EMBOSS: Project Meeting (Mon 10th January 11)


EBI: Peter Rice, Alan Bleasby, Jon Ison, Mahmut Uludag, Michael Schuster

1. Minutes of the last meeting

Minutes of the meeting of 13th December 2010 are here.

2. Maintenance etc.

2.1 Applications


2.2 Libraries

Mahmut has removed one of the AJAX ajdas source files (replaced by DOM parsing) to avoid confusion over source file naming.

2.3 Other

Peter noted that the next plplot library release (5.8.0) will not be out for some time, according to the latest information on their developer mailing list.

Alan suggested contacting Alan Irwin of the plplot project about the source code for the 4.99j library release we first included in EMBOSS to help track the changes we made.

3. New developments

3.1 EMBOSS configuration

Peter described the changes implemented in December. Full details will appear in a new WIKI page emboss.open-bio.org/wiki/Latest_Developments

A new configuration file emboss.standard is installed for all users with a standard set of databases (EDAM, DRCAT and TAX), a standard set of resource definitions for finding these and other databases, and a standard set of server definitions.

Server definitions describe a server which has attributes passed on to all databases, and a cachefile describing each database available from the server. The cachefile is in two locations, one system-wide (with emboss.standard in the share/EMBOSS install directory) and the other in the user's ~/.embossdata directory. Both versions are timestamped, with the most recent copy having priority.

Sets of new applications use EDAM, DRCAT and TAX, including a set of woss* applications to search for EMBOSS applications by EDAM annotation, and a set of drfind* applications to search DRCAT by EDAM annotation, and a set of edam* applications to search EDAM by specific namespaces. A set of onto* applications can also search EDAM and other OBO ontologies.

New ACD datatypes obo, resource and taxon and their output equivalents allow retrieval of entries from these new standard databases.

A new ACD datatype text allows retrieval from a general text database, using any text-based access method that returns an open file. SRSWWW and other methods will need to retrieve single text entries to support this as there is no parser to separate multiple entries in one open file.

3.2 DBX index files

Peter has created DBX index files for the new databases, but thee (especially for TAX) can be very large binary files which seriously upset the CVS server.

It was agreed that the files should be deleted and some other way to handle them should be found. Options include the user generating the files as a post-install step, and distributing them by some other method such as rsync for developers.

Alan and Peter will look into possible ways to reduce the sizes of the index files.

4. Administration

4.1 Hardware

The new backup disk is installed and working. The defective backup disk can now be removed.

The EMBOSS machines were shut down with the computer room shut down over the weekend but are not available this morning. Alan has contacted the systems group. A manual backup was done at 15:30 just before the shutdown.

5. Documentation and Training

5.1 Books

The cover designs look good. Alan has read through the Admin Guide and made notes. There are a few index errors where terms can be 2 pages out, or where there is a better alternative page reference for an index term.

The first author will be responsible for reviewing each of the books.

6. User queries and answers

All done.

7. AOB

The Christmas meal and birthday celebration for Alan and Jon will be on Friday 14th.

8. Date Of Next Meeting

The next EMBOSS meeting will be on Monday 17th January.