EMBOSS: Project Meeting (Fri 1st February 2002)
Alan reported that Phylip 3.6 will be released in the summer but the user interface will not change so we may as well proceed with its incorporation. esim4 has been partly debugged and will be incorporated as part of embassy. He suggested two sections of the web page for porting information, (i) "Has been ported to ..." (for hardware manufacturers who have provided a m/c) and (ii) "Reported to work on ..." (where there are reports that a port has been made but we have been unable to independently verify the claim). He has been helping Tim and Hugh with their work.
Peter has been debugging dbifasta and gcg database retrieval. He has adapted plplot so that it reports back to the program the files that have been written. He has cleaned up function headers in the library code and has ensured that all datatypes are documented. He reported that the reading of lists of sequences was broken but has been fixed. He has generated qatest data for seqret. Duplicate function names have been cleaned up. He will document sequence reading code next.
Thomas has been working on the integration of new EMBOSS programs into SRS. He has been fixing the broken graphical output of pepinfo, enhancing the graphical output etc. He has implemented a script for generating sections for acd files.
Jon has been coding tracing of database hits for psiblasts, seqsort, seqnr and alignwrap. He reported that the pdb parser is finished, including extensive diagnostics, but awaits thorough testing. He has written the pdbtosp application, which parses the swissprot:pdb equivalent table that is provided as a web page by the PDB authors, and writes the table in EMBL-like format database. He has written a new version of the scope application to cope with new format scop parsable files. The new application is called scopparse and reads raw scop parsable files and writes the database in an embl-like format file. He has written the interface application that reads coordinate files and writes files of INTER-chain residue-residue contact information.
Ranjeeva has written the scopseqs application, that parses the embl-like format scop classification file and writes in the same format a file to which domain sequence information derived from structure and sequence databaseshas been added. He is working on statistical methods for combinging the results of multiple database search methodologies.
Hugh has been working on an XML library for graphical output. He has created basic drawing routines including graph drawing. His next job is the integration of his code with EMBOSS.
Tim has been been working on his authenticated server, and has been adding code to ajjava for doing the authentication. He has set up jjl for encryption of the data, and has set up a server on ajbnet for testing of the data. He has written an install script for his jemboss server and has done gui, batch and cpu sections in the acd files.
Gary has been looking at querying local or remote srs servers for sequences.
Next meeting to be held at 10.00 on Friday 8th March, HGMP