Overview and use of standards and formats relevant to MSM

Michael Hucka, Ph.D. – California Institute of Technology, Pasadena, CA James Sluka, Ph.D. – Indiana University, Bloomington, IN

Herbert Sauro, Ph.D. – University of Washington, Seattle, WA

2015 MSM Consortium Satellite Meeting, September 2015, Bethesda, MD, USA

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Conceptual or verbal: descriptions in text

Diagrammatic: graphical representation of objects and relations

Physical: real mock-up of a system or object

Formal: mathematical representation of objects and relations

General types of models

Conceptual or verbal: descriptions in text

Diagrammatic: graphical representation of objects and relations

Physical: real mock-up of a system or object

Formal: mathematical representation of objects and relations

General types of models

Sharing models is important

• Believability of results

• Reproducibility of research

- Publications often lack sufficient detail to reproduce a model

• Reusability of work products

- Easier to reuse ⇒ more likely to be reused

Making models sharable is not always easy

• Sharing requires more work ⇒ time ⇒ funding

• Immature formats and software pose obstacles

• Diversity + complexity = confusion

Motivations for this meeting

Data sharing survey by Tenopir et al., 2011

Tenopir, C., Allard, S., Douglass, K., Aydinoglu, A. U., Wu, L., Read, E., Manoff, M., & Frame, M. (2011). Data sharing by scientists: Practices and perceptions. PloS One, 6(6), e21101.

Overview common formalisms

• Goal: provide background and context

Describe standards and formats useful for a subset of problems

• Goal: provide guidance and starting points

- Scope is limited by time (and us)

‣ Next year, perhaps another satellite can take on another part of the overall patchwork of standards/formats?

Demonstrate actual use

• Goal: provide concrete illustrations

Goals for this meeting

Out

line

General review of common model representation approaches

Overview of standards and formats for a subset of problems

Demonstrations

Discussion of additional related resources

General discussion