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Windows port of contig assembly program

James Bonfield jkb at arran.mrc-lmb.cam.ac.uk
Fri Sep 1 04:14:37 EST 2000

In <005701c0136d$3be99260$7b02a8c0 at nic.in> curiouser at ccmb.ap.nic.in ("Malay") writes:

> >HOWEVER, please note that the windows one is not free. The politics of this
> >are long winded so I won't bother to go into it, but it's sufficient to say
> >that charging for it on Windows will actually secure our long-term aim of
> >keeping the package free on Unix (including Linux).
> I personally think keeping the windows "tinkerers" at bay is slightly
> unfortunate for a package like Staden.

Quite possibly. As I said, personally I'd rather it was all free (even though
I do get a tiny %age of the sales back to me). It could be start of making
the package the "defacto standard" assembly editor, which naturally all of us
here would like! There isn't really a heavy-weight GPLed assembly package
around yet, but the totally-free ones are slowly catching up. If we just
ignore them then the danger is we'll simply be pushed out.

> A GNU sence free will be the easiest way to make something *immortal*.
> Unless you believe that grants will flow forever.

Actually the thinking was that we expected grants to dry up (and so we'd all
be out of a job) unless there's enough income to fund the development. So the
goal was simply to _secure_ the long term future of the package.  OK so making
it completely GPLed would possibly secure the package even more (assuming
anyone else wished to maintain it), but it certainly wouldn't secure our posts
(only 1 person in the group has a permanent position). So there is indeed an
element of self interest here :)

This isn't hypothetical either. Due to the funding shift from "sequencing" to
"analysis" (afterall we all 'know' that all the sequencing has been done now
and so it's not worth investing any money in it...) the group was infact
unfunded for a few months as Rodger was finding it very hard to obtain a new
grant. (The typical response was "you're work is valuable, but we're now
focusing on genome analysis".) The group would have dissolved and further
development of the Staden Package would have ceased if it was not for MRC-LMB
(ie 'here') stepping in and kindly paying our salaries for a few months until
we obtained a new grant. I don't think MRC particularly like the thought of
doing that sort of thing on a regular basis though - hence the
commercialisation on Windows.

What's interesting perhaps is some hybrid licence. I was pondering this quite
a bit earlier in the year (although as I said before, I'm just a programmer
and have no real say in the matter myself). One thought was a modified GPL
licence which allows people to do anything they wish, except to compile the
code on Windows. That way people could be happy with the security of having
public code, but MRC could be sure of keeping an income. Some people would
even see it in a good way; promoting people to switch from Windows to Linux
:-) When I mentioned this to someone once they just asked "But why would
anyone pay for it when the code is all free on Linux?". My answer to that is
"Why would anyone pay for the inferior Windows OS when Linux is free?".

An alternative, and perhaps more mainstream idea, is totally free access for
academics only (ie on both Unix and Windows). In bioinformatics though there's 
just as many (if not more) bright "tinkerers" in industry as academia.

Any suggestions? In a purely hypothetical sense of course - I doubt things are 
likely to change.

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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