Basic Introduction to SBML

The starting point is an appreciation that computational modeling of biological systems is no longer a fringe activity—it's a requirement for us to make sense of our vast and ever-expanding quantities of data. This reality is acknowledged and reinforced by a vast increase this decade in the number of journals, books and articles having computational and systems biology emphases.

At its most basic, computational modeling is no different from modeling as it's practiced by all scientists, whether in biology or elsewhere. The extra but crucial step is casting the model into a formal, computable form that can be analyzed rigorously using simulation and other mathematical methods.

Different representations of models are useful for different purposes. Graphical diagrams of biological processes are useful for visual presentation to humans, but at the level of software, a different format is needed for quantifying a model to the point where it can be simulated and analyzed. That's where the Systems Biology Markup Language (SBML) comes in.

Simply put, SBML is a machine-readable format for representing models. It's oriented towards describing systems where biological entities are involved in, and modified by, processes that occur over time. An example of this is a network of biochemical reactions. SBML's framework is suitable for representing models commonly found in research on a number of topics, including cell signaling pathways, metabolic pathways, biochemical reactions, gene regulation, and many others.

SBML is for software

SBML does not represent an attempt to define a universal language for representing quantitative models. It would be impossible to achieve a one-size-fits-all universal language. A more realistic alternative is to acknowledge the diversity of approaches and methods being explored in systems biology, and seek a common intermediate format—a lingua franca—enabling communication of the most essential aspects of the models.

The adoption of SBML offers many benefits, including: (1) enabling the use of multiple tools without rewriting models for each tool, (2) enabling models to be shared and published in a form other researchers can use even in a different software environment, and (3) ensuring the survival of models (and the intellectual effort put into them) beyond the lifetime of the software used to create them.

SBML is neutral with respect to programming languages and software encoding; however, it's oriented towards allowing models to be encoded using XML. By supporting SBML as a format for reading and writing models, different software tools (including programs for building and editing models, simulation programs, databases, and other systems) can directly communicate and store the same computable representation of those models. This removes an impediment to sharing results and permits other researchers to start with an unambiguous representation of the model, examine it carefully, propose precise corrections and extensions, and apply new techniques and approaches—in short, to do better science.

What can you do with it?

If you're a biologist interested in doing computational modeling, this may be all you need to know about SBML. Today's modern software packages hide the details of SBML and provide you with interfaces that help you focus on your modeling and analysis tasks. You can find out about many SBML-compatible software systems from our SBML Software Guide.

If you're a software developer or an advanced modeler, you probably want to learn just a little bit more about SBML. Step through to our More Detailed Summary of SBML.