I was fortunate to have been rewarded a place to participate
in the EMBL’s course called Computing skills for reproducible research:
software carpentry (acceptance is merit-based), held from the 16th
to the 18th of October 2019.
Heidelberg stunned with its autumn colours, which was a perfect accompaniment
for this great course. I interacted with
many other researchers from diverse backgrounds (human genetics, clinicians,
viticulture, engineering, etc.), some of whom travelled from very far (for e.g. Ghana, Argentina and Peru).
For me the most relevant part of the course was Python
Programing, Pipeline management with Snakemake and version control using command
line Git/GitHub. I am very excited to integrate
SnakeMake to my future projects as the Python extended language helps by
decomposing workflows into smaller steps and automatically determines
dependencies between rules the user creates, which in turn, facilitates
parallelizing pipelines/analysis.
Moreover, in the current ‘reproducible research crisis’ I can foresee
Git/GitHub to be a protagonist, especially with the option of a free private
version so that data sensitive scripts, etc. can be kept in-house.
In short, great lecturers (incl. Cosmos, one of the lecturer’s
Labrador dog), course and venue; recommendable!!
LMV
LMV
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| Heidelberg Palace (Left) | View of Heidelberg from EMBL rooftop (Right) |
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