EMBOSS: Project Meeting (Mon 18th February 08)


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

1. Minutes of the last meeting

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

2. Software Development

2.1 Applications

There is a new release of JASPAR. Alan has updated the JASPAR applications jaspextract and jaspscan to understand the new directories and changed fields. JASPAR now has 3 new sub-databases for conserved non-coding elements (CNE), RNA polymerase II binding sites (POLII) and splice sites (SPLICE).

Peter has a faster version of dbxflat completed. it will need further testing with Alan before deciding which changes to include in the release.

2.2 Libraries

Jon noted that there are some additional sequence formats supported by MUSCLE that should be included in EMBOSS, and it would be useful to check the "clustal" output format matches what MUSCLE expects.

2.3 SoapLab

Mahmut has been answering questions from SoapLab users, and updated the website documentation.

2.4 Other development

Alan reported that the mEMBOSS XP-64 build is working. However, the user who reported an installtion problem with XP-64 has now moved jobs so is unable to test it. For Jemboss it uses 32-bit Java (XP-64 has both included). The Microsoft Visual C++ run-time libraries are bundled in with the installer. Installation instructions are simpler and now only warn against including space characters in the install path.

Alan is bundling a new mEMBOSS version with installed data.

Shaun is making progress with his ACD parser. This has a new grammar to expand abbreviated keywords, and populates a hash table of all captured keywords, then uses this to populate a SoapLab data structure. The parser uses a JAXB tool with Java-XML binding to generate a model consistent with the SoapLab DTD for an AnalysisInstance. It is then easy to generate XML for a populated instance. Peter will look into developing a DTD to keep in step with future ACD changes.

3. Administration

3.1 Patch to 5.0.0

Peter will copy over the patches for sequence reading.

4. Documentation and Training

4.1 Books

Alan is reading through the current draft copy.

4.2 Training

Peter will present a half day tutorial on EMBOSS for users at an EBI course "From sequence to gene: genome resources at the EBI" from March 5th-7th. Mahmut will attend and help with the practical session. See http://www.ebi.ac.uk/training/handson/course_080305_genes.html for details.

4.3 Website

Some pages on the website need to be updated, for example the list of support systems. Text from the books can be used once it has been checked.

Jon is reviewing the application documentation. So far he is about half way through.

5. User queries and answers

dbxfasta is failing for one user at SIB. Peter will investigate.

Sourceforge has been updated with the current set of user queries.

6. AOB

7. Date Of Next Meeting

The next meeting is on Monday 3rd March.