05 September 2008

Center for the Study of Human Polymorphisms: Week 1

I've started my first week at the center Center for the Study of Human Polymorphisms and today we had our first meeting with Mario Foglio and some other to define what will be my job in the following monthes. As I said, I will collaborate with the National Center of Genotyping on Operon, a feasible bioinformatics platform to centralize scientific software and biomedical data with internal results. It was curious because I found that nobody there uses most of the tools used/discussed with the biogang (rss feeds, social bookmarking, etc... ) and I hope I will present some slides about this later.

I will have to re-factoring the current 'C' code of operon (written over BerkeleyDB) to build a new clean C API that will be used some other persons.

What is cool is that this is an open source project and we will host it on google (http://code.google.com/p/polymorphism/).
I've also created a mailing list on google.groups: http://groups.google.com/group/operon-dev, shown my collaborators how to share a calendar on google-calendar (to find what are the possible dates for organizing a meeting) and we have already started to share some documents using google-docs. Thank you google.

The 'C' language was chosen because it is a low-level language and it seems that the developers at the CNG prefer it. I hope I will create some wrappers around this API with some other language. I already know it is possible with java using the Java Native Interface (JNI, see my previous post about this). SWIG (http://www.swig.org/), a tool generating some wrappers in various languages (python, perl...), might also be of hel. Using a Java wrapper will allow us to deploy any application in a java web server such as tomcat.

I've not much played with 'C' since 1998 ( I then played with C++ for 4 years before switching to java) but I (hope) still have some good skills and I know I now have better good programming practice.

That's it for tonight.



Tim Yates said...

I've not used it, but I've heard good things about GlueGen:


Could be worth a quick investigation, as it might save you a few days of JNI hell ;)

Pierre Lindenbaum said...

Cool ref ! Thank you Tim !

NicoR said...

1988? That must be a typo... (except if it took ten years between the calculations and the publication of the results! well, may be...)

Pierre Lindenbaum said...

@nicor, yes that was a typo. It's corrected now. Thanks.