Coding for Reproducible Research

Workshop on code compatible with Reproducible Research using Jupyter notebooks

Resources that are used in this class

• https://github.com/UBEC/ReproducibleResearch/
• https://reproducible-science-curriculum.github.io/rr-jupyter-workshop/
  • https://github.com/Reproducible-Science-Curriculum
• https://github.com/sara-nl/jupyter-bigdata-notebooks

Example of a notebook we use in teaching bioinformatics

• https://github.com/UMCUGenetics/BachelorBfx

---

The outline for today:

1. Get code ready in your environment

   • https://github.com/UBEC/ReproducibleResearch/blob/master/Prepping_RS_Workshop.ipynb

2. Go through Data carpentry intro

   • introduction-RR-Jupyter/notebooks/Intro-to-reproducible-research.ipynb
   • introduction-RR-Jupyter/notebooks/Jupyter_Intro_Background.ipynb

3. A versioned jupyter notebook

   • fork https://github.com/UBEC/ReproducibleResearch
   • clone your own version of ReproducibleResearch
   • open VersionedNotebook through jupyter interface
   • edit the code to perform the desired analysis on the Human IDs
   • commit the code to the repository with a tag
   • run analysis again with different settings for Mouse
   • [origin=False]
   • commit the code to the repository with a different tag
   • check out the versions on github
   • https://github.com/UBEC/ReproducibleResearch/compare/v2.0...v3.1

GIT code example

! git commit -a -m "ID version"
! git tag -a v1.4 -m "ID version"
! git push origin v1.4

4. bio-break

5. See some SPARK in action

   • jupyter-bigdata-notebooks/notebooks/02-spark-intro.ipynb
   • jupyter-bigdata-notebooks/notebooks/03-spark-dataframes.ipynb

---

Tips & Tricks

• https://www.dataquest.io/blog/jupyter-notebook-tips-tricks-shortcuts/

Use Git aware text-editors for libraries/readmes etc

• https://help.github.com/articles/associating-text-editors-with-git/
  • https://atom.io/

Do not put everything under git control:

echo ".ipynb_checkpoints" >> .gitignore

• https://gist.github.com/pbugnion/ea2797393033b54674af
• http://stackoverflow.com/questions/18734739/using-ipython-notebooks-under-version-control

Plotting, embedding, etc...

• https://blog.dominodatalab.com/lesser-known-ways-of-using-notebooks/
• https://plot.ly/python/ipython-notebook-tutorial/

---

Further reading

• https://ropensci.github.io/reproducibility-guide/
• https://git-scm.com/book/en/v2/
  • https://git-scm.com/book/en/v2/Git-Basics-Tagging
• https://github.com/jupyter/notebook
• https://github.com/tanghaibao/goatools

More on getting started

• https://github.com/Reproducible-Science-Curriculum/introduction-RR-Jupyter/blob/master/notebooks/getting_started_with_jupyter_notebooks.ipynb