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EMBOSS: Project Meeting (Fri 20th August 2004)
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Attendees
RFCGR/HGMP:
Alan Bleasby,
Jon Ison,
Gary Williams,
Claude Beazley,
Hugh Morgan
Lion:
Sanger:
EBI:
Peter Rice,
Jaina Mistry,
Lisa Mullan
Visitors:
Apologies:
1. Minutes of the last meeting
Minutes of the meeting of 23rd July 2004 are
here
2. Software Development
2.1 Jemboss
Tim has added a keyword search for the 1-line descriptions of
applications, and a favourites menu for user preferences and the top
10 most used applications, updatable by users. This is saved between
sessions.
2.2 Diffseq
Tim requested an update to diffseq to check on sequence
differences that affect the proteintranslation. Gary will look
into the code.
2.3 EMBASSY Phylipnew (Phylip 3.6)
Jaina has successfully converted 33 out of 35 programs ni her
Masters project. Only a few bugs remain to be fixed. The remaining
programs are "drawtree" and "drawgram" which Peter will convert before release.
Phylip 3.61 is now available.
3. Documentation & Training
3.1 Papers
A paper on the Jemboss alignment editor has been submitted.
Jon's Protein Science paper has been accepted. All the programs
are in EMBOSS and domainatrix. Future work will concentrate on ligands
and protein-protein interactions.
4.2 User survey
Jon is looking for companies and industry users for the user
survey.
So far over 600 replies have been received in the original text
format.
The user survey is now in the form of a web page. A further 200
replies have been received bvy this route. It should be easier for
users to complete - and easier to process the results.
Peter has a script to process the text forms, whcih can be
adapted to save results in web format and further process both sets of
replies.
Strong letters of support have been receieved from two UK universities.
4. Administration
No items.
5. User queries and answers
Gary's current list reviewed. Most new issues were already answered.
6. AOB
6.1 Wish list from ISMB
Jon collated the user requests from ISMB:
- The list of future applications needs updating to encourage other
developers
- We need a table listing all the web and other interfaces
- Some applications have algorithms that could be updated
- LSID support should be included in sequence input
- Abritrary limits in programs such as eprimer3 should be removed.
- Sequence quality information is useful for primer design - this
needs to be read from the appropriate sequence input formats where
available.
- A conversion course for GCG users could be useful. This was
requested by two major user centres, one in the UK and one international.
- Piping of data beween applications could be improved.
- One developer requested a way to read sequence objects from a
string. There are probably many other develoeprs who could benefit
from such a function, whcih should be easy to write (copy text string
to a file buffer, and read as normal).
- Support for DAS distributed annotation systems.
- Applications for SNP locations
- EMBOSS training materials collected from all available sources,
and a comparative review of EMBOSS training courses.
- Functions for RNA folding - look at the Vienna package. Should be
easy to convert to EMBASSY.
- New section in application documentation for a description of the
results, or a review of the curent output file descriptions which can
be quite basic.
- Customisations for local sites - for example the Jemboss
favourites which is already available.
- EMBOSS updates without needing to rebuild Jemboss
- User project management facilities in Jemboss, similar to SeqWeb
and other Web GUIs.
- Seqhound from BluePrint for database access
7. Date Of Next Meeting
Next meeting at 9.30 on September 3, 2004,