Towards anatomic scale agent-based modeling with a massively parallel spatially explicit general-purpose model of enteric tissue (SEGMEnT_HPC).
Towards anatomic scale agent-based modeling with a massively parallel spatially explicit general-purpose model of enteric tissue (SEGMEnT_HPC).
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DOI：
10.1371/journal.pone.0122192
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发表时间：
2015
期刊：
影响因子：
3.7
通讯作者：
An G
中科院分区：
文献类型：
--
作者：
Cockrell RC;Christley S;Chang E;An G
也许生物医学研究界目前面临的最大挑战是整合高度详细的细胞和分子机制来代表临床疾病状态的能力，作为设计有效治疗方法的途径。这在异常组织结构的器官水平病理生理学表征中尤其明显，通过组织学，异常组织结构仍然是疾病诊断和分期的支柱。因此，能够生成解剖尺度的模拟是一个非常理想的目标。虽然计算限制以前限制了多尺度计算模型的规模和范围，但高性能计算（HPC）资源的容量和可用性的进步极大地扩展了生物系统计算模型实现解剖、临床相关规模的能力。肠道疾病是病理生理过程的典型例子，其在空间分辨率的多个尺度上表现出来，在微观、宏观和器官水平上存在结构异常。在本文中，我们描述了一种新颖的大规模并行肠道计算模型，即肠组织_HPC空间显式通用模型（SEGMEnT_HPC），它扩展了现有的肠道上皮模型SEGMenT，以创建细胞间的解剖尺度模拟。我们提出了一个 SEGMEnT_HPC 的示例实现，它模拟回肠贮袋炎的发病机制，以及影响溃疡性结肠炎补救手术后患者的重要临床实体。
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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影响因子：
2.8
作者：
MOSKOWITZ, RL;SHEPHERD, NA;NICHOLLS, RJ
通讯作者：
NICHOLLS, RJ
DOI：
10.1007/978-1-4939-0554-6_16
发表时间：
2014-01-01
期刊：
ENGINEERING AND ANALYZING MULTICELLULAR SYSTEMS: METHODS AND PROTOCOLS
影响因子：
--
作者：
Kang, Seunghwa;Kahan, Simon;Momeni, Babak
通讯作者：
Momeni, Babak
影响因子：
9.5
作者：
Thorne, Bryan C.;Bailey, Alexander M.;Peirce, Shayn M.
通讯作者：
Peirce, Shayn M.
影响因子：
2.5
作者：
Batts, Lorene E.;Polk, D. Brent;Kulessa, Holger
通讯作者：
Kulessa, Holger
影响因子：
4.3
作者：
Cockrell C;Christley S;An G
通讯作者：
An G