EMBOSS: Project Meeting (Fri 6th February 2004)
Alan Bleasby, Gary Williams, Hugh Morgan, Jon Ison
Peter Rice, Martin Senger
Minutes of the last meeting
Minutes of the meeting of 9th January 2004 are
1. Action points
1.1 From this meeting:
1.2 From previous meetings:
MEME documentation is required (action AJB, 2003-02-21)
EMBOSS Ontology commit (PMR, 2003-11-28)
1.3 No longer required:
Prophecy documentation is done
2. Software Development
2.1 Staden open source
James Bonfield described the new open source release of the
Staden package> Staden is now available from staden.sourceforge.net
under a BSD licence. James Bonfield will be maintraining the package,
especially gap4 administration functions for use at the Sanger
The analysis tools such as spin are not currently maintained by
anyone. They have been popular with some EMBOSS users. Peter
volunteered to maintain the EMBOSS/spin interface, and will join the
Staden project on sourceforge.
Peter will check on the possibility of code reuse in EMBOSS
for some of the now non-maintained analysis functions.
Jon has rewritten the documentation and committed code, though
test data is still needed. A paper is in preparation.
Jon reported domainer has a new option to use index numbers or
original numbers for residues.
2.4 Regular expressions
Alan asked whether regular expressions could be used to test
list/selection choices where there is a need to test for only one
Peter will investigate adding an ACD function for these tests.
3. Documentation & Training
4.1 Release 2.8.1
Peter has implemented an "append" attribute for output files, and
corrected Nexus sequence format input.
Alan has completed modifications to EMBOSS and Jemboss for
5. User queries and answers
Gary's current list reviewed. Most new issues were already answered.
All EMBOSS ISMB tutorials were rejected, possibly too specialised for
the audience. Several people plan to attend ISMB and can run ad hoc
7.1 NCBI Blast
Peter reported that NCBI have (again) promised to provide
documentation of the ASN.1 header format for blast databases.
Peter asked everyone to register with Sourceforge and to pass
on their usernames so they can be added to the EMBOSS project.
James explained that "developer" rights are needed to update
web pages over ssh.
It was agreed that the web pages could start as a mirror of the HGMP
pages and then be updated later.
7.3 Student projects
Peter plans to offer an MRes student place for this
summer. Project suggestions to Peter please.
18. Date Of Next Meeting
Next meeting at 9.30 on February 20th, 2004,
Shared Facilities, Hinxton