Course Material for the Software Carpentry workshop Würzburg 2016-10-26/2016-10-27

1 About

This is the course material for the Software Carpentry workshop taking place in Würzburg at October 26th and 27th, 2016. The course is an introduction for novices to the Unix Shell, Python and git.

2 Schedule

2.0 Check installation while people are arriving

2.1 Welcome and introduction [9:00 - 9:30]

• Introduction of the instructors and helpers
• Introduction of the participants
• Photos
• Ice breaker - Sort people by the following values:
  • In which year of your PhD are you?
  • How strong are the computational requirement in your PhD
  • Considerung the course topic - how strong do you feel about knowing this already?
  • Group by research field
• Name tags
• Breaks
• Material of the course
• The etherpad
  • http://pad.software-carpentry.org/p/2016-10-26-Wuerzburg
  • Short URL: http://bit.ly/2emNADR
  • Exercise - add your name to the list of participants
• HackyHour and WUBSyB
• Motivation
  • Access to (bioinformatical) tools that only have CLI
  • Automation
  • Reproducibility / Transparency
• Who has still issue with installation?

2.2 Unix Shell (Konrad) [9:30 - 12:00]

• Files, folders, locations
• Manipulating files and folders
• Connecting tools with pipes
• for loops
• Shell scripting

2.3 Python [13:00 - 16:00]

2.3.0 Installation of Jupyter notebook

2.3.1 Session 1 (Malvika):

• Print, literal constants
• Variables
• String format operators
• Data structures: str, int, float, list, dict
• File handling
• New lines, tab etc., regular expression
• if else startement
• for loop

2.3.2 Session 2 (Markus):

• Function definition: reproducibility
• Doc string, sensible names, arguments

2.3.3 Session 3 (Konrad):

• Importing module and module recommendations (important modules: sys, math, pandas, numpy, scipy, matplotlib, openpyxl, requests, biopython, collections, scikit-learn, )
• Writing scripts

2.4 Git (Markus) [9:00 - 12:00]

• Setup
• Creating a Repository
• Tracking Changes
• Exploring History
• Ignoring things
• Remote repositories

2.5 Open Session [13:00 - 16:00]

This session offers space for further exercises, questions and related topics like open source / open content licenses, open science practices, reproducible research.

• Fill out the post- workshop survey of SWC
• Fill out the feedback form of the GSLS
• Discussion and feedback

3 Sources

• Unix shell - Was created based on Introduction to the Unix Shell for biologists by Konrad Förstner
• Python - Was created based on a SWC course by Malvika Sharan and Toby Hodges
• Git - Was created based on the Software Carpentry introduction to Git for novices course maintained by Ivan Gonzalez and Daisie Huang

4 License

This work by Malvika Sharan, Markus Ankenbrand, Konrad Förstner is licensed under a Creative Commons Attribution 4.0 International License.