دورية أكاديمية
CREDO: a friendly Customizable, REproducible, DOcker file generator for bioinformatics applications.
| العنوان: | CREDO: a friendly Customizable, REproducible, DOcker file generator for bioinformatics applications. |
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| المؤلفون: | Alessandri S; Polytechnic of Turin, Turin, Italy., Ratto ML; Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin, Italy., Rabellino S; Department of Computer Science, University of Torino, Turin, Italy., Piacenti G; Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin, Italy., Contaldo SG; Department of Computer Science, University of Torino, Turin, Italy., Pernice S; Department of Computer Science, University of Torino, Turin, Italy., Beccuti M; Department of Computer Science, University of Torino, Turin, Italy., Calogero RA; Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin, Italy. raffaele.calogero@unito.it., Alessandri L; Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin, Italy.; Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA. |
| المصدر: | BMC bioinformatics [BMC Bioinformatics] 2024 Mar 12; Vol. 25 (1), pp. 110. Date of Electronic Publication: 2024 Mar 12. |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2105 (Electronic) Linking ISSN: 14712105 NLM ISO Abbreviation: BMC Bioinformatics Subsets: MEDLINE |
| أسماء مطبوعة: | Original Publication: [London] : BioMed Central, 2000- |
| مواضيع طبية MeSH: | Software* , Computational Biology*/methods, Reproducibility of Results |
| مستخلص: | 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. (© 2024. The Author(s).) |
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| معلومات مُعتمدة: | CN00000013 National Centre for HPC, Big Data and Quantum Computing |
| فهرسة مساهمة: | Keywords: Bioinformatics; Docker; Open science; Reproducibility; Software sharing |
| تواريخ الأحداث: | Date Created: 20240313 Date Completed: 20240314 Latest Revision: 20240315 |
| رمز التحديث: | 20240315 |
| مُعرف محوري في PubMed: | PMC10935966 |
| DOI: | 10.1186/s12859-024-05695-9 |
| PMID: | 38475691 |
| قاعدة البيانات: | MEDLINE |
Find this article in full text from Springer Verlag. 
Full Text Finder | تدمد: | 1471-2105 |
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| DOI: | 10.1186/s12859-024-05695-9 |