EMBOSS: Project Meeting (Mon 6th August 07)

Attendees

EBI: Peter Rice, Jon Ison, Mahmut Uludag, Martin Senger,
Sanger:
Visitors:
Apologies: Alan Bleasby, Shaun McGlinchey, Rodrigo Lopez, Tim Carver

1. Minutes of the last meeting

Minutes of the meeting of 25th June 2007 are here.

2. Software Development

Software development for EMBOSS was frozen at the last meeting in preparation for release 5.0.0.

2.1 Other development

Following a user request, Mahmut has started to review possible XML output formats, for sequences and reports/features.

Peter recommended Paul Gordon's XML page in Calgary for a list of known formats.

Martin is working with Mahmut on JAX-WS use for SoapLab 2. Shaun's ACD parser is still needed, but a preliminary release of SoapLab 2 can go ahead without it.

3. Administration

3.1 Release 5.0.0

Alan produced the release on July 15th.

4. Documentation and Training

4.1 Books

Jon has drafted the AJAX development sections. Examples will be inserted by hand with the aim of generating them for future updates.

The developer book has separate sections for ACD inputs and for programming using AJAX data structures.

Some AJAX function name cleanup is still required.

The other remaining large section is EMBOSS command line usage for the user book.

5. User queries and answers

We have a request to read sequence data from PDB files. Peter will investigate.

6. AOB

6.1 BOSC and ISMB

Peter attended the Bioinformatics Open Source Conference in Vienna where he gave a talk on EMBOSS. This was followed by ISMB/ECCB (also in Vienna) where the EMBOSS demo was again given to a packed room.

Peter also made contact with the authors of ViennaRNA and MIRA fragment assembly system.

6.2 Accelrys non-support of GCG

Peter reported that Accelrys have issued a statement to all their licensees annoucing the dropping of support for GCG from June 2008, and recommending EMBOSS as a replacement.

Peter has joined an active discussion on the bionet.software.gcg newsgoup (also the info-gcg mailing list) where users are debating their alternatives, and are especially ineterested in the continuing development of the SeqLab interface which was originally available as "GDE". It will be much easier for the remaining GCG users to migrate to EMBOSS if we can support GDE/SeqLab, but this depends on Accelrys finding some way to release the code.

7. Date Of Next Meeting

The next meeting is on Monday 20th August.