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The Bioperl Project

For those interested in bioinformatics and programming, there are several exciting projects going on that are interested to keep an eye out on or maybe even get involved with. One of the oldest ones is The Bioperl Project.

From their site:
'Officially organized in 1995 and existing informally for several years prior, The Bioperl Project is an international association of developers of open source Perl tools for bioinformatics, genomics and life science research.

Facilitated by the Open Bioinformatics Foundation we work closely with our friends and colleagues across many projects including biojava.org, biopython.org, DAS, bioruby.org, EnsEMBL and EMBOSS.

The Bioperl server provides an online resource for modules, scripts, and web links for developers of Perl-based software for life science research. We can also provide web, FTP and CVS space for individuals and organizations wishing to distribute or otherwise make freely available standalone scripts & code. '



This is a flashy UI that can be an alternative of EMBOSS.

That is a really sweet app you made! Thanxxx for mentioning it! Are you involved with the Open Bioinformatics Foundation in any way? If not, you definitely should, that's a really really nice app!

Thanks Edwin!

I used to have a contract with a german company that creates software in the bioinformatics field. It resulted in a few advanced flash apps that are going to be replaced by .NET modules very soon.

Check some more at:

These demos a using static data, but the real apps are visualizing a dynamic information stored in a database. They were originally created for Flash 6 and I wonder is it now possible to have a faster 3D module with the new player features.

There's one more cool application that I haven't found time to prepare for demonstration. It's called Interaction Viewer and displays the relations between proteins inside a cell.

Let me know if you have an idea how these can be utilized by an open foundation.

Those are very nice!

We'd certainly be interested in hosting this as an open source project, at GalaxyGoo. I'm interested in how your managine large data sets with this. I've got a project I'm working on, right now, that has over 3,000 points. It would be fun to compare notes.

Flash 8 does offer improved performance, but I haven't had time to thourougly explore it yet.

By the way, did you see the call for the open alpha for flex?