EMBOSS: Project Meeting (Mon 8th November 10) |
Minutes of the meeting of 11th October 2010 are here.
Alan recommended building under CYGWIN to see messages from undefined functions.
Mahmut is supporting a Japanese Jemboss user.
Axis2C involved installing 9 more DLLs which were compiled because the binary distributions failed to work. It was necessary to recompile without SSL support. Adding SSL may be necessary for some pharmaceutical industry users. Alan will try to reinstall with SSL to test. The problem may be connected to the OpenSSL library naming when it is compiled from source. The build fails to load an axis DLL if SSL is included.
Alan noted that the Ensembl API is incomplete for support of
Ensembl 58.
Michael is reviewing the EFUNC and EDATA documentation errors
for the Ensembl API. Most are now fixed, with 6 modules to be
completed. A correction has been made for a 32-bit size issue in
mEMBOSS. Windows builds use the Visual Studio Express 2010 32-bit
edition.
Michael was at a human genetics meeting last week. There was
interest in using a virtual machine to provide a Linux VM with
APIs. Alan uses Fedora which has a virtualization option. VMs
include Linux or Solaris.
Peter is considering ways to easily define dbx* indexed farm
files, perhaps with a database alias list.
Matus and the others in Bergen are happy. There is discussion on
dropping the topic branch because some topic terms are really
operations. Topics were originally defined as a simple tree for the
BioCatalogue but maybe top level operations terms will meet this need.
The word used in definitions have been made stricter (identification,
prediction, analysis, etc.).
The format branch has 5 top level terms now. These cover XML, HTML,
part-HTML, text and datatype-specific.
Installation has started on Mahmut's machine for 32-bit and 64-bit
versions.
3.3 EDAM
Jon is working on a major revision to be released as
beta_10. The current release has too many top-level terms. New higher
level terms have been added and the remainder reorganised into a
hierarchy under a few broader concepts.
3.4 Data types
Michael would like a variation data type to support users of
Ensembl and UniProt.
4. Administration
4.1 Advisory Board
Peter reported on last week's SAB meeting. He will send the SAB
copies of the presentations, and notes on the discussions. These need
to be reviewed as soon as possible and sent to the SAB members to
help in preparing their report.
4.2 Interim report
The report has been submitted to BBSRC.
4.3 Fedora
Alan noted that Fedora 14 was released on schedule. There are
some issues with PMCIA devices, but this is not a problem for the
EMBOSS machines.
5.0 Documentation and training
5.1 Books
Jon is building indexes for the 3 books. We can generate an
index with Word document page numbers. We need to transform these into
the numbers for the typesetter's proof hard copy pages. When the
indexes have been built, we can limit them to a reasonable number of
words or items and highlight them in the text.
6. User queries and answers
All done.
7. AOB
None.
8. Date Of Next Meeting
The next EMBOSS meeting will be on Monday 22nd November. Next week
there is a clash with a next-generation sequence conference.