**Software** (#) Infrastructure (##) Virtual Core - Turn-key solution for data science [Virtual Core](http://vc.tiago.org) is a turn-key solution to deploy a complete set of data-science core services that can be used as a base infrastructure for big data analysis. The solution is based on [Docker](http://docker.com) and it currently includes: - A LDAP container, along with a web interface (phpldapadmin) - Zabbix-based monitoring - PostgreSQL database server - An extensible software container, currently including Python and R tools for data-science (based on Anaconda) - A user container, where users can log-in and run all data-science application - A file server, capable of routing data from other file servers (e.g. communicate with a Samba server and exposing an NFS interface) - Cluster software (currently only SLURM) - A SLURM-compute container that can be deployed across a cluster (via Docker swarm) - A exploratory analysis server, which includes a Jupyter hub - Plain web server Most communications are SSL secured and the system can work as an adhoc SSL certification authority. The containers can be split across a cluster with Docker Swarm. A wizard is included to get the system up and running as fast a possible. (##) Scientific Cluster (#) Research software (##) Lositan and Mcheza - Detection of genes under selection There are two Jython-based applications available for selection detection: - [Lositan](http://popgen.net/soft/lositan) for co-dominant markers - [Mcheza](http://popgen.net/soft/mcheza) for dominant markers These applications are currently un-maintained but are still widely used. If you run into problems using them, please downgrade your Java version to 1.6. The security model of newer versions is not very friendly towards old Java Web Start applications. lositan.jpg (##) ogaraK - Epidemiology of drug resistant malaria [ogaraK](http://popgen.net/soft/ogaraK) allows the simulation of the spread of drug resistant malaria. It was developed in Groovy and is a Java Web Start application that can also be run on the command-line. ogaraK.png (##) Biopython (co-author) I am one of the many authors of the [Biopython Project](http://biopython.org). 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 Jupyter Notebook format (#) Teaching software Please check my [tutorials page](tutorials.md.html) for teaching software. (#) Ongoing stuff... To be completed [Home](/)