Bioperl-guts: bioPerl (fwd)

Steve Chervitz sac@neomorphic.com
Fri, 16 Apr 1999 06:04:20 -0700 (PDT)


Ewan Birney writes:
 > On Thu, 15 Apr 1999, Steven E. Brenner wrote:
 > 
 > > 
 > > Is anyone interested in this?  Please respond to the list.  (He indicated
 > > that I could forward the message to the list.)
 > > 
 > > Steven
 > > 
 > > ---------- Forwarded message ----------
 > > Date: Thu, 15 Apr 1999 15:29:17 -0700
 > > From: Jim Lindelien <jiml@timelogic.com>
 > > To: "'brenner@hyper.stanford.edu'" <brenner@hyper.stanford.edu>
 > > Subject: bioPerl
 > > 
 > > Dear Dr. Brenner:
 > > 
 > > By way of introduction, I am the senior engineer responsible for the 
 > > DeCypher bioinformatic accelerator produced by TimeLogic, (see 
 > > http://www.timelogic.com/RACE/index.htm) and the company's founder.  I 
 > > wanted to let you know that we would be supportive of anyone at Stanford or 
 > > elsewhere who'd like to code a standardized interface to our systems, and 
 > > will make a loaner available for that purpose.  Also, there are two 
 > > DeCypher accelerators now at Stanford, in Dr Cherry's and Dr Brutlag's 
 > > groups.  Dr. Brutlag has known me for some years now and can vouch for me 
 > > if needed.
 > 
 > I think this is interesting - and if anyone wants to make something for
 > bioperl that would be great. I certainly don't plan to do it ;).

I had some crude scripts that I used for running & parsing Smith
-Waterman searches on a TimeLogic box, but they are about a year old
and likely would need some work. 

 > It should use Steve's yet-to-be-written sequence similarity search
 > interface. Steve - for me this is an important thing to write and commit,
 > because there are a number of us who need to use it (Aaron for his fasta
 > results stuff and myself for HMMER2 stuff).

We should talk more about this. The existing Bio::Tools::SeqAnal.pm
interface was designed to fill this role but hasn't (to my knowledge)
yet been used for anything besides Blast. I think it should be
re-incarnated as Bio::Tools::SeqSimilaritySearch.pm. It has generic
methods like run, parse, and accessors for database size, version,
etc. It could use some more methods for working with hits. SeqAnal.pm
could be a good starting point for discussion. I'm open to suggestions
about design changes.

SteveC

 > > There is a straightforward TCP-IP sockets API in C for UNIX available as 
 > > source code and a UNIX command-line interface for the accelerator, so the 
 > > coding should be pretty simple.  We are happy to modify it as needed to 
 > > expose any required functionality.
 > > 
 > > Please do not hesitate to email me if I can help.
 > > 
 > > Regards,
 > > Jim
 > > ----------------
 > > Not just a fad--DNA is here to stay.
 > > Jim Lindelien VP Engineering 775-833-0200 Ext. 11
 > > 880 Northwood Blvd., Incline Village, NV 89451
 > > TimeLogic Corp. http://www.timelogic.com
 > > 
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 > > 
 > 
 > Ewan Birney
 > <birney@sanger.ac.uk>
 > http://www.sanger.ac.uk/Users/birney/
 > 
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