EMBOSS: Project Meeting (Fri 8th March 2002)


HGMP: Alan Bleasby, Jon Ison, Gary Williams, Waqas Awan, Lisa Mullen, Hugh Morgan, Tim Carver, Damian Counsell
Lion: Peter Rice, Thomas Laurent, Bijay Jassal
EBI: Rodrigo Lopez, Adam Lowe

1. Matters Arising

EMBOSS 2.3.0 released This version of EMBOSS contains two new programs (whichdb and interface) Problems addressed include wildcard database searches failing under some circumstances. Also, missing files in file-list queries no longer cause termination of the programs. The new program 'jembossctl' should not be run by typical users. It is a slave program for a forthcoming Jemboss server. This will hopefully be announced soon.

EMBOSS 2.3.1 released This is a bugfix release. The ChangeLog appears below. As usual, all errors are added to the quality control suite to ensure they don't recur.
est2genome fixed for large alignments (over 40Mbase for est * genomic sequence length) sequence reading for ABI files fixed (and selex files tested) genbank feature input working pepinfo PNG output larger to make the text readable (only affects PNG output) empty sequence file input fails gracefully empty sequence input fails gracefully (and only needs one ^D from stdin)

Alan reported that there have been two new EMBOSS releases (above). He has been working on the setuid part of Jemboss with Tim.

Peter tried to fix PNG problems by using the latest plplot png drivers, but abandoned them as there were too many changes. Instead pepinfo is fixed by a code fix specific to ther plplot PNG source code. He has fixed 3 bugs in est2genome that are apparent for very large sequences (an appropriate qa test has been added). A bug in genbank feature reading has been fixed. Genbank feature tables and tests for selex and abi files have been added to qatest. Helen Davidson (Edinburgh) requested an EMBOSS alternative to gcg assemble.

Jon has been testing the pdbparse application for generating clean files of protein coordinates. He is doing a major documentation excercise on all the protein structure-related applications.

Adam has been working on btrees and dynamic hash tables for indexing. He has not embossified this stuff yet. He has been thinking about updateable indexes and a dispatcher for farming emboss jobs to multiple machines.

Rodrigo has been looking into a port of fasta, but will probably wait a new version is coming out soon. He is working on a port of radar (an application that looks for specific types of repeat in protein sequences) for EMBOSS.

Gary is working on an application for querying local or remote srs servers for sequences.

Lisa reported that a 1/2 day gcg -> emboss conversion course was well received :-) She has been promoting the use of emboss.

Hugh reported that his xml outputing interface has been incorporated into ajax. Basic graphics functions including graphing and dna plotting (cir and lindna) are done. He has converted the iep application to use his software.

Tim has been been working on his jemboss server. He has had a lot of email from people who have been setting it up. He has been testing the jemboss installer.

Damian has been working on an application called structalign for structure-based sequence alignments. He requested library code for 2D arrays of structures. He has been thinking about the biocobbler course.

Thomas has incorporated eprimer3 into SRS. pepinfo now works with Peter's PNG graphics fix.

2. A.O.B.

There were general calls for a wrapper to BLAST and for an implementaion of AMAS.

3. Date Of Next Meeting

Next meeting to be held at 10.00 on Friday 22nd March, HGMP