If you are interested in using Python for Bioinformatics, you might want to check out my new book which provides a comprehensive set of practical recipes in Python covering topics such as: Next-Generation Sequencing, Genomics, Population Genetics, Phylogenetics, Proteomics plus advanced Python tips related to high-performance computing or interacting with R from Python.
The book has a free Github repository.
There are two Jython-based applications available for selection detection:
OgaraK allows the simulation of the spread of drug resistant malaria. It was developed in Groovy.
A very old project is a DSL for pharmacokinetics of drug treatments.
I collaborate with the Biopython project. I am mostly responsible for the Population Genetics module. I was the release manager for a couple of versions, was involved with 2 to 3 conversion and installed the integration server (buildbot). I did other bits like a BioSQL version using the MySQL pure-Python driver. I am currently interested in developing teaching material with IPython Notebooks, to that effect I am converting parts of the Biopython tutorial to Notebook format.
I have been involved in several projects related to automated code translation. For example converting legacy 3270
CA Gen applications to modern web interface ones. On the scientific computing front.
I have also did a semi-automated translation of Fortran to C code in the OpenMalaria simulator.
I have also been involved in the conversion of Python 2 to 3 code (arguably an easier task than the ones above). For example with Biopython and Abjad.
Some tutorials using Jupyter Notebooks
I am also starting to develop a Data Science Course. This is a more ambitious project including text, notebooks and, in the future videos