EMBOSS: Project Meeting (Mon 7th July 08)


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

1. Minutes of the last meeting

Minutes of the meeting of 23rd June 2008 are here.

2. Software Development

2.1 Applications

Alan has modified restrict to report unknown enzyme names.

Jon has added ACD files and code stubs for several utilities to support users migrating from GCG. Peter is completing the code and adding documentation and tests.

The database indexing profiled code has not been completely tested. Release will be postponed until an interim release.

2.2 Libraries

Peter has tested and committed the refactored ajfile code. This completes the major revision of AJAX code in preparation for the developers' book.

2.2 Jemboss

Mahmut has made further improvements to Jemboss including Swing features, refactoring the main window so that resizing extends correctly. Preferences are now saved using Java persistency.

Button actions for directories are cleaned up and apply to the home directory, not to the results directory. This resolved a potential conflict with mEMBOSS on Windows.

Alan will pass on any further feature requests.

2.3 SoapLab

Mahmut noted an increase in SoapLab server jobs to over 1500 per day.

There is an issue with SoapLab error reports failing to include the error code.

3. Administration

3.1 Release 6.0.0

Alan is testing Jemboss new features.

Alan will retest mEMBOSS with the latest ajfile updates.

Alan has tried libtool 2.2 (we currently use 1.5.x). There are no major changes, and testing was successful on Linux, Irix, Solaris and MacOSX. However it failed badly on OSF so any upgrade will be postponed for this release.

EMBASSY package tests need to be completed so Alan can start to build the release distributions. Peter has added a new package myembossdemo to hold test programs and leave myemboss clean for developers. Documentation is needed for the new cbstools and iprscan applications.

Peter is preparing a poster for ISMB.

Alan has contacted Open Bio to ensure the FTP server logs will be preserved. Log files are no longer being rotated and the logfile contemts will be passed on to Alan.

3.2 Funding

As part of the follow-up to the review, Alan has drafted a paper on mEMBOSS.

Peter and Alan are working on a proposal to be submitted later this year.

4. Documentation and Training

4.1 Books

Lisa has sent in her sections and exercises. Additional figures and text have been contributed to the wEMBOSS chapter.

Jon has started XML validation on all files using the latest XMLmind. Paragraph usage and tag order/context issues are fixed.

4.2 Website

No updates

5. User queries and answers

Peter has fixed the mEMBOSS mbossdata issue with use of "cp" to copy files.

A user has noted problems with phylip format when the IDs are too long. This is strictly invalid, but may be made readable in a future release - there is not enough time to make changes for 6.0.0.

6. AOB

Mahmut noted a recent request from SoapLab2 users for an ACD file repository to store standard definitions for third party tools and CGI web pages for SoapLab users. There would be interest in contributing ACD files if EBI could host an archive.

7. Date Of Next Meeting

Peter will be away at ISMB in 2 weeks. There will be a meeting only if major issues arise with the new release.

The next meeting is on Monday 4th August. No new issues.