Discussion
In the above section we have proposed a set of criteria for models in physiome databases, in addition to MIRIAM compliance, by which we hope to facilitate confidence in the use and reuse of biophysically based models of biological and physiological systems. These insist on a transparent connection between experimental data and model representation, and a set of objective model characteristics that will assist in quantifying the scope of a given model.
It would be naïve, however, not to consider the difficulties with implementing such a process. The culture of scientific publishing rewards the creation and publishing of new models rather than critiquing or reviewing existing work. The classification of models according to a set of criteria, as proposed above, may require significant investment of resources and, perhaps, requires new ways to recognize and to provide incentives for individual involvement.
As suggested in the MIRIAM proposal, an initial curation process will be most effective if performed by the model author, rather than post-hoc by a separate curator. However, if models are to fulfill their role, giving qualitative (mechanisms) and quantitative (experimental data) understanding, it will be vital that there is a forum for an open and robust critique of models. This debate could take the form of challenging models with new data sets, as they become available, or critiquing modelling assumptions or approaches used in deriving a model. Developing a forum that encourages open debate amongst experts and users and provides useful information for non experts, while minimizing unproductive conflict, would clearly require skilled mediation and a well established code of conduct. However, as argued in the Introduction, we believe this type of curation will be an essential process for the ongoing development of integrated computational models
We have outlined a preliminary plan that expands the currently proposed criteria for model curation and we assessed four models from our own work against the proposed criteria. We hope that this proposal will itself generate dialogue and debate within the biological modelling community. Our five criteria for model assessment have been selected for their primary relevance to metabolic and electrophysiological models. However, any `final' set of criteria must of course be selected and adopted by the community, and may possibly require the formulation of additional criteria, or even of alternative lists for the classification of models based on other frameworks, e.g. network inference models for gene–gene interactions, or signalling pathways. We see this goal as falling firmly under the aegis of the Physiome Project; motivated by the pressing need to establish standards to facilitate communication and debate about models, to accelerate the use, implementation and review of models and their connection with data by the scientific community.
Acknowledgments
The authors would like to thank Professor Peter Hunter, for helpful discussions. This work was supported. by the Marsden Fund of the Royal Society of New Zealand through grant No. 04-UOA-177 and National Institutes of Health grant No. EB005825.
Footnotes
Glossary available online at http://jeb.biologists.org/cgi/content/full/210/9/1576/DC1
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