EMBOSS: Project Meeting (Mon 12th November 07)


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

1. Minutes of the last meeting

Minutes of the meeting of 1st October 2007 are here.

2. Software Development

2.1 Applications

Alan is still tracing a dbxflat indexing bug that only appears when EMBL release files are processed in a particular order. The crash is in removing an item from a list, but is probably caused by an error elsewhere in the code.

Peter is working through the differences between phylip 3.6 beta and the latest phylip 3.67 to bring the EMBASSY package up to date. Many of the changes to 3.61 were already included in the current PHYLIPNEW release.

Alan will check on the status of testing the MIRA fragment assembly EMBASSY code by the original author.

We have a volunteer to create an EMBASSY package for MUSCLE multiple alignment. So far he is writing the ACD file and testing all MUSCLE options work as documented. Alan's ACD wrapping approach can be used to write the remaining code.

2.2 Libraries

Peter has modified ACD processing so that when standard input is redirected the user cannot be prompted for information and the default value is used.

2.3 SoapLab

Martin released SoapLab2 as a beta version on 28th October. SoapLab2 is aimed at providing much improved support for service providers, and has been rewritten for robustness with the removal of CORBA (AppLab) and Perl utilities. Installation needs only java and ant. SoapLab2 can be deployed in two configurations: as Axis services (axis1deploy for RPC/encoded services) or as JAX-WS (jaxdeploy for document/literal services). Martin is now working on a simple web page front-end (Spinet) to present the inputs and outputs of the SoapLab2 web services, with help text as a mouseover and red annotation for mandatory inputs. Spinet uses stylesheets so customising the appearance is easy.

Remaining tasks include documentation of how to write SoapLab2 ACD files and how to set up the Spinet web page front end.

Mahmut has deployed SoapLab2 at EBI. The new server has been very stable. The old server will need AppLab to be restarted soon. SoapLab2 has 142 EMBOSS tool tests and 50 tests for EMBASSY services.

2.4 Other development


3. Administration

Fedora 8 was released on 8th November. Alan will update the workstations.

Alan suggested drawing up a list of tasks for the release next year. One major task to consider will be updatable database indexes and a further survey of database indexing algorithms.

4. Documentation and Training

4.1 Books

Jon will have complete drafts for all 3 books in the next 2 weeks. Alan and Peter will read through and update text as needed.

Jon will create templates for autogenerated text, update the contents pages, test cross references are valid, and generate everything in the format needed by the publisher.

Peter will update the current parsing scripts to generate the required text. Some new scripts will be needed to extract documentation for QA testing and other parts currently not well documented.

4.2 Website


4.3 Training

Jon presented an EMBOSS session to 40 EMBL predoctoral students. Many of them were unable to use a commandline interface. We need to provide clear examples of how to use programs with various interfaces to illustrate why the command line is the richest way to run the applications.

5. User queries and answers

Jon has added 3 new queries to Sourceforge in the past month.

6. AOB


7. Date Of Next Meeting

The next meeting is on Monday 26th November.