EMBOSS: Project Meeting (Mon 6th September 10)


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

1. Minutes of the last meeting

Minutes of the meeting of 23rd August 2010 are here.

2. Maintenance etc.

2.1 Applications

Jon has completed the EDAM annotation of the EMBASSY packages.

Documentation has also been improved for the one line descriptions and short descriptions for EMBASSY packages.

2.2 Libraries

Alan is investigating whether there is a satisfactory way to configure gsoap. The library requires that the user defines a handful of functions in their own code. This presents problems in linking legitimate applications that do not require those functions. One can end up with either missing functions or circular dependencies. The gsoap library sadly does not allow registration of callback functions.

Jon reported that documentation has now been produced for the true minimum/failrange/maximum ACD mechanism, allowing developers the choice of how applications behave when given inappropriate values.

Michael is making the Ensembl functions available to the EFUNC/EDATA system. He is making extensive function naming changes in order to fit the EMBOSS naming schema/rules.

2.3 Other

The Trend Micro anti-virus software has reported a false-positive hit for mEMBOSS- Investigations by David Bauer have shown that the false signature comes from the embossdata.exe file. He has informed Trend Micro and Alan has made the file available to them.

3. New developments

3.1 Access methods

Mahmut has been investigating DAS, pending the resolution of the GSOAP issues mentioned above. He has working development code to integrate single fully specified DAS sources via DB definitions. He is investigating making the definitions more generic as is done for (e.g.) ensembl database specifications, allowing one definition to be the root of several sources. Parsing of the returned XML from ajseqread will either require ajdas.c/h files in the core library or callbacks using code in the ajseqdb library. It is currently coded using the former less-convoluted, and therefore preferable, approach.

It was also noted that HTTP access is becoming more commonplace in the AJAX libraries. Alan can investigate moving the HTTP primitives, from the ajaxdb library, into the core library. That would provide an opportunity to integrate the new URL code and integration of username/password code into the HTTP access methods.

3.2 EDAM

Jon has implemented some minor fixes to EDAM. He has also provided notes for the EDAM/EMBRACE continuity web site. He highlighted the forthcoming conference on Semantic Web Applications and Tools for Life Sciences in Berlin. An abstract for EDAM/BioXSD has been submitted for a workshop he and Matus are holding there.

4. Administration

4.1 Systems

Alan reported the power failure in the main machine room which killed the EMBOSS file server. All data had to be recovered from backup onto local disc and the backup software redirected accordingly. All server services are now being provided by local workstations pending the arrival of a replacement server.

5. Documentation and Training

5.1 Books

C.U.P. have provided typeset example chapters for the books. It was noticed that section numbering was too deep in some places in the Developer's Guide. Also, tables were not referenced from the fixed text. Jon has provided C.U.P. with corrected files.

6. User queries and answers

Alan will look at the possibility of users' ".embossrc" files being read when using an authenticating Jemboss server.

7. AOB


8. Date Of Next Meeting

Next week is the GMOD meeting in Cambridge. The next EMBOSS meeting will be on Monday 20th September.