EMBOSS: Project Meeting (Mon 17th August 09)


EBI: Alan Bleasby, Jon Ison, Mahmut Uludag
Apologies: Peter Rice

1. Minutes of the last meeting

Minutes of the meeting of 10th August 2009 are here.

2. Maintenance etc.

2.1 Applications

Alan released an updated mEMBOSS.

2.2 Libraries

Peter reported that we need to patch 6.1.0 to fix the problem with SwissProt DE lines reported last week.

If other fixes are identified in time they can be included in the patch.

2.3 SoapLab

Mahmut has changed SOAPLAB jobs exiting with a timeout to report "Terminated by request" rather than report having finished successfully. The timeout has now been set to 5 hours as planned.

Mahmut has completed an update of the SOAPLAB-related sentences in the EMBOSS documentation.

3. New developments

4. Administration


5. Documentation and Training

5.1 Books

Alan has completed proof reading the Developers book. This coming week he will look at prefaces/appendixes/etc and check, along with Mahmut, that the Jemboss chapter conforms to the GUI supplied with 6.1.0. He will get a final confirmation from Lisa that she's OK with the highlighting in the Jemboss chapter.

Jon has updated the list of interfaces. New interfaces and descriptions have been added (Mahmut will write a section on Spinet). The JPRED image in the books was corrupted and has been deleted. All the <systemitem> markup tokens have been checked. Some have been removed (e.g. format names), others have been converted to more specific tokens (e.g. application names). The capitals in proper nouns have been made consistent (e.g. FASTA). More text boxes have been added (e.g. ). In the bibliography Jon has added a new list of papers that cite EMBOSS. He noted that there are 570 such papers in PubMed.

5.2 Website


6. User queries and answers

Mahmut reported that a hanging problem with nthseq in SOAPLAB has gone away after EBI external services applied patches from the ftp server.

7. AOB


8. Date Of Next Meeting

The next meeting will be on Monday 24th August.