EMBOSS: Project Meeting (Fri 12th October 2001)


HGMP: Alan Bleasby, Claude Beezley, Waqas Awan, Jon Ison, Lisa Mullan, Tim Carver, Hugh Morgan
Lion: Thomas Laurent, Peter Rice

1. Matters Arising

Alan has implemented 2D and 3D list sorting functions and a garbage collection function for lists. He has made changes to the function for calculating molecular weights for modified residues. He is working on messaging in EMBOSS.

Claude has added a function for getting help on emboss applications to the corba server. He is fixing some bugs (potential memory leaks).

Waqas has worked with Jon to implement the dichet application. Dichet creates a database of PDB heterogens in swissprot format from a raw text file provided by PDB, and counts the occurences of keywords (the heterogen names) in a directory of PDB files. Dichet has been committed.

Jon has finished coding for porting his PDB file parser into EMBOSS and has modified the program for parsing of heterogens (a new application called coorde will be committed soon). He has worked with Waqas on the dichet application (committed, see above). He has worked with Ranjeeva on seqsort (coding is finished but not yet tested). He has worked with Matt Blades (Leeds University) to modify the filtering and scoring options in the siggen application (new version committed). On behalf of Matt he committed an application called sigplot, for generating plots of the results of sigscan matches of a signature against a sequence database. Jon is testing coorde and will commit a working version soon.

Lisa has been modifying the HGMP introductory course for jemboss.

Tim has continued to work on jemboss and has prettified the program form derived from the acd files. He proposed a "gui" record in the acd definition to indicate whether a program should appear in jemboss or not.

Hugh has been investigating graphics for emboss. He suggested that emboss programs should generate xml output for graphics, with another program reading the xml, displaying the graphics and providing the interactivity. Java will be used for the front-end, and an opengl frame will be used within a java window for more complex graphics (e.g. 3d rendering).

Thomas is working on a script to write sections (input, required, advanced and output) for acd files.

Peter is working on list processing. He reported that memory leakage for feature tables etc has been fixed.

2. Date Of Next Meeting

Next meeting to be held at 10.30 on Friday 26th October, HGMP