ReviewPost screenRecent advances in modeling languages for pathway maps and computable biological networks
Section snippets
Languages, models and systems biology
Systems biology is a multidisciplinary approach to biological and biomedical research that focuses on the complex interactions characteristic of biological systems, often with the aim of discovering the emergent properties of such systems that have proven difficult to elucidate using more reductionist approaches (http://en.wikipedia.org/wiki/Systems_biology). The components of such systems are interdependent and in a state of constant change, and their behaviors depend on their context in situ
Standard languages for biological network analysis
One of the most important uses for standard languages in systems biology is modeling and analyzing biological networks. High-throughput molecular profiling techniques have proven to be effective tools for analyzing biological systems but, because they typically generate long and unadorned lists of analytes (genes, proteins, metabolites, among others), they represent a significant challenge to the researchers tasked with interpreting the results of these experiments [9]. To make analysis
Recent advances in network biology modeling languages
Modeling languages of various kinds have played key parts in biology and chemistry for decades. BioPAX, for example, is a popular language for representing and sharing pathway knowledge [17]. Systems Biology Markup Language (SBML) is an XML-based language for describing and quantifying biological models for use in software [18]. PSI-MI, the Proteomics Standards Initiative Molecular Interaction XML format, is used for data exchange in proteomics [19]. BioPAX, PSI-MI and SBML are compared in [20]
Concluding remarks
The models we use to represent theories of systems biology grow ever larger and more complex as the theories themselves are enriched by continuing research. Recently, more of languages used to express these models have been designed to help model builders take better advantage of information technology, by providing better facilities for data annotation and semantics, analytics, inference, and programmatic simulation. They have also been designed to leverage uniform data structures (such as
Conflicts of interest
T.S. was formerly Chief Technology Officer of the OpenBEL Project, an independent non-profit organization focused on the OpenBEL knowledge engineering platform for the life sciences (http://openbel.org).
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