[Bioperl-l] Re: "Volunteers needed"
bmoore at genetics.utah.edu
Mon Nov 7 09:53:43 EST 2005
Jason Stajich, who has been one of the lead developers in bioperl for
many years now, mentioned last week that:
"Tools::StandAloneBlast could DEFINITELY be improved and needs people
to adopt it...."
Now what the hell is Tools::StandAloneBlast? Blast (and it's relatives
wu-blast and fasta) are probably the most frequently used algorithms in
bioinformatics. They take a nucleic acid or protein sequence as input
and searches for similar sequences in a large database of sequences.
Tools::StandAloneBlast is the module that provides the bioperl interface
to a locally running copy of the NCBI Blast tool. NCBI (National Center
for Biotechnology Information) has written one version of Blast, and
they also maintain a comprehensive database of nucleic acid and protein
sequences and sequence related information. Check out the education
section of the NCBI website (http://www.ncbi.nlm.nih.gov/Education/) and
the Blast handbook
Install a copy of Blast, install the nr sequence database and get
Tools::StandAloneBlast running on one of your machines, and start poking
around that code to see if it can use some improving.
BTW, In Europe, EBI (European Bioinformatics Institue and the Ensembl
project fills a similar niche but from a different angle. It would be
worth becoming familiar with their tools as well because their API is
often more programmer friendly.
P.S. Write a script to use bioperl to blast search the following
sequence against a local copy of the nr database and decide what protein
it is from and why this protein was your friend last Friday night.
> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org [mailto:bioperl-l-
> bounces at portal.open-bio.org] On Behalf Of Jay Hannah
> Sent: Saturday, November 05, 2005 10:09 AM
> To: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] Re: "Volunteers needed"
> On Nov 5, 2005, at 4:50 AM, Ewan Birney wrote:
> > welcome on board - have you tried out BioPerl? It is a rather large
> > project
> > and definitely there are some un-cared for areas that need some TLC.
> > I guess Jason or Aaron might have some ideas, but a good starting
> > place is
> > to download bioperl, go make test and also look at the start of the
> > tutorial.
> > I have no doubt that you'll spot some sub-optimal things on teh way
> > Once that's done I'm not 100% sure where is a good place to start:
> > access
> > of some other internet accessible sequence databases?
> I suspect I may be good at wrestling/smoothing installs, test scripts,
> POD, etc. I have access to Mac OS X, 3 flavors of Linux, and AIX. I'm
> no porting guru, but I'm strong in general Perl, test scripts, CPAN
> installs, web/Internet coding, databases, Apache, Linux, etc. If those
> skills are needed in the Bioperl community I'd be happy to take a stab
> at submitting various patches or tackling whatever.
> The other side of my equation is that I'm thoroughly ignorant in
> biology and genetics. For 10 years I've been data crunching / web
> portaling / e-commercing for companies that have nothing to do with
> this new "hobby." I am, however, committed to learning if I can find a
> niche somewhere in which I can help, no matter how small the
> contribution. I've picked up a few books and am consuming those as
> allows. Turns out genetics and biology are complicated. Who knew?
> It would be fantastic if I could find a local lab that could use my
> help (Omaha, NE USA). Luckily my skills telecommute fairly easily, so
> if any scientist genius type anywhere wants some slave labor I'd
> happily do their bidding under their wing.
> Programming, databases, and Internet interaction are my forte.
> Unfortunately I'm guessing my lack of bio skills render my programming
> skills unusable for much of the work going on...?
> Anyway, I'm just very motivated to help someone doing genetic research
> for the greater good. It would be a great feeling to know that maybe
> someday my labor may help produce something that will help people.
> been working for money for 10 years now, and am attempting a shift in
> focus. Part time. -grin-
> I hope I can help.
> Jay Hannah
> Omaha, NE
> mobile: 402-578-3976
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