EMBOSS: Project Meeting (Fri 12th December 2003)


HGMP: Gary Williams, Hugh Morgan, Jon Ison, Lisa Mullan
Lion: Thomas Laurent
Cambridge Uni:
EBI: Peter Rice

Apologies: Alan Bleasby Rodrigo Lopez Tom Oinn Martin Senger

Minutes of the last meeting

Minutes of the meeting of 28th November 2003 are here

1. Action points

1.1 From this meeting:

1.2 From previous meetings:

EMBOSS Ontology commit (PMR, 2003-11-28)
Convert graphics to grout (PMR, 2003-09-19) postponed to 2.9.0
newcoils/pepcoil merged program (PMR, 2003-11-28)

1.3 No longer required:

2.8.0 release (AJB, 2003-11-28)
Release done, 30th November 2003.

2. Software Development

2.1 ACD enhancements

Peter has added new checks to acdvalid and revised ACD files. These were announced on the emboss-dev list. A new "additional" section should contain all "additional" options. Acdvalid now tests which section each qualifier is in. For boolean switches (like -plot) that are used to turn on/off other qualifiers, there is a new "toggle" ACD type which works exactly like blloean but can have different acdvalid checks.

Future checks in acvalid will include missing knowntype for "string" qualifiers, which will either need a knowntype definition, or be converted to a more specific (or a new) ACD type. To be done for 2.9.0

Jon has made updates to rocplot - top be committed early in 2004

3. Documentation & Training

4. Administration

4.1 AJB reports

Alan has EMBOSS working on an AIX 5.2 machine with 4 IBM power processors.

Alan is expecting a new HP dual-boot HP-UX/Linux-64 machine to replace the current HP-UX machine. Thsi will be the first chance to configure EMBOSS for 64-bit Linux.

5. User queries and answers

Gary's current list reviewed. Most new issues were already answered.

6. CCP11 Software Steering Committee

Jon reported from this weeks' CCP11 steering committee meeting. The Software Steering Committee plans to meet in Hinxton in January. It was proposed that they should try to meet after the EMBOSS meeting on Friday 23rd January. Claude and Hgh should present their work, Tim should present Jemboss, andthere should be an overview of EMBOSS for the new software development panel members. Topics to include future CCP11 development under the next grant.

7. Promoting EMBOSS at ISMB

Peter and Lisa aer proposing tutorials (see next item).

EMBOSS can be shown at a software demo - probably a 1-hour slot to include Jemboss

EMBOSS needs to be included in BOSC - Jon and Peter to investigate the requirements for BOSC> Peter volunteered to do a talk.

EMBOSS CD's can be prepared using funding from the EMBnet quick guide and possibly other sources.

The EMBOSS programming course scheduled for July may be moved to Glasgow before ISMB

Birds of a Feather (BOF) sessions will be a good way to gather EMBOSS users and developers together, and to introduce potential contributors.

Jon volunteered to coordinate ISMB-related efforts.

8. Format for ISMB Tutorial

Lisa has circulated a proposal for an EMBOSS developers tutorial. It was agreed to limit the tutorial to a half day, and to cover the main topics from the programming course.Peter is proposing a tutorial on EMBOSS installation, administration and configuration, including various EMBOSS interfaces. Tim will cover Jemboss. Martin will cover SoapLab.

Peter and Lisa will coordinate these two applications - to be submitted today.

9. AOB

Gary asked about the possibility of retiring one or more CpG island programs to "make check". Gary to ask about the current use of these programs on the mailing lists.

10. Date Of Next Meeting

Next meeting in the New Year, to be held at 9.30 on January 9, 2004, Pompeiian Room, Hinxton Hall