EMBOSS: Project Meeting (Dec 6th 1999)

Attendees

Sanger Centre: Peter Rice, Ian Longden, Richard Bruskiewich
HGMP: Alan Bleasby, Gary Williams, Mark Faller, Val Curwen, Sinead O'Leary
EBI:

1. Matters Arising

Gary collected further contributions for the Xmas kitty. It was agreed that there will be a new kitty from January 1st.

2. General progress on release 0.0.4

Will Gilbert has confirmed that his MSE editor can be released as the first EMBOSS Associated Directory member under the GNU GPL. MSE is already included in the CVS tree and is therefore available through the CVS server. Ian will build a separate distribution for it.

Peter has added "const" throughout ajstr and ajfile. No code changes were needed.

Alan has fixed some memory leaks in AJAX. All strtok calls have been replaced by ajSysStrtok to allow for future parallel code.

Peter will convert ACD help information to tables for the documentation, as for antigenic. Any extra information should be added directly to the ACD files.

Richard plans to parse ACD files directly for the ACEDB interface.

Peter has committed a first draft of dbigcg to index GCG databases. dbiflat (for flat files) and dbiblast (for blast1 and blast2 databases) will follow soon as they need very little additional code.

Ian is working on an EMBASSY version of Joe Felsenstein's PHYLIP package. There is a large number of programs to convert, and various small problems to be resolved.

Richard would like a batch option added soon fpr al applications. "-batch" should generate a command line and submit to a script which would in turn be locally modifiable. Peter will tackle this together with the help tables. There may be some special handling (or restrictions) needed for standard input.

Mark is implementing seqret under disGUIse.

"prima" is now included in Makefile.am with sorting fixed to give a consistent ordering on all Unix systems.

Two new melting options have been added to ajdan, a new data set for thermodynamic calcultion, and a new routine to calculate the product melting temperature.

Peter has added a new attribute "pattern" for strings in ACD so that a regular expression can be provided to validate the input string. It was originally used for date processing in dbigcg.

In order to force protein or nucleic acid sequence types, new qualifiers "-sprotein" and "-snucleic" will be added. To avoid a near clash of names, "-sprompt" will be renamed to "-sask".

3. Any Other Business

None.

4. Next meeting

Next meeting Monday 13th December, 11:00am, usual place.