|
EMBOSS: Project Meeting (Mon 8th November 10)
|
Attendees
EBI:
Peter Rice,
Alan Bleasby,
Jon Ison,
Michael Schuster
Visitors:
Apologies:
Mahmut Uludag,
1. Minutes of the last meeting
There were no meetings for the previous 3 weeks because too many of the team were away.
Minutes of the meeting of 11th October 2010 are
here.
2. Maintenance etc.
2.1 Applications
Alan is looking at eprimer3 where there is a possible
incorrect definition of a directory rather than a full path top a
file.
2.2 Libraries
Peter has recommitted code without the missing functions which
caused problems for the mEMBOSS build.
Alan recommended building under CYGWIN to see messages from
undefined functions.
2.3 Other
Peter has added EDAM.obo and DRCAT.txt to the emboss/data
directory. We may also need a local copy of the sequence ontology (SO)
but for now we can get by using a few internally defined SO terms.
Mahmut is supporting a Japanese Jemboss user.
3. New developments
3.1 Axis2C
Alan has built a new mEMBOSS with all Windows 32-bit
modifications and Axis2C. This involved installing the NASM free
assembler and "mingw" as another compiler for a related install (a
more fully featured compiler than Borland).
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.
3.2 Data access methods
Peter has committed changes to support the new data types.
Alan noted that the Ensembl API is incomplete for support of
Ensembl 58. has some pending updates which are
commented in the source code.
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.
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.
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.
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.
Installation has started on Mahmut's machine for 32-bit and 64-bit
versions.
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.