1<meta charset="utf-8" fmt="-*- markdown -*-"> 2 3 4**Software** 5 6(#) Old stuff 7 8Most that you find below is not maintained anymore. 9 10(##) Research software 11 12(###) Lositan and Mcheza - Detection of genes under selection 13 14There are two Jython-based applications available for selection detection: 15 16- Lositan - for co-dominant markers 17- Mcheza - for dominant markers 18 19[These applications](https://github.com/tiagoantao/lositan) are 20currently un-maintained but are still widely used. If you run into 21problems using them, please downgrade your Java version to 1.6. The 22security model of newer versions is not very friendly towards old Java 23Web Start applications. 24 25 26 27(###) ogaraK - Epidemiology of drug resistant malaria 28 29[ogaraK](https://launchpad.net/ogarak) allows the simulation of the 30spread of drug resistant malaria. It was developed in Groovy and is a 31Java Web Start application that can also be run on the command-line. 32 33(###) Biopython (co-author) 34 35I am one of the many authors of the [Biopython 36Project](http://biopython.org). I am mostly responsible for the 37Population Genetics module. I was the release manager for a couple of 38versions, was involved with 2 to 3 conversion and installed the 39integration server (buildbot). I did other bits like a BioSQL version 40using the MySQL pure-Python driver. I am currently interested in 41developing teaching material with IPython Notebooks, to that effect I 42am converting parts of the Biopython tutorial to Jupyter Notebook 43format 44 45 46(##) Teaching software 47 48Please check my [tutorials page](tutorials.md.html) for teaching software. 49 50 51(##) Infrastructure 52 53(###) Virtual Core - Turn-key solution for data science 54 55[Virtual Core](https://virtual-core.readthedocs.io/en/latest/) is a turn-key solution 56to deploy a complete set of data-science core services that can be 57used as a base infrastructure for big data analysis. The solution is 58based on [Docker](http://docker.com) and it currently includes: 59 60- A LDAP container, along with a web interface (phpldapadmin) 61- Zabbix-based monitoring 62- PostgreSQL database server 63- An extensible software container, currently including Python and R tools for data-science (based on Anaconda) 64- A user container, where users can log-in and run all data-science application 65- A file server, capable of routing data from other file servers (e.g. communicate with a Samba server and exposing an NFS interface) 66- Cluster software (currently only SLURM) 67- A SLURM-compute container that can be deployed across a cluster (via Docker swarm) 68- A exploratory analysis server, which includes a Jupyter hub 69- Plain web server 70 71 72Most communications are SSL secured and the system can work as an 73adhoc SSL certification authority. The containers can be split across 74a cluster with Docker Swarm. A wizard is included to get the system up 75and running as fast a possible. 76 77 78 79 80[Home](/) 81 82<!-- Markdeep: -->
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