EMBOSS: Project Meeting (Fri 3rd August 2001)
Alan Bleasby, Gary Williams, Lisa Mullan, Tim Carver, Ranjeeva Ranasinghe, Waqas Awan
1. Matters Arising
EMBOSS 2.0.0 includes:
1. Feature table reading: EMBL, Swissprot and PIR feature tables are
handled by rewritten library routines. Tables can currently be
read and written (or interconverted) in native or GFF formats.
For the applications programmer an internal key/value pair
structure greatly simplifies use.
2. Report Handling: Stub code to enable application output to be
selected in (a range of) standard output report formats has
been included. The feature tables above use one of these
formats. More report formats will be added during the lifetime of
the 2.x.x series. Release 3.0.0 of EMBOSS will mark the completion
of this phase.
3. Code purification: All library code and applications are tested
for memory handling before release. To our knowledge the code does
not leak a single byte in normal use. A "purify" script is provided
(mainly for developers).
4. Quality control: code has been written, supplied and used for
testing code prior to release. This ensures that applications
produce the same output (where appropriate) after changes to
the library etc. A QA test script is provided/
5. Code modification: almost all the source code has been revamped
since the 1.x.x series. All functions, including those in
applications, have unique names. This now allows you to navigate
the entire source code using SRS.
6. Protein structure code has been added and, although not yet
complete, this marks one of many new directions for applications.
EMBOSS 2.0.1 fixes an indexing problem with DBIGCG and split entries.
It also incorporates handling of the Selex format as used in the
HMMER 2.1.1 has been converted for EMBOSS and appears in the
download directory (ftp://ftp.uk.embnet.org/pub/EMBOSS/) as
the 'embassy' package HMMER-2.1.1.tar.gz
Alan was at the ISMB meeting and held an ACD workshop and Open Source
demonstration. He has incorporated HMMER and selex format into EMBOSS.
Release version 2.0.1 with a fix for dbigcg.
Lisa was at the ISMB meeting, giving a training talk about EMBOSS.
Tim s working on the java interface to EMBOSS. Discussions with Peter
and Thomas about the new section and endsection implementation.
Gary has commited listor which writes a list file of the logical OR of
two sets of sequences. He is working on estscan to find ORF.
Thomas has been modifying SRS to integrate EMBOSS programs.
Peter was also at the ISMB meeting. With Thomas will be produce a list
of changes to the ACD files to incorporaate sections. The sections are
likely to be
2. Date Of Next Meeting
Next meeting to be held on Friday 3rd August , HGMP