Open source software infrastructure for computational biology and visualization

Effects of magnetogastrography sensor configurations in tracking slow wave propagation

Magnetogastrography (MGG) is a non-invasive method of assessing gastric slow waves (SWs) by recording the resultant magnetic fields. MGG can capture both SW frequency and propagation, and identify SW dysrhythmias that are associated with motility disorders. However, the impact of the restricted spatial coverage and sensor density on SW propagation tracking performance is unknown. This study simulated MGG using multiple anatomically specific torso geometries and two realistic SW propagation patterns to determine the effect of different sensor configurations on tracking SW propagation. The surface current density mapping and center-of-gravity tracking methods were used to compare four magnetometer array configurations: a reference system currently used in GI research and three hypothetical higher density and coverage arrays. SW propagation patterns identified with two hypothetical arrays (with coverage over at least the anterior of the torso) correlated significantly higher with simulated realistic 3 cycle-per-minute SW activity than the reference array (p = 0.016, p = 0.005). Furthermore, results indicated that most of the magnetic fields that contribute to the performance of SW propagation tracking were located on the anterior of the torso as further increasing the coverage did not significantly increase performance. A 30% decrease in sensor spacing within the same spatial coverage of the reference array also significantly increased correlation values by approximately 0.50 when the signal-to-noise ratio was 5 dB. This study provides evidence that higher density and coverage sensor layouts will improve the utility of MGG. Further work is required to investigate optimum sensor configurations across larger anatomical variations and other SW propagation patterns.

A mathematical model of the effects of anoctamin-1 loss on intestinal slow wave entrainment

The interstitial cells of Cajal (ICC) generate electrophysiological events called slow waves that regulate the motility of the gastrointestinal (GI) tract. Recent studies have demonstrated that the Ca²⁺-activated Cl^- -channel, encoded by the anoctamin1 (Ano1) protein, has a major role in regulating intestinal slow waves and motility. The main aim of this study was to develop a multi-scale mathematical model capable of simulating both normal slow wave entrainment and the effects of Ano1 knockout (KO) on the normal activity. A biophysically-based cell model was adapted to simulate the effects of Ano1 KO at the cellular level. A 10mm one-dimensional (1D) model was then developed to simulate entrained intestinal slow wave propagation. Cellular KO at levels of 100% and 20% were applied to a varying-sized middle region of the 1D model. The main finding was that the level of loss of entrainment increased as both cellular and spatial Ano1 KO levels increased, mostly manifesting as ectopic activation. In the future, this model will be extended and used in combination with Ca²⁺ -imaging data to quantitatively investigate the effects of Ano1 loss in ICC.

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

Experimental progress in investigating normal and disordered gastric motility is increasingly being complimented by sophisticated multiscale 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 (GI) electrical activation. At the organ level, high-resolution electrical mapping and modeling studies are combined 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 multiscale challenges in basic and clinical GI research.

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

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.