Open Call project, 2022 Ribo-seq data analysis
Project Outcome
In this project, the SSC enabled the researcher to address maintainability and reproducibility issues, and to increase the quality of the software being developing in the lab, Rp-Bp. This software allows to predict translated open reading frames (ORFs) from ribosome profiles using an unsupervised Bayesian approach. Isolation and deep-sequencing of ribosome-protected RNA fragments (ribosome footprints) provides a genome-wide snapshot of the translatome at sub-codon resolution. Rp-Bp can be used for ORF discovery, or simply to estimate periodicity in a set of Ribo-seq samples; Rp-Bp also automatically classifies ORFs into different biotypes or categories, relative to their host transcript.
Through the SSC support, the code refactoring requirements were evaluated, to identify and resolve selected dependency conflicts. A test suite was added. Further, the software was packaged on PyPI and bioconda, and a minimal CI/deployment pipeline was implemented. Pre-built docker containers were also provided. Further, the software was improved with an interactive reporting dashboard.
The support of SSC has been a springboard for me to adhere to best practices in software development. This had a positive impact on my performance as a software developer. They provide really good knowledge transfer.
Dr. Etienne Boileau, Postdoctoral Researcher at Klaus Tschira Institute for Computational Cardiology/Internal Medicine III: Heart, Vascular and Lung
Enabling new research
Through this collaboration with the SSC, the researcher has built capacity for better coding (best practices for software development, Continuous Integration, etc.), which was very beneficial for the researcher. As the researcher is mostly working by himself on the code, it was also a real “collaborative” experience for them, experiencing how GitHub can be used in collaborative software development. As a result, a new tool is being developed, that builds on rp-bp.
Resulting publications
- ECCB2024, Turku 16-20 September, 2024
- 28th Annual Meeting of the RNA Society, Singapore, May 30 to June 4, 2023
