Towards Anatomic Scale Agent-Based Modeling with a Massively Parallel Spatially Explicit General-Purpose Model of Enteric Tissue (SEGMEnT_HPC)
Authored by Gary An, Robert Chase Cockrell, Scott Christley, Eugene Chang
Date Published: 2015
DOI: 10.1371/journal.pone.0122192
Sponsors:
United States National Institutes of Health (NIH)
Platforms:
C++
Model Documentation:
Other Narrative
Flow charts
Model Code URLs:
Model code not found
Abstract
Perhaps the greatest challenge currently facing the biomedical research
community is the ability to integrate highly detailed cellular and
molecular mechanisms to represent clinical disease states as a pathway
to engineer effective therapeutics. This is particularly evident in the
representation of organ-level pathophysiology in terms of abnormal
tissue structure, which, through histology, remains a mainstay in
disease diagnosis and staging. As such, being able to generate anatomic
scale simulations is a highly desirable goal. While computational
limitations have previously constrained the size and scope of
multi-scale computational models, advances in the capacity and
availability of high-performance computing (HPC) resources have greatly
expanded the ability of computational models of biological systems to
achieve anatomic, clinically relevant scale. Diseases of the intestinal
tract are exemplary examples of pathophysiological processes that
manifest at multiple scales of spatial resolution, with structural
abnormalities present at the microscopic, macroscopic and organ-levels.
In this paper, we describe a novel, massively parallel computational
model of the gut, the Spatially Explicitly General-purpose Model of
Enteric Tissue\_HPC (SEGMEnT\_HPC), which extends an existing model of
the gut epithelium, SEGMEnT, in order to create cell-for-cell anatomic
scale simulations. We present an example implementation of SEGMEnT\_HPC
that simulates the pathogenesis of ileal pouchitis, and important
clinical entity that affects patients following remedial surgery for
ulcerative colitis.
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