PMC:4342829 / 7630-9276 JSONTXT

{"project":"2_test","denotations":[{"id":"25880925-21943907-14893500","span":{"begin":192,"end":194},"obj":"21943907"},{"id":"25880925-12611808-14893501","span":{"begin":354,"end":356},"obj":"12611808"},{"id":"25880925-21685047-14893502","span":{"begin":442,"end":444},"obj":"21685047"},{"id":"25880925-17032683-14893503","span":{"begin":458,"end":460},"obj":"17032683"},{"id":"25880925-21685047-14893504","span":{"begin":1171,"end":1173},"obj":"21685047"},{"id":"25880925-17032683-14893505","span":{"begin":1212,"end":1214},"obj":"17032683"}],"text":"Ensuring standardisation allows systems biology models to be reused outside of their original context: in different simulators, under different conditions, or as parts of more complex models [31]. To this end, we have made five of the six models (the exception is the spatial model of D. melanogaster) available in Systems Biology Markup Language (SBML [32]) format, allowing for their simulation in multiple software tools, including AMIGO [33] and COPASI [34]. Even when defined in a standard format such as SBML, large models such as the genome-wide kinetic model of S. cerevisiae may give different results when simulated in different software environments. The inherent size and stiffness of genome-scale systems biology models create new challenges to be addressed for their robust simulation by systems biology tools [25]. To address this problem all the models have been consistently formatted, with their dynamics provided both in C and in Matlab. Additionally, a benchmark consisting of a parameter estimation problem has been defined for every model, for which ready-to-run implementations are provided in Matlab (optionally with the use of the AMIGO toolbox [33]) and, in some cases, also in COPASI [34]. The availability of ready-to-run implementations is a highly desirable practice in computer science, since it ensures reproducibility of the results. Calibration results with state of the art optimization methods are reported, which can serve as a reference for comparison with new methodologies. Additionally, suggestions on how to compare the performance of several methods are also given in the Results and discussion section."}