DynSysMod: A Framework for Modeling Composite Dynamic Systems
Jennifer Leaf
TCSS 702: Design Project Final Report
August 17, 2007
http://faculty.washington.edu/gmobus/SystemsScience/DynSysMod-JenniferLeafFinalPaper.pdf
A system is a collection of elements that interact to function as a single, larger entity. The field of computer simulation and modeling oncerns the creation of abstract representations of real systems and the execution of the system models in a virtual environment, to explain or predict the behavior of the real systems. System dynamics is the field of study that models systems whose behavior is heavily influenced by feedback (that is, the outputs of the system are recycled back into the system as inputs) and examines their behaviors over time. While many system dynamics modeling applications have been developed, they are lacking the ability to define multiple, independent types of flows through the system, and the ability to run different sections of the model at varying time resolutions. The application, DynSysMod, described in this project report, provides a description language and simulation execution engine to exercise system dynamics models of varying complexity. This tool will be especially useful in modeling energy systems and other types of systems that require multiple types of flows, and where different parts of the model should be executed at different rates. The framework developed in this project provides a solid foundation for system dynamics modeling and future expansion of modeling functionality.
PlantSBM: The Plant Systems Biology Modelling project
The aim of this project is to develop a web-based portal which will make available, in open-source format, those plant growth models which are identified as most relevant to the needs of the UK plant systems biology and crop science communities. The first priority will be to implement ten such existing models, representing at least one each from the following categories: a temperate monocot, a temperate dicot crop species; Arabidopsis; a bioenergy crop; a plant-soil interaction model; a nutrient uptake and usage model; a highly complex model (50+ parameters)
The models, which are currently available in a range of formats, will be represented in an open-standard declarative XML format. Use of a declarative language makes it possible to display the models in a variety of ways, depending on the needs of user communities, and facilitates model transformation (e.g. simplifying a complex model). It also provides an efficient mechanism for making much of the model metadata available automatically through its internal structure.
Full proposal (public version): BBR outline Ougham et al public.pdf