Bioperl-guts: bioPerl (fwd)
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 <firstname.lastname@example.org>
> > To: "'email@example.com'" <firstname.lastname@example.org>
> > 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.
> > 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
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