Windows port of contig assembly program

James Bonfield jkb at arran.mrc-lmb.cam.ac.uk
Fri Sep 1 08:02:40 EST 2000

In <002f01c01411$e9a55520$7b02a8c0 at nic.in> curiouser at ccmb.ap.nic.in ("Malay") writes:

> I am actually quite disheartened to see Staden package going in the line of
> GCG. It has definitely the potential of becoming the defacto standard for

I don't think it's going along the GCG line. GCG was completely commercial. We 
are totally committed to keeping it completely free for academics on Unix, and 
we can even provide the source code. It's not GPL though, so if you modify the 
source code you have to be content with no being able to redistribute it. We
do however fold back in any (good) source improvments. However I guess most
people aren't willing to submit such a thing to a non GPL package.

GCG also suffered from the fact that it was mostly made up of free programs
anyway. It's definitely important to put a nice uniform interface to such
tools, but there's only so much money people will part with to get something
that's free (and the "nice uniform interface" wasn't particularly nice).

We have been working on an interface to EMBOSS too, so to that extent maybe we 
are falling into the GCG trap. However I think our interface (in Nip4 and
Sip4) is substantially easier and more powerful than the native EMBOSS ones,
so hopefully that really does add something important.

> Sometimes I feel it is quite easy to get funding in countries like India,
> where I must say government has been quite liberal in funding projects. My
> only hope Rodger goes to *public*, literally for funding and initiate an
> international effort to keep the project beyond the clutches of any control
> and make it GPL. I guess a GPLed Staden will wash out any other commercial
> sequence analysis program.

I suspect that we may find it easier to get funding improving a GPL package
than improving a semi-commercial one. The danger of the commercial route, even 
if it is only one one single platform, is that we're then considered to be
able to fund ourselves. (And at present there's no sign of that.)

> What we require is just a push and some strong intention.

Intention isn't always enough. We're bound by contracts.

James Bonfield (jkb at mrc-lmb.cam.ac.uk)   Tel: 01223 402499   Fax: 01223 213556
Medical Research Council - Laboratory of Molecular Biology,
Hills Road, Cambridge, CB2 2QH, England.
Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/

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