EMBOSS: Project Meeting (Fri 12th November 2004)


RFCGR/HGMP: Alan Bleasby, Jon Ison, Gary Williams,
Sanger: Tim Carver
EBI: Peter Rice, Lisa Mullan, Amandine Schuurman


1. Minutes of the last meeting

Minutes of the meeting of 1st October 2004 are here

2. Software Development

2.1 ACD ontology

Peter described Amandine's student project. Amandine is a visitor from Namur in Belgium. She has been annotating ACD files with the relations between output files (and their contents) and input files and parameters.

Cases where the relationships are complex - for example, dependencies on selections and lists, or on boolean options, have been clearly annotated.

The results will be translated into ACD markup in a future release, and will also indicate (helped by acdvalid analysis) which applications are candidates for splitting into two or more simply-defined programs.

2.2 Developers Course Requests

Alan reported the following requests from attendees on this month's developers' course:

2.3 Domainatrix

Jon has added a function for all versus all alignments in Nucleus.

2.4 Access Methods

Peter has added a database access method for Seqhound services from BluePrint.

Peter has also added a similar database access method for Entrez utilities from NCBI.

Both are provided as beta versions in CVS.

2.5 Genetic Codes

Gary has checked and updated the genetic code files - NCBI had updated some of the minor start codons.

2.6 Jemboss

Tim has updated libraries for apache axis to version 1.4.2, to work with java 1.5.

2.7 Diverge request

Gary reported a request for a program like GCG's diverge.

3. Administration

No items.

4. Documentation & Training

4.1 PDB parsing paper

Jon has a solution for mmCIF output by using a Brookhaven utility to convert to PDB. He will look into providing mmCIF output format, and adding residue-level descriptions.

4.2 ASEAN Workshop

Peter and Lisa reported on the ASEAN course at CBI in Beijing.

5. User queries and answers

Gary's current list reviewed. Most new issues were already answered.

6. AOB

7. Date Of Next Meeting

Next meeting at 9.30 on January 14th, 2005,