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Molbio Software Standard

Ramin Charles Nakisaramin r.nakisa at ic.ac.uk
Thu Apr 1 17:57:47 EST 1993

Thanks to all the people have responded to my cunning plan.  If you
missed it, I simply suggested that we (molecular biologists) worked out
what molbio programs we needed and wrote them ourselves.

Amos Bairoch sent me a message saying that he had done _exactly_ this
between 1984 and 1988, and this gave rise to PC/Gene.  He said that
after you reach a certain critical mass of programs, administration just
becomes too much, and at this point he handed over to a company which
could take over the upkeep.

IMHO we can get around the Corporate Critical Mass by simply setting out
a standard format for molbio programs.  The standard shouldn't be too
strict; that would take all the creative fun out of programming.  It
should be easy to use and portable and give programs a common "feel", so
that if you have used one of the programs, you know what to expect in
the rest.  I always find that the problem with public domain software is
in the variety of interfaces - I don't want to learn more than one
syntax! Documentation should be standard too.  Although it's unpleasant
to write, once there is a template it is much easier to fill in the
gaps. Given that we can establish a standard, preferably without too
many flame-wars, we can write a simple front end to package all the
pieces into a ragged whole.  Complaints and queries should go to each
program's author, splitting the onus.

Here is an outline to discuss:

* The source is written in C.  C really is very portable and as an added
  bonus it allows us to use Don Gilbert's amazing ureadseq module to
  read and write sequences in all the standard formats.  This would also
  allow us to build up a standard library of functions, so that we don't
  have to re-invent the wheel with every program.

* It should work when compiled for MS-DOS, Windows (quickwin), Macintosh
  (simple window format?), UNIX and X.

* It must be able to read and write all the standard sequence formats.

* There should be a standard interface.  The most portable interface is
  one that consists of only printf and scanf.  A standard graphic
  interface would be very difficult to define in a platform-independent
  way.  Compiler's can usually produce basic windows for windowing
  operating systems eg. the quickwin library on the MS C/C++ 7.0 compiler.

* It should offer sensible default parameters when possible, and
  use standard command-line switches.

* Graphic output should be in at least two formats: Postscript and HPGL

* All source should be included and beautified.

If you have ever used particularly good/bad molbio software then here is
your chance to have a say before it's written!
< Ramin Charles Nakisa, "She walks in beauty Tel:    071 589-5111 x 6729   >
> Biophysics Section,   As the night of      FAX:    071 589-0191          <
< The Blackett Lab,     starry skies and     EMAIL:                        >
> Imperial College,     cloudless climes..."         ramin at ic.ac.uk        <
< London SW7 2BZ.                                    mbrcn at seqnet.dl.ac.uk >

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