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The status of the Staden Package

Staden Package Administrator staden-admin at arran.mrc-lmb.cam.ac.uk
Thu May 1 00:54:29 EST 2003

As most of you will know despite it receiving excellent referee
reports and the highest possible banding the MRC recently declined to
fund my grant application to continue the development of our package
at the MRC Laboratory of Molecular Biology (LMB).  Thanks for all your
messages of support and outrage, but the decision has not been

I feel that to solve the licencing problems which would have arisen
with the current release of the package the best solution is to make
available a licence which will enable the package to run on any
machine in perpetuity. MRC have agreed we can do this and the licence
file is now in the ftp site and should be used to replace your
existing file(s).

We also obtained permission to make a final beta release of the
package available. This contains current projects in various states of
completion, some of which are already, or would soon have become
important new components of the package. Please see the Release Notes
for details. This release requires no licence file and is in the ftp
Further information is available at
In order for the package development to have continued at LMB the
collective knowledge and effort of the whole group was required.  MRC
have declined to fund that, but they have now agreed with my
recommendation that the package could become Open Source.  However
this only makes sense if it is certain that there are sufficient
resources available to make it a success. For this to be so requires
enough people volunteering to work on the package on the necessary
platforms and to add their changes back. The whole operation also
needs a coordinator. I request that users discuss the form that an
open source licence should take and volunteer their services to help
in this effort via the bionet.software.staden newsgroup (or the WWW
gateway at http://www.bio.net/). Some of the people emailing have said
they were willing to pay to keep the package going.  If the
volunteered resources are insufficient it may be necessary to resort
to some fee paying system.  Again this should be discussed via the
newsgroup, as can any other ideas for trying to keep the package going.
The staden-package and staden-admin emails are unlikely to be manned
after April.  James has taken a position at the Sanger Institute where
he will continue to work on parts of the package. Kathryn, Mark and
Yaping are looking for work.  Their email addresses are in the package
web site.  At present I have no firm plans.
Unless things change unexpectedly, you are on your own now and need to
help one another via the newsgroup. There are enough of you to make it
succeed, but it's up to you.
Personally I hope the package can continue to be useful and is
developed further. From your emails it is clear that, like us, you see
that there is much that needs doing and that the package is the ideal
platform for many of the interesting and important new sequence
related projects that lie ahead. I felt that with the power and
flexibility of gap4, plus a new assembly engine and finishing methods,
in combination with our mutation detection tools and extensions to
spin, we were about to create an even more powerful system for the
Thanks for your support.
Rodger Staden

Staden Package Administration         mailto:staden-admin at mrc-lmb.cam.ac.uk
MRC Laboratory of Molecular Biology,  http://www.mrc-lmb.cam.ac.uk/pubseq/
Hills Road,                           
Cambridge,  CB2 2QH, UK.              

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