Overview of Research Education Program
FAIR DOs (Findable, Accessible, Interoperable, Reusable: Development Of Simulations) is a research education program in the modeling and simulation of digestive and renal neurobiology. The main thrust of FAIR DOs is to educate the next generation of researchers and clinicians in the neural regulation of digestive and renal epithelia through taught modules and supervised modeling projects that make use of SPARC datasets, maps, and models. Overall, FAIR DOs aims to provide about 35/45 hours of training to students, with each student research project producing one publication in the Physiome journal–launched by the International Union of Physiological Sciences. The SPARC Portal will provide findability to these student- generated open-access models and associated data, as well as accessible interactivity via the O2S2PARC simulation platform. Overall, the FAIR DOs effort will provide a unique educational, mentored experience that will also generate a SPARC ecosystem of interoperating models that coherently study the neurobiology of digestive and renal epithelial transport. From a didactic “Systems” perspective, this ecosystem of models will be organized to follow the teaching narrative of the British Medical Association “Medical Physiology 3rd Ed.” textbook, supplemented with recent literature, setting the stage to further leverage SPARC resources for education in the future.
Course: PHOL 429: Biophysical Modeling and Simulation of Cellular Transport
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Offered: Spring 2024 at Case Western Reserve University
Lecture Program (1 credit): MWF 2:00-3:30 PM for 4 weeks
Mentored Research Program (2 credits): MF 2:00-2:50 PM
- Full syllabus description: PHOL 429 Syllabus
- Lead instructors
- Walter F. Boron, MD, PhD (walter.boron@case.edu)
- Rossana Occhipinti, PhD (rossana.occhipinti@case.edu)
- Leadership/Organizing Committee
- Walter F. Boron, MD, PhD (walter.boron@case.edu)
- Bernard de Bono, MD, PhD (b.debono@auckland.ac.nz)
- Jeffrey Grethe, PhD (jgrethe@ucsd.edu)
- Peter Hunter, PhD (p.hunter@auckland.ac.nz)
- Maryann Martone, PhD (maryann@ncmir.ucsd.edu)
- David Nickerson, PhD (d.nickerson@auckland.ac.nz)
- Rossana Occhipinti, PhD (rossana.occhipinti@case.edu)
Format and Meeting times
This class will be offered as a two-module class/semester: a taught 4-week Lecture program, followed by a 11-week Research program. Students can take the class for either 1 credit hour (“Lecture Program”) or 3 credit hours (“Lecture Program + Research Program”).
Module I: Lecture Program (1 credit)
- Meeting Times: Mondays, Wednesdays, Fridays, 2:00-3:30 PM for 4 weeks (10 lectures)
- Format: Live lectures with students attending the class in person. Participating faculty from UCSD and University of Auckland will deliver lectures via Zoom with students in the classroom. Each of these lectures will be followed by a small-group tutorial in which the teaching faculty and TAs will discuss the material covered in the preceding lecture. All lectures and tutorials will be recorded.
- Content overview: Core Topics to provide the background knowledge on computational methods, Stimulating Peripheral Activity to Relieve Conditions (SPARC) resources, and epithelial transport physiology.
- Evaluation: In class mini-exam through multiple choice and short answer questions.
Module II: Mentored Research Program (2 credits)
- Meeting Times: Mondays, Fridays, 2:00-2:50 PM in class tutorials. Every two weeks one class (Friday) will be allocated for group discussions of the assigned research projects.
- Format: Guided research and in class tutorials/group discussion. At the beginning of this module, students will receive a list of potential research projects. After a student chooses a project, the student will be paired with program faculty with relevant expertise for independent study under their guidance. Students generally will work in pairs on two parallel projects (so that each can still be first author on the term paper/publication plus, perhaps, a co-shared first authorship). Pairing of students will account for complementary expertise (e.g., a student with a more quantitative background will be paired with a student with a more biological background)
- Content overview: Tutorials covering examples of applications for the material learned in the previous module and discussion of research projects.
- Evaluation: At the end of the semester (in week #15), students will deliver a brief in class presentation of their project. Students will submit the final term paper by week #16 of final exams.
Course description
This course is a graduate-level course 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.
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 use SPARC data and models, and leverage SPARC infrastructure. The Lecture program is a required pre-requisite for the research program.
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.
Prerequisites and/or intended student population
There are no prerequisites for this course. This is a graduate-level class, and it is recommended that students have completed undergraduate-level biology, chemistry, mathematics, and physics courses appropriate for pre-medical or pre-dental programs.
Recommended and/or Required textbook(s) and/or other supplies
Textbook: “Medical Physiology”, 3rd Edition, Boron & Boulpaep Eds (freely accessible online via ClinicalKey when students are connected to the Case network either on campus or via VPN).
SPARC resources are freely available from the website ‘https://sparc.science’. Recommended and required reading will come from the online materials such as journal articles and e-textbooks freely available to all students at Case.
Learning objectives and Course Goals
Module I: Lecture Program
- Improved breadth of knowledge about computational methodologies, familiarity with the NIH SPARC effort and its resources, as well as a well-grounded working knowledge about epithelial transport physiology and control by the ANS.
- The Lecture program will cover five main Core Topics: (1) Biophysical modeling theory, (2) Biophysical modeling tools, (3) The NIH SPARC effort, (4) Neurophysiology review, (5) Computational knowledge management.
Module II: Mentored Research Program
- Hands on experience with building a computational model in CellML including research, creation, execution and results analysis