Not specifically. There is no reason why SBML models could not be stored in a database, nor is there any reason why you could not use SBML as a schema. However, this was not the motivation for creating SBML. An SBML model is meant to encode a consistent view of knowledge of a biological system. SBML is not meant to encode a large set of potentially conflicting knowledge about such a system.

The Systems Biology Markup Language (SBML) is a machine-readable format for describing qualitative and quantitative models of biochemical networks. It can also be used to express the interactions of biochemical networks with other phenomena. By a ''biochemical network'', we mean a system consisting of biochemical entities linked by chemical reactions that alter, transport and/or transform the entities.

Database identifier annotations can be created using CellML metadata in SBML Level 2; see the specification for CellML Metadata, in particular Section 4.10, ''Biological Entity''. SBML elements derived from SBase have a metaid attribute, which should contain a value unique to the SBML document. RDF elements can use this value as a reference to the specific element. Its possible to use a simpler form of database identifier annotation than that shown in the CellML specification.

Yes. You may create and modify database schemas (i.e. structures) via code. Both SQL commands and DDA objects may be used. VistaDB 3 supports CLR Procs which let you store managed .NET source code (C#, VB.NET) in the database, thereby providing even more power and flexibility than Stored Procs. TSQL Stored Procs will be added in a later release (see roadmap).

No. Since applications may rely on a certain standard structure, this should not be modified. For this reason, MySQL AB cannot support bugs or other issues which result from modifying INFORMATION_SCHEMA tables or data.

Yes. Any just about any third party HTML template (or your existing site HTML) can be applied to AspDotNetStorefront as a skin, giving you control over your store's appearance. We also have skin designers who are familiar with our product.

The overall structure of the database tables that store information: user profile data, content metadata, or pure structured information. In the simplest case, a database schema has a single database table of user information. Each record (row) within this table might represent a unique customer, with each field (column) representing relevant customer information (address, city, phone number, etc.).

The Schema is a blueprint of all objects in the domain and when first created a default Schema exists which contains definitions for users, computers, domains etc. Because of this, you can only have one schema per domain as you cannot have multiple definitions of the same object. The default schema definition is defined in the SCHEMA.INI file that also contains the initial structure for the NTDS.DIT (storage for the Directory data). This file is located in the %systemroot%\ntds directory.

SBML is designed to enable the exchange of biochemical network models between different software packages. The aim is to (1) enable the enable the exchange of models between software tools with little or no human intervention, thus allowing the tools to be properly integrated; and (2) enable these models to be published in electronic form alongside, for example, peer-reviewed journal articles. The emphasis in SBML is on supporting quantitative models.

SBML model consists of a set of chemical entities linked by reactions that can transform one entity into another or transport entities between compartments. A compartment in SBML is a location having a defined size or extent (which may be in terms of volume, area, or length). Every chemical species in an SBML model must be located in a compartment. SBML can represent not only biochemical networks, but also quantitative models of interaction between these networks and other phenomena.

SBML originated out of a workshop on software platforms for systems biology held in the year 2000 with funding by the Japan Science and Technology Corporation (JST). The original authors were Michael Hucka, Andrew Finney, Herbert Sauro and Hamid Bolouri, but SBML is now very much a community effort. Please see Section 8 for more details about the history of SBML. See Section 7 about how you can participate in SBML's evolution.

The Systems Biology Markup Language is formally defined in specification documents (see Question 4.2).

SBML is being developed in a series of levels, where each level adds new features and fixes problems with the previous level. The lowest-numbered levels provide fundamental features that are common to all biochemical network models. Higher-numbered levels add more features that are specific to particular classes of tools. Any level can be used as a standard for interchanging models.

The Systems Biology Markup Language (SBML): A medium for representation and exchange of biochemical network models Hucka, M., Finney, A., Sauro, H. M., Bolouri, H., Doyle, J. C., Kitano, H., Arkin, A. P., Bornstein, B. J., Bray, D., Cornish-Bowden, A. , Cuellar, A. A., Dronov, S., Gilles, E. D., Ginkel, M., Gor, V., Goryanin, I. I., Hedley, W. J., Hodgman, T. C., Hofmeyr, J.-H., Hunter, P. J., Juty, N. S., Kasberger, J. L., Kremling, A., Kummer, U., Le Novère, N., Loew, L. M., Lucio, D.

First you have to fill the "relation", "table_coords" and "pdf_pages" configuration variables.

A Derby database is a group of schemas, each with its own set of tables, all of which are defined by the same data dictionary (the system tables in the SYS schema). On disk, the database is a set of data files (located in the seg0 directory) and a set of transaction log files (located in the log directory). Transactions cannot span databases, but they can span schemas in the same database.

Trac no longer has the schema in plain SQL since it was necessary to abstract the table creation in order to support other database platforms. However, the structure in db_default.py still provides a representation of the schema. To get a definitive schema for your install: prompt> sqlite3 /path/to/tracdata/yourinstance/db/trac.db sqlite> .schema

InterMine is an object-based query system that uses a PostgeSQL database. InterMine can work with any data model, for FlyMine we have a biological model that is based on the sequence ontology. InterMine is designed to allow you to adapt the data model easily for your own data. It also includes code to import data from several standard bioinformatics file formats and will soon be compatible with the chado schema.

No changes need to be made to the application's schema. DataXtend RE automatically adds its own Control and System tables to the existing schema for tracking change-capture and maintaining DataXtend RE meta data, respectively. Some other products also do not require database changes, but instead require applications to be specially rewritten to access the database through their proprietary method. Other products require significant database changes.

Yes. If your schema was not designed for replication you may have even more significant challenges than designing from scratch. You need to be concerned about the same issues as a new design but have a more limited set of options for dealing with design issues. In many cases your application will have to be coded to provide a solution.

The registration pages for the mailing list and the web forum are accessible from http://sbml.org/forums.

The list of tools supporting SBML has grown to over 100 at the time of this writing, and it is no longer feasible to maintain a list in this FAQ. Instead, we refer readers to the front page of the web site http://sbml.org, which gives a list of software and provides links to more information about them.

The BioModels Database provides a database of many dozens of models that have been published in the literature. The models in the database have been checked by humans to correspond to the publication and have been annotated with links to other data resources to make searching easier.

SBML Level 2 Version 1 was finalized in June 2003. SBML Level 2 Version 2 is in final draft stage and expected to be finalized in 2006. New development is oriented towards SBML Level 3.

The idea is that the units associated with every math entity in a model should be precisely defined, while at the same time allowing for reasonable default unit definitions. The set of math entities important in this regard includes variables, parameters and the result of equations.

We recommend SBML Level 2, despite the fact that at the moment more tools support Level 1, because Level 2 fixes known problems with Level 1 and we anticipate that Level 2 will be forward-compatible with Level 3.

Don't Panic. Few if any packages support all aspects of SBML. Depending on what you wish do with a model you can either ignore features that are not relevant to your tool or report errors when certain features are used. In most cases a simulator will simply report an error if it encounters a feature that it is unable to support.

SBML development has been and continues to be motivated and directed by the systems biology community. The process is managed by the SBML Editors (see next question), but they do so under the control of the community. The editors collect proposals for changes to SBML from the SBML Working Groups and from other groups and individuals, and then seek to establish a consensus in the community about how to proceed with the proposals.