Staden Package: new 1997.1 release

James Bonfield jkb at mrc-lmb.cam.ac.uk
Mon Dec 8 10:45:21 EST 1997

The latest release of the Staden Package (1997.1) has just been
released. The most important features of this release are listed
below, although the complete changes (of which there are many more
than listed below) are on our web pages at:


For a quick pictorial overview of the most recent components, see


James Bonfield

1997.1 Release Notes Summary

An entirely new program named Nip4 is now available. This is the first
release of our replacement for nip (the Nucleotide Investigation
Program). The key features are a good graphical user interface, methods to
import external data and algorithms, and direct communication with Gap4.

Nip4 is designed to allow tight integration of third parties
algorithms. The organisation of the code makes it straightforward for other
groups to add their own algorithms to the programs. Coupled with our use of
dynamic loading this means that these additional functions can be made
available as compiled code by their authors, hence allowing them to retain
complete control of their distribution. We believe this will be an
attractive option for many people developing new algorithms: they can
concentrate on the algorithms without worrying about the user interface,
and they can make them available as an additional option to a (we wish!)
widely used program. Further documentation on the processes involved will
be made available in the new year, however we are interested in feedback on
this topic now.

*	Many bug fixes

*	Automatic contig ordering function

*	Find internal join (and other) result auto-navigation

*	Improved editor search methods (by quality, discrepancies, and
	from file).

*	Communication mechanism to allow direct manipulation linking
	of cursors in Gap4 and external programs. (This is currently
	possible between Gap4 and Nip4).
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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