Improving Collaboration by Standardization Efforts in Systems Biology

Andreas Dräger, Bernhard Ø. Palsson
2014 Frontiers in Bioengineering and Biotechnology  
Collaborative genome-scale reconstruction endeavors of metabolic networks would not be possible without a common, standardized formal representation of these systems. The ability to precisely define biological building blocks together with their dynamic behavior has even been considered a prerequisite for upcoming synthetic biology approaches. Driven by the requirements of such ambitious research goals, standardization itself has become an active field of research on nearly all levels of
more » ... rity in biology. In addition to the originally envisaged exchange of computational models and tool interoperability, new standards have been suggested for an unambiguous graphical display of biological phenomena, to annotate, archive, as well as to rank models, and to describe execution and the outcomes of simulation experiments. The spectrum now even covers the interaction of entire neurons in the brain, three-dimensional motions, and the description of pharmacometric studies. Thereby, the mathematical description of systems and approaches for their (repeated) simulation are clearly separated from each other and also from their graphical representation. Minimum information definitions constitute guidelines and common operation protocols in order to ensure reproducibility of findings and a unified knowledge representation. Central database infrastructures have been established that provide the scientific community with persistent links from model annotations to online resources. A rich variety of open-source software tools thrives for all data formats, often supporting a multitude of programing languages. Regular meetings and workshops of developers and users lead to continuous improvement and ongoing development of these standardization efforts. This article gives a brief overview about the current state of the growing number of operation protocols, mark-up languages, graphical descriptions, and fundamental software support with relevance to systems biology. algorithm ontology; LEMS, low entropy model specification; MAMO, mathematical modeling ontology; MIASE, minimum information about a simulation experiment; MIBBI, minimal information for biological and biomedical research; MIRIAM, minimal information required in the annotation of models; NCBI, National Center for Biotechnology Information; NuML, numerical mark-up language; OBO, open scripts, which are specific to certain computational environments and that are not very reproducible are of small benefit for the scientific community and progress of the field (Lloyd et al., 2004) . The development of standardized data formats, models, and computational methods have paved the way toward the evolution and maturation of systems biology into a main-stream field of research (Macilwain, 2011) . Sufficient annotation and metadata of models, experiments, and other data enhance the reproducibility of biomedical ontologies; ODE, ordinary differential equation; OMEX, open modeling exchange format; OMG, object management group; OSB, open-source brain; OWL, web ontology language; PDE, partial differential equation; PharmML, pharmacometrics mark-up language; PHML, physiological hierarchy mark-up language; RDF, resource description framework; SBGN, systems biology graphical notation; SBGN-ML, systems biology graphical notation mark-up language; SBML, systems biology mark-up language; SBOL, synthetic biology open language; SBRML, systems biology result mark-up language; SBW, systems biology workbench; SED-ML, simulation experiment description mark-up language; SVG, scalable vector graphics; SWIG, simplified wrapper and interface generator; TEDDY, terminology for the description of dynamics; URI, uniform resource identifier; W3C, world wide web consortium; XML, eXtended mark-up language.
doi:10.3389/fbioe.2014.00061 pmid:25538939 pmcid:PMC4259112 fatcat:yvsizmtklreanfa6oybwaifccm