Software Carpentry Course

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

Heidelberg Palace (Left) | View of Heidelberg from EMBL rooftop (Right)

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