[Bioperl-l] another use of Perl for biology

Heikki Lehvaslaiho heikki at ebi.ac.uk
Tue Feb 25 18:36:36 EST 2003


I had a quick look at your site. 

Coming in totally unprepared is was quite difficult to get a picture of
what you are working on in practical terms. The whole system is there
but it has not been broken into manageable chunks. I had to dig into one
of the posters to find out what what OSIS stands for (Object-oriented
Systematics Information System).  It looks really ambitious and complex.
You are using graphical interfaces to model taxonomic problems by
reusing basic classes, right? I can not get the feel of how stable are
your basic classes? In other words, is the development now focused on
connecting and using these basic classes rather than trying out
different ways of modelling basic units in systematics? How about the
ontology? Do you have a graphical representation of the current class
model(s)? Is there now a consensus in the field  how these things should
be modelled? Are you confident you model can tackle most real life

We do not have practically nothing related to taxonomy/biodiversity in
bioperl, but I'd love to see something. If your basic atomic classes are
in stable stage, it'd be grand if could consider putting them into
bioperl with some sample scripts. That would be a quick way for other
people to get feel of your approach and give you feedback.



On Tue, 2003-02-25 at 17:07, Guillaume Rousse wrote:
> I just updated the web site of OSIS, a software framework developped in my 
> laboratory.
> This project aims to create a shared code base to build systematics 
> application from a common trunk instead of reinventing the wheel constantly, 
> as molecular biology community already do with biojava, bioperl, and similar 
> projects.
> The only implementation available currently is in Perl, and the only use case 
> is related to database management, but the project scope is wider.
> It is of course a free software project, so all comments, critics or 
> contributions are welcomed.
> The web site is located at http://lis.snv.jussieu.fr/~rousse/recherche
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