors and Affiliations

  1. Enhanced Regenerative Medicine, Istituto Italiano di Tecnologia, Genoa, Genova, Italy

    Gabriella Panuccio

  2. Department de Informática, Universidade do Minho, Braga, Portugal

    Miguel Rocha

  3. Computer Science Department, University of Vigo, Vigo, Spain

    Florentino Fdez-Riverola

  4. Institute for Artificial Intelligence and Big Data (AIBIG), Universiti Malaysia Kelantan, Kampus Kota, Kota Bharu, Malaysia

    Mohd Saberi Mohamad

  5. Biotechnology, Intelligent Systems and Educational Technology (BISITE) Research Group, University of Salamanca, Salamanca, Salamanca, Spain

    Roberto Casado-Vara

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Nogueira-Rodríguez, A., López-Fernández, H., Graña-Castro, O., Reboiro-Jato, M., Glez-Peña, D. (2021). Compi Hub: A Public Repository for Sharing and Discovering Compi Pipelines. In: Panuccio, G., Rocha, M., Fdez-Riverola, F., Mohamad, M., Casado-Vara, R. (eds) Practical Applications of Computational Biology & Bioinformatics, 14th International Conference (PACBB 2020). PACBB 2020. Advances in Intelligent Systems and Computing, vol 1240. Springer, Cham. https://doi.org/10.1007/978-3-030-54568-0_6

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