Open Source Software Infrastructure for Computational Biology and Visualization

Blackett, Shane; Bullivant, David; Stevens, Carey; Hunter, Peter

doi:10.1109/iembs.2005.1615879

Cited by 5 publications

(6 citation statements)

References 2 publications

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“…71, 72 CMISS is another example of a continuum software package that has been applied to solve GI electrophysiological models. 53, 73 In both environments, systems of differential equations are solved over a geometric mesh using a discrete method, such as the finite element method. The individual environments differ in approach to constructing the geometric mesh and numerical procedural setup.…”

Section: Computational Techniquesmentioning

confidence: 99%

Toward the virtual stomach: progress in multiscale modeling of gastric electrophysiology and motility

O’Grady

Gao

et al. 2013

WIREs Mechanisms of Disease

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Experimental progress in investigating normal and disordered gastric motility is increasingly being complimented by sophisticated multi-scale modeling studies. Mathematical modeling has become a valuable tool in this effort, as there is an ever-increasing need to gain an integrative and quantitative understanding of how physiological mechanisms achieve coordinated functions across multiple biophysical scales. These interdisciplinary efforts have been particularly notable in the area of gastric electrophysiology, where they are beginning to yield a comprehensive and integrated in-silico organ modeling framework, or ‘virtual stomach’. At the cellular level, a number of biophysically-based mathematical cell models have been developed, and these are now being applied in areas including investigations of gastric electrical pacemaker mechanisms, smooth muscle electrophysiology, and electromechanical coupling. At the tissue level, micro-structural models are being creatively developed and employed to investigate clinically significant questions, such as the functional effects of ICC degradation on gastrointestinal electrical activation. At the organ level, high-resolution electrical mapping and modeling studies are combining to provide improved insights into normal and dysrhythmic gastric electrical activation. These efforts are also enabling detailed forward and inverse modeling studies at the ‘whole body’ level, with implications for diagnostic techniques for gastric dysrhythmias. These recent advances, together with several others highlighted in this review, collectively demonstrate a powerful trend toward applying mathematical models to effectively investigate structure-function relationships and overcome multi-scale challenges in basic and clinical gastrointestinal research.

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Section: Computational Techniquesmentioning

confidence: 99%

Toward the virtual stomach: progress in multiscale modeling of gastric electrophysiology and motility

O’Grady

Gao

et al. 2013

WIREs Mechanisms of Disease

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“…25,26 Another standard has been developed to describe spatiotemporal variations throughout the tissue (FieldML). 25 Finite element (FEM) and boundary element method software environments, such as CMISS and CHASTE, 27,28 have also been applied in multiscale simulations of the GI tract. 29,30 Recently, a new generation of open-source, distributed-memory architecture software packages, such as OpenCMISS, has been developed.…”

Section: The Virtual Esophagusmentioning

confidence: 99%

The virtual esophagus: investigating esophageal functions in silico

Yassi

Gregersen

et al. 2016

Annals of the New York Academy of Sciences

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Esophageal and gastroesophageal junction (GEJ) diseases are highly prevalent worldwide and are a significant socioeconomic burden. Recently, applications of multiscale mathematical models of the upper gastrointestinal tract have gained attention. These in silico investigations can contribute to the development of a virtual esophagus modeling framework as part of the larger GIome and Physiome initiatives. There are also other modeling investigations that have potential screening and treatment applications. These models incorporate detailed anatomical models of the esophagus and GEJ, tissue biomechanical properties and bolus transport, sensory properties, and, potentially, bioelectrical models of the neural and myogenic pathways of esophageal and GEJ functions. A next step is to improve the integration between the different components of the virtual esophagus, encoding standards, and simulation environments to perform more realistic simulations of normal and pathophysiological functions. Ultimately, the models will be validated and will provide predictive evaluations of the effects of novel endoscopic, surgical, and pharmaceutical treatment options and will facilitate the clinical translation of these treatments.

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“…-SCIRun (software.sci.utah.edu/scirun) is our own example of a general purpose, problem-solving environment that has found extremely broad application both within biomedicine (Johnson et al 2002;Henriquez et al 2004;Stinstra et al 2005;Wolters et al 2006;Jolley et al 2008) and in areas as diverse as nuclear physics (Sanderson et al 2004;Jones et al 2007) and combustion (Parker 2006). -CMISS (www.cmiss.org) also has a very broad technical scope and application domain (Blackett et al 2005), and is the basis of many simulation studies in bioelectric fields and biomechanics of the heart and other organs (Hooks et al 2002;Garny et al 2003;Nash 2005), respiratory physiology (Tawhai et al 2000) and bioelectric fields in the gastrointestinal system (Pullan et al 2004). -SIMBIOS (simbios.stanford.edu) is a newly emerging software system from the NIH-funded Center for Physics-based Simulation of Biological Structures (Schmidt et al 2008).…”

Section: (B ) Software Infrastructurementioning

confidence: 99%

“…CMISS (www.cmiss.org) also has a very broad technical scope and application domain (Blackett et al . 2005), and is the basis of many simulation studies in bioelectric fields and biomechanics of the heart and other organs (Hooks et al .…”

Section: Introductionmentioning

confidence: 99%

Subject-specific, multiscale simulation of electrophysiology: a software pipeline for image-based models and application examples

MacLeod

Stinstra

Lew

et al. 2009

Phil. Trans. R. Soc. A.

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Many simulation studies in biomedicine are based on a similar sequence of processing steps, starting from images and running through geometric model generation, assignment of tissue properties, numerical simulation and visualization of the results—a process known as image-based geometric modelling and simulation. We present an overview of software systems for implementing such a sequence both within highly integrated problem-solving environments and in the form of loosely integrated pipelines. Loose integration in this case indicates that individual programs function largely independently but communicate through files of a common format and support simple scripting, so as to automate multiple executions wherever possible. We then describe three specific applications of such pipelines to translational biomedical research in electrophysiology.

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Open Source Software Infrastructure for Computational Biology and Visualization

Cited by 5 publications

References 2 publications

Toward the virtual stomach: progress in multiscale modeling of gastric electrophysiology and motility

Toward the virtual stomach: progress in multiscale modeling of gastric electrophysiology and motility

The virtual esophagus: investigating esophageal functions in silico

Subject-specific, multiscale simulation of electrophysiology: a software pipeline for image-based models and application examples

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