EMBOSS: Project Meeting (Mon 4th August 08)

Attendees

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

1. Minutes of the last meeting

Minutes of the meeting of 7th July 2008 are here.

2. Software Development

2.1 Applications

Jon has identified some applications from Mike's PhD project that can be added to EMBASSY.

2.2 Libraries

The PCRE regular expression library ha sbeen through several releases since it was included in EMBOSS. Peter will update the PCRE library from 4.3 to 7.7. This may allow reporting of all matched to patterns with a range of lengths which current find one match for each possible start position.

2.3 SoapLab

Nothing to report.

3. Administration

3.1 Release 6.0.0

Release 6.0.0 was produced on schedule (15th July 2008).

Release 6.0.1 was released the same day to fix issues with graphics and the JEMBOSS interface to mEMBOSS.

4. Documentation and Training

4.1 Books

Jon has finished XML validation and checking links.

4.2 Website

No updates

4.3 Publications

Jon will write a first draft for an EMBOSS paper covering the main package.

Other papers were also discussed.

5. User queries and answers

There is an outstanding question on fuzznuc results showing only a subset of overlapping wildcard pattern matches. This is caused by the PCRE regular expression library - Perl-compatible expressions find one match for such patterns. See the PCRE library update above.

Phylip sequence format restricts input files to 10 character identifiers. Longer identifiers cause a failure to read the data but no message identifying the problem. This can be fixed by testing for a valid file with longer identifiers, and by testing phylip output for long or non-unique identifiers.

A user reports that allversusall uses a local alignment and can report very short local matches.

6. AOB

Peter has been at BOSC and ISMB in Toronto where there was much interest in EMBOSS. He will report in detail at the next meeting.

7. Date Of Next Meeting

The next meeting is on Monday 18th August.