EMBOSS: Project Meeting (Mon 18th August 08)

Attendees

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

1. Minutes of the last meeting

Minutes of the meeting of 4th August 2008 are here.

2. Software Development

2.1 Applications

Alan has started work on deletion of entries in the B+ tree dbx indexing applications. Deletion is implemented for the top half of the tree, he is now working on the leaf nodes and secondary indexes.

Peter is checking the modifications made to the profiled code to make sure that all results match the current release.

Peter has reviewed the data files used by dan to improve documentation and to standardise the free energy values to 25C. The free energy values are ignored by all code at present and are recalculated for a specific temperature.

2.2 Libraries

Alan will modify the pattern matching code to use a brute force method for variable length matches so that all possible matches can be returned. The current library code returns only the first match for each start position. Peter will update the Perl-compatible regular expresssion library code to version 7.7. This may allow us to return all variable length matches more efficiently using the library.

2.3 SoapLab

Mahmut has updated the SoapLab WU-Blastservices to use the new jdispatcher endpoint.

Modifications to enable LSF support were not trivial as the SoapLab service description refers to a Java classname. Martin has been contacted for advice.

The ExecuteThread class executes jobs, used standard input and records standard output and standard error. The basic iomplementation has been tested apart from temporary input files (e.g. for mwcontam) as this needs a tmp directory visibvle on both systems. Tests used EMBOSS5. External services have now installed EMBOSS 6.0.1.

Legacy derived services support should be dropped. The inputs need a web servcie call for each attribute. Only a few clients have used these services. Mahmut will try to contact the users.

3. Administration

3.1 Release 6.0.0

Alan has added patches and updated mEMBOSS. These include multiple sequence support in jaspscan, a fix to digest and a fix for PCRE missed matches in fuzznuc

4. Documentation and Training

4.1 Books

Jon is marking up the text of Lisa's chapter updates.

4.2 Publications

Jon has drafts of EMBOSS papers, using text from the manuals.

5. User queries and answers

6. AOB

7. Date Of Next Meeting

The next meeting is on Monday 1st September