@article{Draeger2014,
  author   = {Dr\"ager, Andreas and Palsson, Bernhard {\O}.},
  title    = {Improving collaboration by standardization efforts in systems biology},
  journal  = {Frontiers in Bioengineering},
  year     = {2014},
  volume   = {2},
  number   = {61},
  month    = dec,
  abstract = {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 granularity 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 on-line resources. A rich variety of open-source
	software tools thrives for all data formats, often supporting a multitude
	of programming 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, markup languages, graphical
	descriptions, and fundamental software support with relevance to
	systems biology.},
  doi      = {10.3389/fbioe.2014.00061},
  issn     = {2296-4185},
  keywords = {model formats, modeling guidelines, ontologies, model databases, network
	visualization, software support},
  pdf      = {https://www.frontiersin.org/articles/10.3389/fbioe.2014.00061/pdf},
  url      = {https://www.frontiersin.org/articles/10.3389/fbioe.2014.00061/full}
}