Video Conference Link

https://meet.gwdg.de/b/car-a2m-gns-44g

Dates

Due to strotng interest, we will have two occurences of the workshop:

• Dec. 10 & 11 2020
• Jan. 14 & 15 2021

Please sign up for only one event.

Registration

The registration in online at https://workshops.evolbio.mpg.de/event/36/registrations/

Topics

The workshop covers:

• Basic use of the command line
• Version control with git
• Best practice in writing computer code (the workshop uses Python but the ideas are applicable to any language)
• Setting up a repository in GitHub/GitLab with license, tests, README, etc

Timetable (preliminary)

The material is designed for a two days workshop. Suggested timetable:

Day I

• 11:00 - 11:15 Introduction, check for installations
• 11:15 - 12:00 An introduction to command line
• 12:00 - 12:30 Lunch
• 12:30 - 13:15 An introduction to Python
• 13:15 - 13:30 Coffee break
• 13:30 - 16:00 Git and closing remarks

Day II

• 11:00 - 12:00 Best practices discussion
• 12:00 - 12:30 Lunch
• 12:30 - 14:00 GitLab
• 14:00 - 16:00 Continuous Integration with GitLab

Further reading

A number of sources that provide excellent guidance and references on the development of scientific software:

• "Share and Enjoy": Publishing Useful and Usable Scientific Models
• "Top Tips to Make Your Research Irreproducible"
• "Ten Simple Rules for the Open Development of Scientific Software"
• "Re-run, Repeat, Reproduce, Reuse, Replicate: Transforming Code into Scientific Contributions"
• "Gene name errors are widespread in the scientific literature."
• "A Guide to Reproducible Code in Ecology and Evolution"