From owner-comp-bio@hgmp.mrc.ac.uk Tue Apr 24 00:43:48 2001 Return-Path: Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 981EA17AFE for ; Tue, 24 Apr 2001 00:43:47 +0100 (BST) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id D503E17AFD for ; Tue, 24 Apr 2001 00:43:45 +0100 (BST) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6023) id 688A717AFE; Tue, 24 Apr 2001 00:43:42 +0100 (BST) Received: from localhost (localhost [127.0.0.1]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id B879A17AE8 for ; Mon, 23 Apr 2001 20:55:42 +0100 (BST) Received: from mr1.ash.ops.us.uu.net (mr1.ash.ops.us.uu.net [198.5.241.86]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id CCBDD17AE4 for ; Mon, 23 Apr 2001 20:55:37 +0100 (BST) Received: from gap.cco.caltech.edu by mr1.ash.ops.us.uu.net with ESMTP (peer crosschecked as: gap.cco.caltech.edu [131.215.139.43]) id QQkmap17364 for ; Mon, 23 Apr 2001 19:55:34 GMT Received: (from news@localhost) by gap.cco.caltech.edu (8.9.3/8.9.3) id MAA15503; Mon, 23 Apr 2001 12:41:57 -0700 (PDT) To: bionet-biology-computational@uunet.uu.net From: "Herbert Sauro" Newsgroups: bionet.biology.computational Subject: Systems Biology Markup Language - Level 1 Organization: California Institute of Technology, Pasadena Message-ID: <9c20i3$f4d@gap.cco.caltech.edu> X-Priority: 3 X-MSMail-Priority: Normal X-Newsreader: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Date: Tue, 24 Apr 2001 00:43:42 +0100 (BST) Sender: owner-comp-bio@hgmp.mrc.ac.uk Precedence: bulk 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. .