EMBOSS: Project Meeting (Mon 12th May 08)


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

1. Minutes of the last meeting

Minutes of the meeting of 28th April 2008 are here.

2. Software Development

2.1 Applications

Alan has added an EMBASSY package wrapping iprscan with 12 applications including an HMM scan of Pfam called fprintscan. We can now drop pscan from EMBOSS as it is out of date. The package also includes wrappers to signalp and tmhmm with a very limited subset of options.

Alan has added signalp and tmhmm to EMBASSY. Note that these applications are not completely open. Academics can download the original executables, but commercial users need to apply for a licence. The DTU website in Denmark has other applications for antigenic sites and other motifs which could be wrapped in a new EMBASSY package.

2.2 Jemboss

A user reported problems with Jemboss installation. They were corrected by following the recommended install procedures.

When reporting the version number, Jemboss should show the version of the server.

Mahmut has worked through the first half of the Jemboss feature requests. Most related to graphics data and sequence list concepts.

2.3 SoapLab

Mahmut has corrected javascript validation for minimum and maximum values on the Spinet web interface. The changes will be checked with Martin later this week.

2.4 Other

Shaun has a parser which now handles basic ACD files including SoapLab's custom XML. The eclipse toolkit provides an extension point that can be used for scripting EMBOSS applications.

3. Administration

3.1 Patch to 5.0.0

3.2 Funding

Peter and Alan will present EMBOSS for an EBI internal review on 6th June in preparation for the next round of funding proposals.

4. Documentation and Training

4.1 Books

Peter has almost completed reading through the draft administrator's guide and will return it to Jon later this week.

Jon has received the draft of the wEMBOSS chapter and requested some more text and additional screenshots.

4.2 Training

4.3 Website

Jon has updated the application descriptions and is working through the algorithm documentation.

5. User queries and answers

No new issues.

6. AOB

Peter has submitted an abstract to BOSC and a poster to ISMB in Toronto. The conferences start just after the 6.0.0 release.

7. Date Of Next Meeting

May 26th is a public holiday. The next meeting is on Monday 9th June.