EMBOSS: Project Meeting (Mon 23rd May 11)
1. Minutes of the last meeting
Minutes of the meeting of 16th May 2011 are
2. Maintenance etc.
Peter fixed tcode to report results for non-coding nonsense
data by expanding the y-axis to cover the threshold values.
Peter fixed graphics applications to correctly report separate
XY plots for multiple input sequences. The application example results
need to be carefully checked before the release.
Peter has fixed tests for dbigcg and ontoget in
the Visual Studio builds.
Martin has prepared a new test distribution which Mahmut
has tested on the London Data Centres. Some issues with message part
attribute names need to be discussed. The latest SoapLab should be
3. New developments
3.1 Access methods
Mahmut has updated DAS and wsdbfetch access. As dbfetch returns
metadata in the same form as wsdbfetch we can auto-generate the server
cache files. Dbfetch access provides the same data resources as
wsdbfetch without the Axis2C dependency.
Mahmut has extended CHADO access with some example GFF
files. Sequence-region lines are added to the output.
FlyBase CHADO access is under development, and not yet included in the
QA tests. It should be usable by the release.
Michael noted the need to map Ensembl and GFF features. In
Ensembl all features are chromosome based but can be mapped to other
Michael has updated to Ensembl 61 and committed the code
changes. Server cache files are committed for Ensembl and
Ensembl genomes with 100-400 databases in showserver plus alias
names. The databases are dumped in alphabetical order, as are the
Ensembl 62 is now out. Most changes are in variations. Some more
testing is needed for the API.
Michael would like help in assigning EDAM links to Ensembl
Mahmut looked into MRS support. The support for formats is not
good but there is help on the query interface.
3.2 New applications
Peter has extended textget to report text from sequence
or obo entries where the appropriate format name has a text parser
that can find the end of an entry. Some cleanup is needed to remove
attempts to read these entries as sequence or obo directly.
Applications that create server cache files need a standard naming
convention for the release. They should also have a standard interface
to ask for server name or other details.
Mahmut suggested adding comment lines to server cache files to
explain how the file was created.
Peter proposed adding a variation object to ACD and AJAX to
make use of the Ensembl API and for reading/writing VCF file format.
Mahmut suggested explicit support for paired-end reads for NGS
Peter would like to update the EMBOSS version number to
"220.127.116.11" on all systems so that QA tests give consistent
results. This failed on Unix as the extra digit is not valid for the
build utilities. Peter will consult Alan on the best
Mahmut is interested in installing Ubuntu as a windows
application using Wubi. Michael offered to demonstrate
the use of VirtualBox by Ensembl to test Unix distributions under
5. Documentation and Training
6. User queries and answers
8. Date Of Next Meeting
Next week is a public holiday. The next EMBOSS meeting will be on
Monday 6th June.