Scientific computing, Python, Bioinformatics, Genomics and Population Genetics


Python for Bioinformatics

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 github repository.


Most of my Python code is related to bioinformatics and scientific computing. But here you will also find content related to containerization of Python applications via Docker and IPython Notebook-based tutorials. Tutorials range from a wide range of topics like bioinformatics, population genetics and even music.


In the Bioinformatics page you can find Python libraries (including my collaboration with the Biopython project), but also complete, easy to use applications for selection detection (based on Jython). There is also a pharmacogenetics simulator developed in Groovy and a Domain-Specific Language for pharmacokinectics developed in Scala.


Other than bioinformatics, I have been involved in research spanning malaria epidemiology, population genomics and genomics of humans and anopheline mosquitoes (the main vectors of malaria), conservation genomics, estimation of effective population size and selection detection.

I also maintain a separate website with information about population genetic workshops which I helped organize and live bioinformatics tools