[Bioperl-l] Re: "Volunteers needed"

Mon Nov 7 10:39:22 EST 2005

Course I must not have actually posted the proper name in my email,  
it's real name is Bio::Tools::Run::StandAloneBlast - don't want that  
to throw Jay for a loop at the get-go....

There are certainly things that we can use just plain-old perl help  
on if you aren't comfortable with the bioinformatics and biology  
concepts.

I will post some more information this week about efforts on a new  
Bioperl website which will help aid the efforts in tracking TO-DO  
projects and a cleaner and simpler website interface.  I'll be  
looking for volunteers to help with the new site content and  
migrating (and editing) the text from the existing site.   Part of  
the new site will be a wiki which will allow tracking and commenting  
on particular sub-projects that need help.  I've started collecting  
my thoughts on what we need to work on and will post the URL where  
others can contribute to the list.  I hope this sort of work will  
help direct people towards the projects that need help.

Best,
-jason

On Nov 7, 2005, at 9:53 AM, Barry Moore wrote:

> Jay-
>
> 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
> http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=handbook.chapter.610).
> 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.
>
> Barry
>
> 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.
> MSTAGKVIKCKAAVLWELKKPFSIEEVEVAPPKAHEVRIKMVA
>
>> -----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:
> DB
>>> 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
> time
>> allows. Turns out genetics and biology are complicated. Who knew?
>> -grin-
>>
>> 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.
> I've
>> 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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>
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--
Jason Stajich
Duke University
http://www.duke.edu/~jes12