From owner-metabolic-reg@net.bio.net Mon Sep 20 22:03:00 1999 Path: biosci!newsfeed.stanford.edu!newsfeed.berkeley.edu!demos!news.stack.serpukhov.su!not-for-mail From: "Alex Sel'kov" Newsgroups: bionet.metabolic-reg Subject: Re: Universal format for storing pathways and models Date: Tue, 21 Sep 1999 01:58:09 +0400 Organization: Not organized Lines: 68 Message-ID: <937860976.418122@sirius.shome.eu.org> 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> <937852968.19861.0.nnrp-07.c2de3927@news.demon.co.uk> NNTP-Posting-Host: sirius.stack.net X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Cache-Post-Path: sirius.shome.eu.org!unknown@lamb.empproject.com X-Cache: nntpcache 2.3.3 (see http://www.nntpcache.org/) > Is there a public specification of EMP, I've never seen one even though I've > looked. In 1994 EMP was published on CD and companion book contains fromat descripsion. Parsers also availiable. But anyway we need to develop "commertial grade" formal specifications, programmers API, user guide e.t.c. Long delay with so trivial steps also trivial - funding. Only in this year we can seriously think about development, (I mean not prototypes and pilots but normal development: with schedule, internal standarts, documented production process, professional team e.t.c) and most of urgent things will be completed by the end of this year. > 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. > DBsolve, by example :) Not a big news, because DBsolve and EMP/MPW have common roots. I can't say that we have good format or we have "community- frendly" products. I can say exactly opposite - we have unsatisfactory format at present time (with some kludges like SGML-like netlist for metabolic pathways exporting). But we have also good understanding how such things must be done. By the way, you know any simulation software wich can import metabolic pathways, stoichiometric matrixes e.t.c. from KEGG or Boehringer? ;) > > 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. > And why not to think about other possible applications? Visualisation software? Database search engines? Another software packages? > > 2. "What?" > > What what? > What to do. Formal specifications which explains concepts. > > 3. "How?" > See pmb document. > > I see. This is implementation. I can say only one thing - this solution is perfectly fits if you need exchange with a very few model by occassion. But when we speak about thousands of models with many various tools working simuntaniously on the same data - you can't base your work on formats like pbm. Definitely not. In any case I can't say that pbm is "bad" or "good". Simply such format unfotutantely can't solve our (by example) problems. Regards, as .