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HUB (Heidelberg Unseminars in Bioinformatics) about IPython and chemoinformatics
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##HUB (Heidelberg Unseminars in Bioinformatics) about IPython and chemoinformatics This repository contains material for HUB 21

Location and date

BioMed X, Im Neuenheimer feld 583, Heidelbeg, 21 January 2016

How to run code from this repo

I recommend Anaconda Python distribution with Python 2.7. In Anaconda terminal type jupyter notebook and navigate to folder with notebooks.
You can install RDKit (chemoinformatics library) with conda install -c rdkit

If you can't install Python on your computer you can use to experiment with Jupyter (rdkit is not available in

Pair programming presentation can be converted to html and served with:

jupyter nbconvert Pair\ programming.ipynb --to slides --post serve --ServePostProcessor.port=8910

Current plans are to include this:

  • short intro about BioMed X
  • an ice-breaker - maybe the 'classic' standing in a line/grid to describe our experience coding, which we can also use for teaming people up for later activities - a group of experienced coders goes to the part of the room where people haven't done any coding before, and we find experienced partners for each of them
  • a demo from Samo of IPython in chemoinformatic context
  • maybe someone else demos something similar using a different language (R? Perl?)
  • pair-programming together, using examples from Rosalind

angle we'd use to publicise the event would be:

  • never coded before? come and try out coding with experts, to see what it's like
  • interested in seeing what iPython/jupyter can do? come along and check it out - especially if you're into chemoinformatics - note that similar stuff is available for other languages
  • chance to try out pair programming

For this, we'll ideally have a bunch of people joining the event who will bring their own laptops, have appropriate software set up and running, so that we have enough laptops to pair-program with everyone - if not, maybe we try doing it in groups of 3.


  • prepare intro notebook
  • install instructions
  • list optional chemo/bioinfo and visualisation libs
  • check how to make jupyter work with other programming languages
  • guest wifi vouchers
  • buy beer
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