EMBOSS: Project Meeting (Mon 7th August 2006)


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

1. Minutes of the last meeting

Minutes of the meeting of 10th July 2006 are here.

2. Software Development

2.1 XML and DOM Library

Alan is working through Hugh's old ajgraphxml code which used a different DOM library. This had a massive code bloat effect and unwanted dependencies on libxml2 and in turn glib.

For XML work Alan has looked at Microsoft's VDW Virtual Desktop for HTML Authoring which is free and has a good XML editor.

Peter will check XMLspy pricing for machines at EBI and other options for home use.

2.2 Release 4.0.0

Alan reported that ViennaRNA was rebuilt. Peter noted that the online documentation for ViennaRNA needs updating to replace a few blank sections with a note to "see the original Vienna RNA documentation".

Peter has a fix for a reported bug in reversed sequence positions in dreg and fuzznuc. He also has an alternative way to resolve Henrikki Almusa's changes to make sure reports are not empty, by writing a header and tail when the report is closed. The existing 4.0.0 code has the problem that a search through an entire database currently reports no hits found for each sequence. 3.0.0 ignored sequences with no hits.

2.3 Other development

Alan has modified Eamino.dat to make alanine an aliphatic amino acid. Peter noted that the amino acid categories are hard-coded in pepstats and need to be derived from the data file.

Shaun is looking into Axis and JAX-WS for EBI webservices, starting with a simple service for water.

Mahmut has built SoapLab for EMBOSS 4.0.0 on a test server (emboss16). The current server is still running 2.8.0 - frozen to prevent service interfaces changing until EMBOSS command line qualifier names stabilised. However the underlying dispatcher was pointing to a release 2.9.0 installation. There is a memory leak in SoapLab, avoided for now by increasing the memory allocation for tomcat.

Tim reported extended EMBL features are working with Artemis in the modified splitter and union applications. Peter will aim to make include files for feature format definition files (Efeatures and Etags) so that Sanger can maintain a modified file with their extra source feature tags and other Artemis extensions.

3. Administration

3.1 Planning Release 5.0.0

Tim listed a few additions needed to make GFF version 3 feature tables fully compatible with the standard.

Alan plans to standardize the use of size_t and unsigned integers throughout the code to avoid compilation warnings.

3.2 Test systems

Alan plans further testing on the IBM and HP loan machines once the network switch is upgraded.

4. Documentation and Training

4.1 Books

Alan and Peter will meet Cambridge University Press to update on progress with the 3 books.

4.2 Training

Peter will contact possible sponsors for an autumn developers course outside Hinxton.

5. User queries and answers

The list was reviewed. All issues were resolved.

6. AOB


7. Date Of Next Meeting

The next meeting is on Monday 21st August.