This is a multi-part message in MIME format. You need a MIME compliant mail reader to completely decode it. --=_-=_-EKPDHAPAANABMCAA Content-Type: text/plain; charset=us-ascii Content-Language: en Content-Length: 249 Content-Transfer-Encoding: 7bit It seems my web-based email doesn't used fixed-width fonts. I am re-sending my previous email as a plain *.txt file. Cheers! Serge Need a new email address that people can remember Check out the new EudoraMail at http://www.eudoramail.com --=_-=_-EKPDHAPAANABMCAA Content-Type: text/plain; charset=us-ascii; name="proposed_action_plan.txt" Content-Language: en Content-Length: 2546 Content-Transfer-Encoding: 7bit Hello all! May I suggest the following courses of action for the next few weeks? May June July 1 2 3 4 1 2 3 4 1 2 3 4 DESIGN Recruitment (ALL) *-----* Formation of a Design Committee *-* Design Work *-----*-------* 1st Draft * Approve Final Design * DEVELOPMENT Interface with ext. *---------------------* web servers (Sean) (e.g. BLAST@NCBI) Writing parsers *---------------------* (Nico) Miscellaneous code *---------------------* c/o Serge Study other BioXXX *---------------------* to aid design (Greg) Test/critique *---------------------* existing code (Andres, Frank, other SF members) The design phase may appear to be too long for some, but this is a long-term project (which hopefully will outlive us all) and viewed in that context, two months isn't too big a deal. Also, the DEVELOPMENT that goes in parallel with DESIGN is meant to fill the appetite of people more inclined to coding. We can identify modules that could be written in a way that would be easy to integrate into whatever final design is adopted by the end of July. I vote to have such development focus on code that interface with external data or applications (local or web-based) because that seems to interest most of our potential users. What do you think? This early, I have something for the last group (Andres, Frank, etc.) to look at: the xlevdist() method. The xlevdist() method is my own version of PHP's levenshtein() function. They both return an integer that is a measure of the difference between two strings. I wrote xlevdist() because of the 256-character limit of levenshtein(). You can view the source code at the CVS repository (GenePHP folder, etc.inc.php file, inside the SeqMatch() class, if I'm not mistaken.) I have two problems with this. One is that it *SEEMS* to give wrong answers when given a very short string and a very long one (as arguments). (Well, I hope it's just my imagination!) My second problem is this: how should function xlevdist() be modified to allow for user-defined weights (for substitution, deletion, insertion operations such as the BLOSSUM matrix)? The algorithm for levenshtein is described here: http://www.merriampark.com/ld.htm#WHATIS It also has code written in Java that implements the algorithm. Many thanks! Regards, Serge --=_-=_-EKPDHAPAANABMCAA--