[Biojava-l] Newbie to list

[Thomas Down]

On Tue, Mar 12, 2002 at 12:25:26AM -0800, James Kwong wrote:
> 
> I'm interested in doing a project involving bioinformatics for my
> masters project in comp sci and contribute to the biojava project.  I'm
> wondering if any of you have any suggestion as for new projects needed
> for biojava.
> 
> My background:  I have an undergraduate degree in biochemistry and
> currently pursuing masters degree in computer science.  Hopefully when I
> finish, I may work in the field of bioinformatics.
> 
> I browsed through the biojava and bioperl websites and the bioperl's
> project list (http://bio.perl.org/Projects/areas.html) appears a bit
> outdated from the timestamp on the bottom of the page.  Does biojava
> have anything on workflow and/or phylogenetic trees?


Hi...

There's actually been some discussion about workflow management
quite recently.  Have a look in the mailing list archive at
the thread ``LIMS framework - an open-bio project proposal'':

    http://biojava.org/pipermail/biojava-l/2002-March/002327.html

As for phylogeny...  No code for that yes.  There is, though,
an object model which allows storage of multiple sequence
alignments and (in the current CVS trunk) some taxonomy code.
So those might be helpful starting points if you wanted to work
in that direction.

Would you be interested in writing new phylogeny algorithms?
Or parsers/object models to facilitate the use of existing
tools?  Either way, it could be an interesting project.

Good luck -- and don't hesitate to drop a message to this list
if you've got any questions,

    Thomas.