GP and Arka -- software for molecular biology

January Weiner nospam_jweiner1 at ix.urz.uni-heidelberg.de
Wed Feb 14 14:01:21 EST 2001


[ Gary Williams ]
> I was very interested to hear of your bioinformatics package.

> We are doing something very similar - EMBOSS
> http://www.hgmp.mrc.ac.uk/Software/EMBOSS/

Wow, seems like I was forcing an open door. I should have examined the SAL
database more carefully. Why didn't you put your package into the freshmeat
database?

> EMBOSS is a collection of Open Source command line tools written in ANSI C.
> You might like to join our project, or contribute some software to it?

Well, we have compatible licenses, and it shouldn't be very hard. BTW, I see
that Peter Rice is working at LION Bioscience, and our group has a
collaboration with this company -- interesting. One thing about my programs
is that I try to keep them as ANSI and lightweight as possible. I will
definitely download your developer tree and look at the source.

> We are always interested in GUIs for EMBOSS.
> Could Arka be adapted to be an interface to EMBOSS?

Why, yes, quite easily. Basically, it is a very simple thing: you have
three windows -- stdin, stderr and stdout. You can save or modify them.
Then, you have a sort of database holding information about my command-line
tools programs: names, options, short descriptions of the programs and
options etc. Right now it is hard-wired into the program, but the next
version will just read a configuration file which will be much more flexible.

You can run any program included in the "database" or issue an arbitrary
command -- you have a command history (stored before exiting) and I plan to
extend it to build little "macros" which will be in fact just /bin/bash
scripts. 

Apart from that, there are two graphical utilities: one for showing simple
GC content graphs (which I did for learning to program gtk+) and one for
showing 3D graphs of arbitrary data (which I did because I needed to
visualize DNA structures). 

Unfortunately, Arka is not portable. This is gtk+, and though there is gtk+
in Windows, there is also a lot of Unix-specific code in my program, so
basically Arka is Linux-specific. 

Best regards,
January

-- 
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AG Herrmann, Zentrum für Molekulare Biologie, Universität Heidelberg
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