From owner-metabolic-reg@net.bio.net Tue Oct 05 07:07:00 1999 Path: biosci!newsfeed.stanford.edu!newsfeed.berkeley.edu!dispose.news.demon.net!demon!news.demon.co.uk!demon!fssc.demon.co.uk!not-for-mail From: "Herbert M Sauro" Newsgroups: bionet.metabolic-reg Subject: Re: how do I define the l mtarix from MCA in maple? Date: Tue, 5 Oct 1999 09:00:51 +0100 Message-ID: <939110454.6941.0.nnrp-08.c2de3927@news.demon.co.uk> References: <7taqr6$ip8$1@reader1.wxs.nl> NNTP-Posting-Host: fssc.demon.co.uk X-NNTP-Posting-Host: fssc.demon.co.uk:194.222.57.39 X-Trace: news.demon.co.uk 939110454 nnrp-08:6941 NO-IDENT fssc.demon.co.uk:194.222.57.39 X-Complaints-To: abuse@demon.net X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2014.211 X-Mimeole: Produced By Microsoft MimeOLE V5.00.2014.211 Lines: 44 I'm sure there is more than one way to skin the cat here (apologies to cat lovers but I'd be interested to learn of other cat skinning approaches with regard to the link matrix) but one way to compute the L matrix is to use the following algorithm: Algorithm: L = tr (echelon (tr (m))) where tr is the transpose, echelon computes the fully *reduced* row echelon and m is the stoichiometry matrix. I'm not sure what the syntax would be in matlab. Also I think there is a way of using svd which is probably the recommended way but I haven't explored this avenue. Not that the reduction of the stoichiometry matrix to a fully reduced echelon may involve row exchanges which means you *must* carry out the same exchanges in the stoichiometry matrix. Note that the freeware indigo package will carry this operation out for you automatically and the algorithm above is a line taken from an indigo script.. Available from http://members.tripod.co.uk/sauro/biotech.htm See the download page. Hope that helps Herbert Sauro FRANK BRUGGEMAN wrote in message news:7taqr6$ip8$1@reader1.wxs.nl... > I'm a PhD student at the Free University of Amsterdam and I'm working on > mathematical modelling of biochemical pathways and I'm trying to implement > reder's method for metabolic control analysis in Maple but uptill now I have > not been able to implement the computation of the L-matrix satisfactorily. > Does anyone know how I can calculate the link matrix in maple? > > Thank you very much for your time, your sincerely Frank Bruggeman > > Please reply to, frankb@bio.vu.nl > > > .