Browsing by Author "Cooling, Michael T."

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    Harmonizing semantic annotations for computational models in biology
    (Oxford University Press, 2019) Neal, Maxwell Lewis; Konig, Matthias; Nickerson, David; Mısırlı, Goksel; Kalbasi, Reza; Drager, Andreas; Atalag, Koray; Chelliah, Vijayalakshmi; Cooling, Michael T.; Cook, Daniel L.; Crook, Sharon; De Alba, Miguel; Friedman, Samuel H.; Garny, Alan; Gennari, John H.; Gleeson, Padraig; Golebiewski, Martin; Hucka, Michael; Juty, Nick; Myers, Chris; Olivier, Brett G.; Sauro, Herbert M.; Scharm, Martin; Snoep, Jacky L.; Toure, Vasundra; Wipat, Anil; Wolkenhauer, Olaf; Waltemath, Dagmar
    Life science researchers use computational models to articulate and test hypotheses about the behavior of biological systems. Semantic annotation is a critical component for enhancing the interoperability and reusability of such models as well as for the integration of the data needed for model parameterization and validation. Encoded as machine-readable links to knowledge resource terms, semantic annotations describe the computational or biological meaning of what models and data represent. These annotations help researchers find and repurpose models, accelerate model composition and enable knowledge integration across model repositories and experimental data stores. However, realizing the potential benefits of semantic annotation requires the development of model annotation standards that adhere to a community-based annotation protocol.Without such standards, tool developers must account for a variety of annotation formats and approaches, a situation that can become prohibitively cumbersome and which can defeat the purpose of linking model elements to controlled knowledge resource terms. Currently, no consensus protocol for semantic annotation exists among the larger biological modeling community. Here, we report on the landscape of current annotation practices among the COmputational Modeling in BIology NEtwork community and provide a set of recommendations for building a consensus approach to semantic annotation.
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    Minimum information about a simulation experiment (MIASE)
    (PLOS, 2011-04) Waltemath, Dagmar; Adams, Richard; Beard, Daniel A.; Bergmann, Frank T.; Balla, Upinder S.; Britten, Randall; Chelliah, Vijayalakshmi; Cooling, Michael T.; Cooper, Jonathan; Crampin, Edmund J.; Garny, Alan; Hoops, Stefan; Hucka, Michael; Hunter, Peter; Klipp, Edda; Laibe, Camille; Miller, Andrew K.; Moraru, Ion; Nickerson, David; Nielsen, Poul; Nikolski, Macha; Sahle, Sven; Sauro, Herbert M.; Schmidt, Henning; Snoep, Jacky L.; Tolle, Dominic; Wolkenhauer, Olaf; Le Novere, Nicolas
    Reproducibility of experiments is a basic requirement for science. Minimum Information (MI) guidelines have proved a helpful means of enabling reuse of existing work in modern biology. The Minimum Information Required in the Annotation of Models (MIRIAM) guidelines promote the exchange and reuse of biochemical computational models. However, information about a model alone is not sufficient to enable its efficient reuse in a computational setting. Advanced numerical algorithms and complex modeling workflows used in modern computational biology make reproduction of simulations difficult. It is therefore essential to define the core information necessary to perform simulations of those models. The Minimum Information About a Simulation Experiment describes the minimal set of information that must be provided to make the description of a simulation experiment available to others. It includes the list of models to use and their modifications, all the simulation procedures to apply and in which order, the processing of the raw numerical results, and the description of the final output. MIASE allows for the reproduction of any simulation experiment. The provision of this information, along with a set of required models, guarantees that the simulation experiment represents the intention of the original authors. Following MIASE guidelines will thus improve the quality of scientific reporting, and will also allow collaborative, more distributed efforts in computational modeling and simulation of biological processes.