Quality assurance for biological and medical applications inside Debian
Description of the project: The Covid-19 pandemic made it obvious that Free Software in medicine and biology can provide tools to care for global health. The Debian Med project has packaged a lot of applications used in medicine and biology. In previous Outreachy projects starting in 2016 until last year several packages got Continuous Integration tests. It turned out that these tests are extremely helpful to ensure the quality of the software in the focus of the Debian Med team. Besides testing single packages it needs to be verified that related sets of packages are playing well together and are packaged in a way that the user can expect the maximum performance out of the packages (for instance by ensuring that MPI features are used if available and the hardware features are used as best as possible).
Confirmed Mentor: AndreasTille
How to contact the mentor: tille@debian.org
Confirmed co-mentors: Nilesh Patra nilesh@debian.org
Deliverables of the project:Continuous integration tests for all Debian Med applications (life sciences, medical imaging, others), Quality Assurance review and bug fixing
Desirable skills: Background in bioinformatics, medical imaging could be an advantage, but interest in scientific software and reading relevant documentation and papers might be sufficient. Debian packaging skills are an extra plus but can be taught in the project run.
What the intern will learn: Detailed insight into the software maintained by the Debian Med team, bug triaging in scientific software, Debian packaging skills, optimising bioinformatics and other scientific tools
Application tasks: Pick bugs like 890788, 909713, 970309, 970312, 970404, 970597, 970598 or 970599 and try fixing it - asking the mentor for help is perfectly fine and actually recommended. This is on one hand proof that the student is able to understand Debian packaging and understands the actual topic at a sufficient level.
Recommended reading:
[MUST] Building in a clean chroot: any one of sbuild, pbuilder, cowbuilder. We recommend "sbuild".
Examples: freebayes, dazzdb, snap-aligner, ncbi-seg, bio-rainbow, maffilter
Related projects: SummerOfCode2016/Projects/BioToolsTesting, SummerOfCode2017/Projects/QA_BiologyApps, ?Continuous_Integration_for_biological_applications_inside_Debian, SummerOfCode2019/ApprovedProjects/CIforDebianMed SummerOfCode2020/ApprovedProjects/DebianMedQAGSoC and Outreachy Project Proposal: Quality Assurance and Continuous integration for applications in life sciences and medicine
* Getting in touch: Please subscribe to the mailing list and feel free to ask for help there. Mentors and co-mentors can be contacted at their email addresses mentioned above.