EMBOSS: Project Meeting (Feb 15th 1999)

Attendees

Sanger Centre: Peter Rice, Ian Longden
HGMP: Gary Williams, Alan Bleasby, Sinead O'Leary, Thon de Boer, Mark Faller
EBI:

1. Matters Arising

None

2. Progress on Release 0.0.4

The HGMP CVS tree is set up. PR is running a copy at HGMP. IL will be added.

IL has tested the string library through purify and fixed several bugs and inconsistencies. Purify is now also installed at HGMP.

AJB would like to look further into the automake and autoconf files.

The current CVS tree is almost ready for release to EMBnet developers.

PR has not yet looked into the WISE code, but will do so to identify useful code for the EMBOSS libraries.

3. Documentation

TDB has a draft of ACD documentation. PR has provided comments and some additional data. This will be included, and the document added to the main Web pages.

PR proposed a simple syntax for conditionals:

ifeq: cmpname [ default: $(sequence.type) value: P
                true: blosum62    false: dnasimple ]

Separate "if" types could be defined for various conditionals. An "else" could be allowed to negate the prvious if, or it could be covered by the syntax above.

ACD examples are needed for applications that would make use of this.

4. New applications

The current list of applications (in the release, under development, and proposed) was reviewed.

All EGCG applications were reviewed. Some were defined as "obsolete". Some were already in EMBOSS (for example many are sequence conversion applications replaced by "seqret" and "seqretall"). Others were assigned either as needing replacement or as general functions that would be needed (for example "pattern matching"). In some cases they were assigned to external packages (e.g. CINEMA) to be integrated.

Most were assigned to HGMP for development. See the applications web pages for the full list.

5. Any other Business

Sequence output from applications could be in database format, producing a (possibly indexed) database from a set of output sequences. In this way, "seqretall" could become a general database building utility.

An EMBOSS database format could be included in this, together with GCG and blast databases.

6. Next meeting

Next meeting postponed to Tuesday 23rd February, afternoon, in the Sanger Centre Informatics meeting room. Exact time to be notified later.

Peter Rice, Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton Hall, Cambridge, CB10 1SA, UK.