[Bioperl-l] (repost) virtual gel from chromatogram, staden library on Windows

[Jonathan Epstein]

I see my original post from May 6th in the archives, but didn't see a copy of it in my incoming mail, so I'm taking the liberty of reposting this.  My apologies if this is a duplicate for others.

Many thanks to Chris for fixing the listserv!

Jonathan

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Hi,

One of our investigators wants to create virtual sequence gels from ABI chromatogram files.  While I remain unconvinced regarding the merits of this idea, meanwhile I'm trying to determine feasibility.

I found that ABI.pm in the BioPerl distribution requires a Staden library at:
  ftp://ftp.mrc-lmb.cam.ac.uk/pub/staden/io_lib/  

I would like to come up with a Windows or Windows/Linux solution to the original problem if practical, but would settle for a Linux-only solution, especially because I can probably turn this into a web application.

I was able to compile library version 1.8.7 (the last version which explicitly says it was tested on Windows) using gcc on Windows, but past experience suggests that I'm going to have trouble with this when I try to integrate it with the Visual C-compiled versions of BioPerl and ActivePerl.


So, my questions are:
(1) does anyone know of an inexpensive pre-existing software tool for recreating virtual sequence gels?  This seems like the simplest solution, since a custom (but free) BioPerl-made solution isn't likely to have a wide array of users
(2) what version(s) of the Staden library have been tested on Windows, and are any such available pre-compiled with the Microsoft compilers?
(3) any suggestions as to which which graphics packages (e.g., Tk) are likely to be the most friendly for producing a virtual gel?  I have a passing familiarity with Tk, and need to use wxPython for another project so am willing to invest some effort in learning wxperl.

TIA,

Jonathan 


Jonathan Epstein                                Jonathan_Epstein at nih.gov
Head, Unit on Biologic Computation              (301)402-4563
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