EMBOSS: Project Meeting (Fri 6th February 2004)


HGMP: Alan Bleasby, Gary Williams, Hugh Morgan, Jon Ison
Lion: Thomas Laurent
Sanger: James Bonfield
Cambridge Uni:
EBI: Peter Rice, Martin Senger

Apologies: Rodrigo Lopez Tom Oinn

Minutes of the last meeting

Minutes of the meeting of 9th January 2004 are here

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 Institute.

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.

2.2 Rocplot

Jon has rewritten the documentation and committed code, though test data is still needed. A paper is in preparation.

2.3 Domainer

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 option. Peter will investigate adding an ACD function for these tests.

3. Documentation & Training

4. Administration

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 FreeBSD systems.

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 demonstrations.

7. AOB

7.1 NCBI Blast

Peter reported that NCBI have (again) promised to provide documentation of the ASN.1 header format for blast databases.

7.2 SourceForge

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