[Bioperl-l] Emerging from obscurity

Paul-Christophe Varoutas paul-christophe.varoutas@curie.fr
Thu, 11 Jan 2001 01:48:13 +0100

Hi everybody,

I am writing because I would like to start contributing to the bioperl 
project. But first of all let me introduce myself:

I am finishing my PhD at the Curie Institute in Paris, France. My subject 
is molecular genetics in yeast, and more particularly the study of the 
initiation of meiotic recombination.

Apart from molecular genetics, I have a rather strong background in 
algorithmics and programming, that I developped by studying alone and 
interacting a lot with people studying computer science. One of my favorite 
fields is OOP: a have read a lot of books on OOP design and have experience 
in designing projects using UML and implementing them in C++. I started 
using C++ on 1992 and ever since I have implemented lots of sexually 
attractive object classes, such as various types of neural networks 
(backpropagation nets, BAMs (bidirectional associative memories) and FAMs 
(like BAMs but integrating  fuzzy logic), various cryptographic algorithms, 
and a basic collection of bioinformatics objects (that was before I 
discovered bioperl ;-) ), that I then used to develop some small 
appications, the coolest one probably being a program doing ORF prediction 
using Fourier transforms.

As for Perl, I started learning it on 1995 (that was the year of the 5.001 
release). Slowly but steadily it has become my favorite language. I use it 
extensively to do virtually *everything*, including solving my small 
everyday problems, such as doing file management, automating various 
internet activities (from more low-level operations using the IO::Socket:: 
modules to FTP/telnet sessions and web stuff), automating the very few 
biocomputing needs I've had for my PhD project. I also use perl for CGI 
I am fascinated by the power of regular expressions (I am reading 
"Mastering Regular Expressions" for the second time, and I am even more 
fascinated than the first time I read it, I'm still discovering astonishing 
details and realizing there is so much to learn about them), and try to use 
them whenever/wherever I can  B-) .

I discovered the bioperl project two years ago and I am following with big 
interest the discussion groups for almost a year. Many times I wanted to 
just jump in the discussions, but I didn't because I knew I would have no 
time to deal with it on top of my other activities.

So, after this rather long introduction, here is the subject of my mail: 
like all of you, I want to participate in making bioperl better.

As I mentionned above I am finishing my PhD, so I don't have much time for 
the moment. But will have finished the experimental part of my PhD by the 
end of January, so I will have some time to spare. I will probably pass 
large amounts of time in front of a macintosh writting my article and PhD. 
I *hate* macs (my favorite mac software is telnet for loging to our unix 
servers or to my home PC), and participating in the bioperl project will 
prevent me from getting insane :-).

I was thinking about participating in the discussions about the OOP design 
of bioperl, participating in the biocorba interoperability project, but for 
the moment I would prefer starting with something more "smooth", after all 
I am not (yet) familiar with all bioperl modules. So doing something that 
can get me more familiarized with the whole set of the bioperl modules 
should be a good start.

I figured out that I can help with some aspects of bioperl that can 
contribute to the enlargement of the bioperl community.
So, here is what I propose to do:

- Help figuring out bioperl 0.7 cross-platform compatibility with the MacOS 
platform. Almost all french labs use macintosh computers, and our lab has a 
lot of mac boxes with various types of processors and various versions of 
MacOS (from 7.5.3 to 9.0). Todd Richmond and Mark Colosimo have already 
pointed out that there are a lot of compatibility problems, their posts are 
going to be my starting point. I would like to make a list of all problems, 
figure out which ones can be solved reasonably easily, and make at least a 
subset of bioperl work on MacOS "Classic" (non-MacOS X) platforms, which is 
what most Mac people use, and most probably will continue using.

- Contribute to Shelly's effort for compatibility with the Windows NT/2000 

- Participate in the documentation project of bioperl. I know that there 
are already people working on various aspects of the documentation, so I 
would like Ewan / Hilmar to tell me what you prefer: participate in one of 
the ongoing projects or initiate another project to do something that is 

I am very glad to contribute to the bioperl group, you are doing some 
exceptionally good work out there.

(For those who are reading this line, thank you for reaching so far  :-)   ).


Paul-Christophe Varoutas
Institut Curie - Section de Recherche - UMR144
Laboratoire de Genetique Moleculaire de la Recombinaison
26, rue d'Ulm
75248 Paris cedex 05