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JigCell Models, Use Cases, and Walkthroughs

The ultimate purpose of the modeling that we do is to understand and explain the underlying mechanisms driving the physiology of the organisms under study. When trying to explain models, the modeling process, and the software involved, we have developed terminology to address the differing aspects to the process.

Modelers naturally create models, which are artifacts that embody the descriptive information in question. Our modeling community has agreed that SBML is the standard language used to define models. Thus, along with reaction equations, differential equations, wiring diagrams, English language explanation, and other forms of presentation, we attempt to provide a valid SBML file for all of our models.

Separate from the models themselves is the process by which modelers do their work. A use case is a description of the process used to perform a particular modeling task on a particular model. It is a user-centered description of the activities performed by a user to accomplish a particular goal.

A walkthrough is a sofware-centered description of the steps taken when using a particular sofware system to accomplish a particular task or series of tasks on a particular model. Walkthroughs are useful for explaining how a particular software system is meant to be used.

As part of our work on JigCell, we have studied and documented the modeling process, both from the standpoint of modeling as a creative endeavor, and from the standpoint of modeling as a formal process.

Over the past 10 years, the Tyson lab has worked extensively on three models, and has published these models in various forms in the Biology literature. The simplest one attempts to explain the biochemistry of M-phase promoting factor (MPF) in Xenopus oocyte extracts, which we typically refer to as the "frog egg model." A more complicated model attempts to explain the cell cycle for the budding yeast Saccharomyces cerevisiae. In addition, we have done preliminary work toward modeling the circadian rhythm of Drosophila melanogaster.

To help people understand what we do and the software that we provide, we provide web pages containing both use cases and walkthroughs related to our modeling efforts.

• The Frog Egg model, use case, and walkthrough.
• The Budding Yeast cell cycle model and use case.
• The Generic Eukaryotic cell cycle model and use case.
• See our initial efforts on modeling circadian rhythms.
• Models of the Tyson Lab: This document is somewhat out of date, but it provides multiple representations for the Frog Egg Extract and Budding Yeast Cell models. Each model is show in terms of its wiring diagram, its JigCell representation, its differential equations, and its SBML representation.