From owner-metabolic-reg@net.bio.net Mon Sep 20 17:49:00 1999 Path: biosci!newshost.lanl.gov!arclight.uoregon.edu!hammer.uoregon.edu!newshub.northeast.verio.net!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: Universal format for storing pathways and models Date: Mon, 20 Sep 1999 19:42:46 +0100 Message-ID: <937852968.19861.0.nnrp-07.c2de3927@news.demon.co.uk> References: <40EF164E4C27D31192760000F847DF32519954@ukz206.ggr.co.uk> <937692632.667327@sirius.shome.eu.org> <7s216b$ug5$1@nnrp01.ops.uunet.co.za> <937750899.40114@sirius.shome.eu.org> 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 937852968 nnrp-07:19861 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: 47 Alex Is there a public specification of EMP, I've never seen one even though I've looked. Is there any simulation software that can import and export EMP? If so what sorts of things can the program do, I'd be interested. > From my point of view, we always have three questions: > > 1. "Why?" Because Gepasi and Scamp wanted to talk to each other. There have been a number of occasions when I wanted to run Geapis models but couldn't and I'm sure Pedro (Mendes) sometimes had the same problem but the other way round. > 2. "What?" What what? > 3. "How?" See pmb document. > > And when I see detailed answer only on question #3 I have strange feelings > that I miss something :) > > I don't think that such subset totally unrelated to us :) First of all EMP was > initially created to support cell clock modelling. Working on enzyme kinetics > EMP extention is one of our primary tasks now. We also have some pilot- > projects like http://wit.mcs.anl.gov/ERM/ (at this stage we decide > totally redesign this extension). Our metabolic pathway (and regulatory > pathway) extensions also need good presentaion format. > I'm personnaly wery interested in good format covering reactions. > But good format must deal with many things: support for easy database > storing and retrieval, support for visualization e.t.c. We have a long > development history and wasted many man/years (bad design, > incorrect desigions) so I can say that good solutions unfortunately > rare exist :) > > Regards, > > as Herbert .