The popularity of systems biology has brought about a rise of interest in the computational modeling of biological networks. These can be metabolic networks, signaling networks, and others. It is natural for researchers to want to use the same computational models with different software tools. The Systems Biology Markup Language (SBML) has become the most widely-used common representation format for storing qualitative and quantitative models of biochemical reaction networks. At the time of this writing, nearly 60 software tools world-wide claim to support SBML, and the number has been growing every month. The high number of citations of the paper probably reflects the recent increase in activity in this area.

The paper is about a software technology, so in that sense, it is neither about a new discovery nor experimental methodology. However, it is definitely a technology useful to others. SBML is a machine-readable format for storing models in a software-tool-independent manner, allowing users to move models more easily between tools that store, edit or analyze biochemical reaction networks. SBML also makes it easier for researchers to develop such models collaboratively and then publish them in electronic form. Prior to the development of SBML, these models were often stored in proprietary formats, each associated with a specific tool.

Many biologists today, especially in the field of systems biology, are studying the chemical reactions occurring within the cells of living organisms in order to try to understand the molecules and processes involved. It requires careful, detailed analysis. It is also prone to errors due to poorly-expressed assumptions and the inherent difficulty of keeping track of all the details involved. One of the ways to help make the activity more systematic and rigorous is to create mathematical representations, or models, in which every important detail is made explicit. When formulated in a way that can be manipulated by a computer program, these models can be simulated or "run" by a computer, allowing a researcher to study the predicted behaviors of the model and compare the predictions to actual biological observations. In this way, they can learn if their understanding—as embodied in the model—matches the experiments.

As in any scientific field, researchers doing computational modeling need to be able to exchange the results of their work. An important part of their results are the models themselves. Our article describes a document format for storing these models in a way that is not tied to a particular piece of software. This format is called the Systems Biology Markup Language (SBML). It is analogous to HTML, except that instead of describing how to place text on a page in a browser for human consumption, SBML describes the elements making up a computational model of a biological reaction network for consumption by other software tools. SBML today can be written and read by many different software applications that are popular with systems biologists. It means biologists can more easily exchange their models, and benefit from each other's work.

In the year 2000, Herbert Sauro, Andrew Finney, and Mike Hucka were recruited by Hamid Bolouri to join the JST ERATO Kitano Symbiotic Systems Project at Caltech. The project was headed by Hiroaki Kitano and John C. Doyle; its aims included the development of SBML as well as the Systems Biology Workbench (SBW), a software framework for the integration of software tools in systems biology. We have continued to develop SBML and associated software since that time.