CREDO: a friendly Customizable, REproducible, DOcker file generator for bioinformatics applications
Abstract Background The analysis of large and complex biological datasets in bioinformatics poses a significant challenge to achieving reproducible research outcomes due to inconsistencies and the lack of standardization in the analysis process. These issues can lead to discrepancies in results, und...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2024-03-01
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| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12859-024-05695-9 |
| _version_ | 1827315716366270464 |
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| author | Simone Alessandri Maria L. Ratto Sergio Rabellino Gabriele Piacenti Sandro Gepiro Contaldo Simone Pernice Marco Beccuti Raffaele A. Calogero Luca Alessandri |
| author_facet | Simone Alessandri Maria L. Ratto Sergio Rabellino Gabriele Piacenti Sandro Gepiro Contaldo Simone Pernice Marco Beccuti Raffaele A. Calogero Luca Alessandri |
| author_sort | Simone Alessandri |
| collection | DOAJ |
| description | Abstract Background The analysis of large and complex biological datasets in bioinformatics poses a significant challenge to achieving reproducible research outcomes due to inconsistencies and the lack of standardization in the analysis process. These issues can lead to discrepancies in results, undermining the credibility and impact of bioinformatics research and creating mistrust in the scientific process. To address these challenges, open science practices such as sharing data, code, and methods have been encouraged. Results CREDO, a Customizable, REproducible, DOcker file generator for bioinformatics applications, has been developed as a tool to moderate reproducibility issues by building and distributing docker containers with embedded bioinformatics tools. CREDO simplifies the process of generating Docker images, facilitating reproducibility and efficient research in bioinformatics. The crucial step in generating a Docker image is creating the Dockerfile, which requires incorporating heterogeneous packages and environments such as Bioconductor and Conda. CREDO stores all required package information and dependencies in a Github-compatible format to enhance Docker image reproducibility, allowing easy image creation from scratch. The user-friendly GUI and CREDO's ability to generate modular Docker images make it an ideal tool for life scientists to efficiently create Docker images. Overall, CREDO is a valuable tool for addressing reproducibility issues in bioinformatics research and promoting open science practices. |
| first_indexed | 2024-04-24T23:02:39Z |
| format | Article |
| id | doaj.art-75ad9c145c0c4f70b80f3e75ae7b3efa |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-04-24T23:02:39Z |
| publishDate | 2024-03-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-75ad9c145c0c4f70b80f3e75ae7b3efa2024-03-17T12:40:23ZengBMCBMC Bioinformatics1471-21052024-03-0125111610.1186/s12859-024-05695-9CREDO: a friendly Customizable, REproducible, DOcker file generator for bioinformatics applicationsSimone Alessandri0Maria L. Ratto1Sergio Rabellino2Gabriele Piacenti3Sandro Gepiro Contaldo4Simone Pernice5Marco Beccuti6Raffaele A. Calogero7Luca Alessandri8Polytechnic of TurinDepartment of Molecular Biotechnology and Health Sciences, University of TorinoDepartment of Computer Science, University of TorinoDepartment of Molecular Biotechnology and Health Sciences, University of TorinoDepartment of Computer Science, University of TorinoDepartment of Computer Science, University of TorinoDepartment of Computer Science, University of TorinoDepartment of Molecular Biotechnology and Health Sciences, University of TorinoDepartment of Molecular Biotechnology and Health Sciences, University of TorinoAbstract Background The analysis of large and complex biological datasets in bioinformatics poses a significant challenge to achieving reproducible research outcomes due to inconsistencies and the lack of standardization in the analysis process. These issues can lead to discrepancies in results, undermining the credibility and impact of bioinformatics research and creating mistrust in the scientific process. To address these challenges, open science practices such as sharing data, code, and methods have been encouraged. Results CREDO, a Customizable, REproducible, DOcker file generator for bioinformatics applications, has been developed as a tool to moderate reproducibility issues by building and distributing docker containers with embedded bioinformatics tools. CREDO simplifies the process of generating Docker images, facilitating reproducibility and efficient research in bioinformatics. The crucial step in generating a Docker image is creating the Dockerfile, which requires incorporating heterogeneous packages and environments such as Bioconductor and Conda. CREDO stores all required package information and dependencies in a Github-compatible format to enhance Docker image reproducibility, allowing easy image creation from scratch. The user-friendly GUI and CREDO's ability to generate modular Docker images make it an ideal tool for life scientists to efficiently create Docker images. Overall, CREDO is a valuable tool for addressing reproducibility issues in bioinformatics research and promoting open science practices.https://doi.org/10.1186/s12859-024-05695-9ReproducibilityBioinformaticsDockerOpen scienceSoftware sharing |
| spellingShingle | Simone Alessandri Maria L. Ratto Sergio Rabellino Gabriele Piacenti Sandro Gepiro Contaldo Simone Pernice Marco Beccuti Raffaele A. Calogero Luca Alessandri CREDO: a friendly Customizable, REproducible, DOcker file generator for bioinformatics applications BMC Bioinformatics Reproducibility Bioinformatics Docker Open science Software sharing |
| title | CREDO: a friendly Customizable, REproducible, DOcker file generator for bioinformatics applications |
| title_full | CREDO: a friendly Customizable, REproducible, DOcker file generator for bioinformatics applications |
| title_fullStr | CREDO: a friendly Customizable, REproducible, DOcker file generator for bioinformatics applications |
| title_full_unstemmed | CREDO: a friendly Customizable, REproducible, DOcker file generator for bioinformatics applications |
| title_short | CREDO: a friendly Customizable, REproducible, DOcker file generator for bioinformatics applications |
| title_sort | credo a friendly customizable reproducible docker file generator for bioinformatics applications |
| topic | Reproducibility Bioinformatics Docker Open science Software sharing |
| url | https://doi.org/10.1186/s12859-024-05695-9 |
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