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Staden Package .. Comments.

David Philip Judge dpj10 at mole.bio.cam.ac.uk
Wed May 7 03:09:34 EST 2003

Hello Bernadette,

For the last 18 years or so I have run practical courses in various 
places showing pwoplw how to use bioinformatics tools. The Staden 
package has been the mainstay of most of the sessions I have organised.

Stopping funding for this package is an unbeleivably inappropriate 
decision. Particularly as Rodger was about to release so many new 
innovations in the package.

I append the reply I made to Rodger's original announcement of the MRC's
funding blunder. If it would be helpful to you for me to elaborate in 
anyway, please just ask.

Dave Judge


Dear Rodger, James, Kathryn, Mark, Yaping,

Devastating!? A rare occasion when the word is hardly adequate I feel.

I suppose I must begin by apologising for taking too lightly your claims 
that your work might not get funded this time round. I fear I have only 
a small understanding of how these decisions are made, but I truly could 
not see how a product of such high profile and quality as your software 
could be overlooked. Particularly given the huge number of committed 
users and the exciting imminent developments to which you refer in your 

As you know, I have taught the use of Bioinformatics tools for the last 
18 years. Your software has been the mainstay of my practical sessions 
for all of this time. I have had the pleasure of introducing your 
package to a great number of its users in the course of these years. 
Your software has been uniformly well received as reliable, well 
documented and easy to use. In particular, people have enjoyed your 
interactive graphical displays (far in advance of any rival software 
that I have used) and the way that your package can be easily integrated 
with software from other sources (I am thinking particularly of phred, 
phrap etc. for sequencing project management and the EMBOSS package for 
sequence analysis). This integration often enabling easy access to 
software whose native interface is crude. In the case of the EMBOSS 
package, your software also enhances the programs output by adding the 
advanced graphical features of your package.

If work is truly to cease on the package, I will regret not seeing the 
release of your new assembler which James has enthusiastically described 
to me on several occassions. Your ideas on the use of read pairs, 
confidence values and dealing with repeats sounded very exciting. Also, 
I had looked forward to the first official release of your new "long 
sequence" alignment program. I have already generated useful results 
with the test versions. Also, I was looking forward to using James's new 
automatic finishing suggestion tools once they had completed testing at 
the Sanger Centre.

Even more regretable will be the abandoning of your impressive work on 
tools for people involved in mutations studies (largely Mark's work I 
beleive). These features have generated great interest in the sequencing 
courses we have run since their inclusion in the package. On several 
occassions I have even been asked to show people these features during 
courses aimed at a more general audience. I can assure you that the 
ceasation of this work will be sorely regretted by the increasing number 
of people involved in this kind of work.

Personally, as you know, I was particularly following your progress with 
Kathryn's spin program and all the new ideas (particularly Yaping's work 
on the "sequence editor") you planned to incorporate in the near future. 
I saw this, together with the EMBOSS package, as the most promising 
combination of software for people wanting to run sequence analysis 
programs on their own workstations whilst (with the SRS capabilities 
incorporated into EMBOSS) accessing sequence databases remotely. This 
would be particularly powerfull once the EMBOSS people can be persuaded 
(as I am confident they will be) to produce a windows compilation to 
work with your well established windows version. I think I can claim 
myself to be "devastated" at the loss of this possibility as I intended 
to build a complete set of new course material around a combination of 
the Staden and EMBOSS packages running on personal LINUX and Windows 
workstations. I am convinced that teaching this combination would have 
been the way to dissuade people from wasting funding intended for 
research on hugely expensive commercial software packages.

Finally, it is a shame that your suggestion that the package be made 
open source was rejected. Of course your package has commercial 
potential, but I do hope the MRC now realise that recognising this fact 
is not sufficient. Their last attempt to commercialise your programs 
appeared to benefit no-one. It did however delay access to a windows 
version of your programs to everyone for a number of years. However, I 
feel sure they will have benefitted from their unfortunate experiences 
and will do a much better job this time?

yours, still hoping for a sensible outcome,

David Judge

Staden Package Administrator wrote:

 > Hello,
 > You are on the list of people with licences for our software. I am
 > sorry to have to inform you that the Staden Package is no longer
 > available or supported as the MRC has decided to withdraw our funding.
 > Last year I submitted, to MRC, a three year grant proposal of 443k,
 > almost all of which was to pay salaries. The application gained
 > extremely positive referee reports and the MRC Molecular and Cellular
 > Medicine Board awarded it their highest banding for both past and
 > proposed work. Despite this, and with knowledge of the large number of
 > groups who are going to be badly affected, the MRC has decided not to
 > fund us. The current funding finishes at the end of April - just a few
 > weeks - and James Bonfield, Kathryn Beal, Mark Jordan and Yaping Cheng
 > will lose their jobs and receive no redundancy pay.
 > Before we saw the favourable referees reports I asked MRC if, in the
 > event of our funding being cut, the package could be made Open Source
 > so that we and others could continue to develop and support it even if
 > no longer working for MRC. This seemed to us the best way of
 > safeguarding users and the careers of the group. MRC refused, saying
 > the package had potential commercial value.
 > The official who phoned to tell us the funding decision said he had
 > "devastating news". For us this is certainly true. I have been working
 > on various versions of the package for over 25 years, James for 11 and
 > Kathryn for 7. It is also very frustrating as we had so much work
 > nearly ready for release.
 > If this decision is going to affect the work of you and your
 > colleagues, or if you have any other comments or suggestions please
 > reply to this email and, if you think it might help, send a copy to
 > the MRC Chief Executive George Rada george.rada at headoffice.mrc.ac.uk
 > Rodger Staden

David P. Judge            Tel   : +44-1223-333614
Room G12-13,                 FAX   : +44-1223-333992
Department of Genetics,   Email : dpj10 at mole.bio.cam.ac.uk
University of Cambridge,
Tennis Court Road,

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