Genetic Cloning with Debian
Mentor: SteffenMoeller
Summary: Improve the interplay of several tools for preclinical research and write respective tutorials
Required skills:
- good reading and writing skills
- strong interest in computational biology and genetics
- Perl
- wxWindows
- Java
Description: Several routine tasks in preclinical research are a continuous nuisance with Open Source tools on any OS. Debian has an edge since it offers a series of applications that address most of those routine issues. This availability the upstream developers had not been anticipated by the developers of those contributing tools. Also, some tools need a bit of maintenance to update their URLs.
- A student of the mentor is preparing a Bachelor thesis to dissect the tool 'GENtle' [1] for genetic cloning into several smallish units that would then communicated by the exchange of files. The cloning workflow would then be orchestrated by the bioinformatics workflow suite Taverna [2]. To continue an earlier effort on packaging Taverna for Debian [3] is suggested as another 2011 GSoC project.
Challenges:
- Completely understand how to plan genetic cloning experiments with Taverna and write a tutorial on it
Improve the fragments of GENtle
do not only rely on ClustalW but alternatively also on other alignment tools of Debian
allow GENtle to run PerlPrimer
extend usability as suggested here.
- Some mainenance for whatever one might observe on the way
Update URLs e.g. for Ensembl for PerlPrimer
- prepare for some eye candy, e.g.use of svg icons, the use of standard icon collections and their extension by own work
Aims: Strategically, this project reminds ourselves that Debian is more than the packaging of readily available software. It is also about gluing components together or to prepare for it. The most tangible result is the time saving for all the molecular biologists out there using GENtle, ?PerlPrimer and friends. The tutorial introducing to these tools will attract more to our distribution and be of high educational value.
References:
[1] GENtle gentle.sourceforge.net
[4] PerlPrimer
Applications:
- Nancy