Tuesday, May 13, 2014

Project Description

I just realized that I made the mistake of not describing the project I will be working on this summer. I proposed the implementation of the arrays package within JSBML since SBML core lacks an efficient representation of regular structures (elements that are used over and over).  Of course the arrays package is just syntactic sugar to the modeling language, just like the Hierarchical Model Composition package, which is an extension in SBML to construct hierarchical models.
This means that you can construct the exact same models without these packages. However, from the modeling standpoint, it becomes much easier to design models when you can construct models hierarchically and in arrays form, especially when you want to model a population of cells.

The arrays package is used to avoid the tedious work of copying over something multiple times. I think arrays is good when you want to indicate multiple elements share the same attributes since X[0] and X[1] are referring to X where as X_0 and X_1 could be two completely different things (this would be bad practice but name conventions are suggested, not enforced).

The arrays package has been proposed.  In order for the arrays package to be officially integrated into SBML, two modeling tools have to support the package. Hopefully, other tools make use of the arrays package because I think it is a nice feature. Also, I hope that the arrays package helps revive the Dynamic Structures package, which is currently stalled (there are some nice discussion about this package though).

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