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Gene Expression Tools from a Technical Perspective: Current Approaches and Alternative Solutions for the KnowSeq Suite

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Bioinformatics and Biomedical Engineering (IWBBIO 2022)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 13346))

Abstract

The precision and personalized medicine is declared as the next revolutionary paradigm in the current health outlook. With this assumption, many challenges must be faced to achieve that paradigm shift. One of these important challenges is the creation and development of tools with the capability of exploiting biological data to infer or extract new and relevant knowledge. In this sense, these tools must fulfill a set of requirements such as scalability, security and a user-friendly design. That is the way to change the users scope from technicians to all type of researchers, physicians and other non-technical users. Along this article, a review of several gene expression analysis tools has been addressed, with the aim of studying their pros and cons. Then, two different implementations are proposed taking into account the current state of KnowSeq R/Bioc package, with the purpose of showing different use cases to migrate one concrete tool to a web application.

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Notes

  1. 1.

    https://mlflow.org/.

  2. 2.

    https://optuna.org/.

  3. 3.

    https://www.ray.io/.

  4. 4.

    https://mazamascience.github.io/beakr/.

  5. 5.

    https://rdocumentation.org/packages/fiery/versions/0.2.3.

  6. 6.

    https://cran.r-project.org/web/packages/ambiorix/readme/README.html.

  7. 7.

    https://redis.io/.

  8. 8.

    https://www.rabbitmq.com/.

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Acknowledgements

This work was funded by the Spanish Ministry of Sciences, Innovation and Universities under Project RTI2018-101674-B-I00 titled “Computer Architectures and Machine Learning- based solutions for complex challenges in Bioinformatics, Biotechnology and Biomedicine”, in collaboration with the Government of Andalusia under the projects P20_00163 and CV20-64934. The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of this manuscript.

Author information

Authors and Affiliations

  1. CoE Data Intelligence, Fujitsu Technology Solutions S.A., Camino del Cerro de los Gamos, 1, Pozuelo de Alarcón, 28224, Madrid, Spain

    Daniel Castillo-Secilla

  2. Instituto de Investigación Biosanitaria ibs.GRANADA, CIBER de Epidemiología y Salud Pública (CIBERESP), Escuela Andaluza de Salud Pública, Avda. de Madrid, 15. Pabellón de Consultas Externas 2, 2a Planta, 18012, Granada, Spain

    Daniel Redondo-Sánchez

  3. Department of Computer Architecture and Technology, University of Granada. C.I.T.I.C., Periodista Rafael Gómez Montero, 2, 18014, Granada, Spain

    Luis Javier Herrera, Ignacio Rojas & Alberto Guillén

Authors
  1. Daniel Castillo-Secilla
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  2. Daniel Redondo-Sánchez
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  3. Luis Javier Herrera
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  4. Ignacio Rojas
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  5. Alberto Guillén
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Corresponding author

Correspondence to Daniel Castillo-Secilla .

Editor information

Editors and Affiliations

  1. Marcelina Siebold Guest Relations Dept., University of Granada, Granada, Spain

    Ignacio Rojas

  2. Faculty of Sciences, University of Granada, Granada, Spain

    Olga Valenzuela

  3. ETSIIT. CITIC-UGR, University of Granada, Granada, Spain

    Fernando Rojas

  4. ETSIIT, University of Granada, Granada, Spain

    Luis Javier Herrera

  5. University of Granada, Granada, Spain

    Francisco Ortuño

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Castillo-Secilla, D., Redondo-Sánchez, D., Herrera, L.J., Rojas, I., Guillén, A. (2022). Gene Expression Tools from a Technical Perspective: Current Approaches and Alternative Solutions for the KnowSeq Suite. In: Rojas, I., Valenzuela, O., Rojas, F., Herrera, L.J., Ortuño, F. (eds) Bioinformatics and Biomedical Engineering. IWBBIO 2022. Lecture Notes in Computer Science(), vol 13346. Springer, Cham. https://doi.org/10.1007/978-3-031-07704-3_33

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  • DOI: https://doi.org/10.1007/978-3-031-07704-3_33

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  • Publisher Name: Springer, Cham

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  • Online ISBN: 978-3-031-07704-3

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