Multiscale Computational Modeling in Vascular Biology: From Molecular Mechanisms to Tissue-Level Structure and Function - Multiscale Computer Modeling in Biomechanics and Biomedical Engineering - page 229

Fig. 5 Illustration of a possible approach to couple intracellular signaling models (ISM), agent
based models (ABM), and constrained mixture models (CMM) to enhance computations of
vascular behaviors
programs because they are well established, readily available, and easy to learn,
which, importantly, will facilitate the sharing of our multiscale model. Matlab is a
general-purpose simulation tool, and Netlogo, written in Java TM , is freely down-
loadable from http://ccl.northwestern.edu/netlogo/ and is the most widely used
agent-based modeling software [ 63 ]. Our group has previously published a mul-
tiscale model that unites ISM with ABM using a Java TM -based umbrella program
to run an ISM and an ABM in parallel [ 49 ], for the study of tissue morphogenesis
during embryonic development. The umbrella program will interface the ISM,
ABM, and CMM through the use of text files that can be imported and exported by
both Matlab and Netlogo, which will store inputs and outputs of each module and
be used to communicate predictions from one level of scale to the next. Netlogo
extensions are capable of running Java TM code, and the Java TM code will open and
run Matlab.
Model validation is an important check to confirm the model is accurate and
stable. Box 2 describes a possible strategy for validating a three-tiered multiscale
model.