[Population Modeling] Introduction

[Leandro Watanabe]

Hello,

My advisor, Chris Myers, and I found about about this group through Jacob
Barhak in the SBML mailing list. Looks like there are some interesting work
going on in population modeling and we have some work that relate to this
topic. Hopefully we can contribute to this group. Here is a brief
description:

     In a modeling perspective, standards are important for the ability to
share and reuse models. The importance of modeling standards is higher than
ever with the rising number of computer-aided design (CAD) tools being
developed because it grants interoperability between tools. In the
systems/synthetic biology fields, the most widely used modeling language
for simulation is the Systems Biology Markup Language (SBML
<http://sbml.org/Main_Page>), which allows the representation of
quantitative models. SBML has many features that allow the representation
of chemical reaction networks, discrete event models, and ordinary
differential equations (ODEs) models.

    SBML supports extensions that increases the usability of the standard
for different applications. The arrays package has been proposed to allow
the representation of regular structures more concisely. The arrays package
<http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/arrays> in
SBML has been used for the representation of population models in the
systems/synthetic biology domains
<http://pubsdc3.acs.org/doi/full/10.1021/acssynbio.5b00242> within the iBioSim
tool <http://www.async.ece.utah.edu/ibiosim>. In particular, the arrays
package was used to construct a lattice-based model of cellular populations
to identify the behavior of genetic circuits in different cells when placed
in an environment that allows cell-cell interactions. This is just one of
the many applications of the arrays package, which could potentially be
used for many other applications such as disease models.

Looking forward to hearing about your work and learning from you.

Thanks,
Leandro
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