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Comment: Quality assurance for biological applications inside Debian
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| '''Description of the project:''' The Debian Med project has packaged a lot of [[applications for bioinformatics|http://blends.debian.org/med/tasks/bio]]. In GSoC 2016 a big step for Continuous Integration of the most important applications regarding to the usage statistics provided by popularity contest was done. While it would be important to continue this effort to cover even more applications with sensible testing in this work some other tasks to enhance the quality of the Debian Med packages were uncovered. 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). | '''Description of the project:''' The Debian Med project has packaged a lot of [[http://blends.debian.org/med/tasks/bio|applications for bioinformatics]]. In GSoC 2016 a big step for Continuous Integration of the most important applications regarding to the usage statistics provided by popularity contest was done. While it would be important to continue this effort to cover even more applications with sensible testing in this work some other tasks to enhance the quality of the Debian Med packages were uncovered. 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). |
Quality assurance for biological applications inside Debian
Description of the project: The Debian Med project has packaged a lot of applications for bioinformatics. In GSoC 2016 a big step for Continuous Integration of the most important applications regarding to the usage statistics provided by popularity contest was done. While it would be important to continue this effort to cover even more applications with sensible testing in this work some other tasks to enhance the quality of the Debian Med packages were uncovered. 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: Andreas Tille
How to contact the mentor: tille@debian.org
Confirmed co-mentors:
Deliverables of the project: Enhanced packages for bioinformatics covering whole workflows of users as best as possible
Desirable skills: The student should have a background in bioinformatics. Debian packaging skills are an extra plus but can be taught in the project run.
What the intern will learn: Detailed insight into the bioinformatic tools inside Debian, Comparing and benchmarking biotools, Debian packaging skills, Optimising bioinformatics and other scientific tools
Application tasks: Pick a bug out of the list 848326, 848329, 848332, 848333, 848334, 848335 and try fixing it. This is on one hand proof that the students is able to understand Debian packaging and understands bioinformatics at a sufficient level
Related projects: SummerOfCode2016/Projects/BioToolsTesting, SummerOfCode2017/Projects/Benchmarking