From owner-comp-bio@hgmp.mrc.ac.uk Mon Apr 30 21:26:50 2001 Return-Path: Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 9CE0E17B7A for ; Mon, 30 Apr 2001 21:26:45 +0100 (BST) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id B044317B89 for ; Mon, 30 Apr 2001 21:26:34 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6023) id 0BA6F17B7F; Mon, 30 Apr 2001 21:26:14 +0100 (BST) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 415F317AA4 for ; Sat, 28 Apr 2001 18:19:17 +0100 (BST) Received: from sprettur.isnet.is (sprettur.isnet.is [193.4.58.19]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 2433517AA9 for ; Sat, 28 Apr 2001 18:19:02 +0100 (BST) Received: from teapot30.bigpond.com ([139.134.5.3]) by sprettur.isnet.is (8.11.1/8.11.0/isnet) with ESMTP id f3SHIxT95586 for ; Sat, 28 Apr 2001 17:18:59 GMT (envelope-from news@teapot30.bigpond.com) Received: (from news@localhost) by teapot30.bigpond.com (8.8.8+Sun/8.8.8) id DAA14905; Sun, 29 Apr 2001 03:05:14 +1000 (EST) To: bionet-biology-computational@moderators.isc.org Message-ID: <3AEAFB61.77E48909@bigpond.com> From: Mark Addinall Organization: That's IT X-Mailer: Mozilla 4.75 [en] (X11; U; Linux 2.2.16-22 i686) X-Accept-Language: en MIME-Version: 1.0 Newsgroups: bionet.biology.computational Subject: Re: Systems Biology Markup Language - Level 1 References: <9c20i3$f4d@gap.cco.caltech.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: newsfeeds.bigpond.com 988477453 144.134.88.147 (Sun, 29 Apr 2001 03:04:13 EST) NNTP-Posting-Date: Sun, 29 Apr 2001 03:04:13 EST Date: Mon, 30 Apr 2001 21:26:14 +0100 (BST) Sender: owner-comp-bio@hgmp.mrc.ac.uk Precedence: bulk Herbert Sauro wrote: > > We would like to announce the release of the final specification for Level 1 > of SBML (the Systems Biology Markup Language). It is available from > > http://www.cds.caltech.edu/erato > > SBML is a description language for simulations in systems biology. It is > oriented towards representing biochemical networks that are common in > research on a number of topics, including cell signaling pathways, metabolic > pathways, biochemical reactions, gene regulation, and many others. SBML is > the product of close collaboration between the teams developing BioSpice > (http://gobi.lbl.gov/~aparkin/), Gepasi (http://www.gepasi.org/), DBSolve > (http://websites.ntl.com/~igor.goryanin/), E-Cell http://www.e-cell.org/), > Jarnac (http://members.tripod.co.uk/sauro/Jarnac.htm), StochSim > (http://www.zoo.cam.ac.uk/comp-cell/StochSim.html), and Virtual Cell > (http://www.nrcam.uchc.edu/). > > The motivations for developing SBML stem from the current inability to > exchange models between biochemical network simulation/analysis tools. The > lack of a common standard for exchanging models poses two problems for > researchers. > > First, models cannot be shared directly between tools because the file > format used by each tool is unique and nontransferable. This makes it > difficult if not impossible for a researcher to exchange models. Second, > when a simulator is upgraded or is no longer supported, models developed in > the `old' system become stranded and unusable in any other simulator. This > later scenario has already happened on a number of occasions, with the > resulting loss of the model to the scientific community. With the recent > roliferation of new biochemical simulators, this situation can only get > worse. > > We have kept the base definition of SBML as simple as possible, so that > simulator developers will not find it too difficult to implement support for > SBML in their tools. > > This base definition, called SBML Level 1, is the result of merging > modeling-language features from a number of existing software packages, and > encompasses the minimal information required for biochemical models. > Additional structures and facilities will be added to SBML in subsequent > levels; among the features we are developing for SBML Level 2 are > hierarchical models and spatial characteristics. By freezing subsets of > features in SBML definitions at incremental levels, we hope to provide the > community with stable standards to which software authors can design to, > while at the same time allowing the simulation community to gain experience > with the language definitions before introducing new elements. > > The effort perhaps closest in spirit to SBML is CellML > > (http://www.cellml.org). CellML is an XML-based markup language designed for > storing and exchanging computer-based biological models. The constructs in > CellML tend to be at a more abstract and general level than those in SBML > Level 1, and describe the structure and underlying mathematics of cellular > models in a very general way. By contrast, SBML is closer to the internal > object model used in model analysissoftware. Because SBML Level 1 is being > developed in the context of interacting with a number of existing simulation > packages, it is a more concrete language than CellML and may be better > suited to its purpose of enabling interoperability with existing simulation > tools. However, CellML offers viable alternative ideas, and the developers > of SBML and CellML are actively engaged in ensuring that the two > representations can be translated between each other. With thanks, could you or I cross post this to aus.science? Very interesting indeed. Regards, Mark Addinall .