Biophysical Modeling and Simulation of Cellular Transport. 1 -

Catalog description

This course is designed to provide hands on experience in computational modeling of the neural regulation of digestive and renal epithelia through a lecture-based module and supervised modeling projects that make use of datasets, maps and models assembled and made available through the Stimulating Peripheral Activity to Relieve Conditions (SPARC) program of the National Institutes of Health (NIH). The SPARC program is a large NIH project aimed at understanding the anatomy and physiology of the autonomic nervous system (ANS) and its connections to develop new therapies based on the emerging science of neuromodulation. The Lecture program will provide talks and small group tutorials introducing SPARC, concepts of open science, and modeling methodologies relevant to epithelial cells (including transporters & channels) and their control by the autonomic and enteric nervous systems. Students can take this first part as a 1 credit hour. The Research program will provide students with a mentored experience in the development, testing, and textbook-linked publication of a Findable, Accessible, Interoperable, Reusable (FAIR) model that simulates epithelial transport. These models will be generated using SPARC data and models, and leveraging SPARC infrastructure. The outcome of this reproducibility project will be submitted to an online repository. Students will be given the opportunity to publish their models in the Physiome journal (or another journal that publishes computational models). Physiome is an open access journal, launched by the International Union of Physiological Sciences (IUPS) that publishes reproducible and reusable mathematical models of physiological processes, where the experimental details and model validation have been published in a recognized 'primary' peer-reviewed journal. For the FAIR DOs ('Findable, Accessible, Interoperable, Reusable Development of Open Simulations') educational Physiome papers, the Medical Physiology textbook by Boron & Boulpaep will be regarded as the primary publication. Dr. Peter Hunter is the Editor-in-Chief of Physiome and Dr. Walter Boron is a co-editor of Medical Physiology. Drs. Nickerson & Occhipinti are members of the Editorial Board of Physiome.