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Epithelium: The lightweight, customizable epithelial tissue simulator

Drag, Melvyn I
http://rave.ohiolink.edu/etdc/view?acc_num=osu1430011382

Abstract Details

2015, Master of Mathematical Sciences, Ohio State University, Mathematics.
Epithelial tissue performs many important functions in animals, such as preventing contamination, transporting gases and nutrients, and fluid secretion. Macroscopically, epithelial tissue can be thought of as the layer of an animal that separates it from the exterior world. The geometrical and topological features of epithelial tissue make it amenable to computational modeling. There are several simulation codes in existence which reproduce certain aspects of epithelial tissue morphogenesis, wound healing, and equilibration, but to the best of our knowledge only one of them is freely available to the public. Unfortunately, installation and use of this software requires expertise in a unix-like operating system and advanced knowledge of several programming languages. With this in mind, I have developed Epithelium, a lightweight epithelial tissue simulator which compiles easily on any unix-like system, and which can also be distributed as precompiled binaries. The code has very few dependencies, and these dependencies are likely already satisfied by the default packages installed on a Linux or Mac computer. For users with access to NVIDIA GPUs, Epithelium comes in stable and beta parallel versions. In Epithelium simulations are fairly easy to design and run via several configuration files, the source code is highly modularized, and the algorithms used therein are extensively documented. As such, this code is useful for reproducing previous results, and for quickly designing new computational biology experiments of epithelial tissues.
Ed Overman (Advisor)
Marcos Sotomayor (Advisor)
48 p.
Biology; Computer Science; Mathematics
parallel computing; epithelial tissue

Recommended Citations

Citations

  • Drag, M. I. (2015). Epithelium: The lightweight, customizable epithelial tissue simulator [Master's thesis, Ohio State University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=osu1430011382

    APA Style (7th edition)

  • Drag, Melvyn. Epithelium: The lightweight, customizable epithelial tissue simulator. 2015. Ohio State University, Master's thesis. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=osu1430011382.

    MLA Style (8th edition)

  • Drag, Melvyn. "Epithelium: The lightweight, customizable epithelial tissue simulator." Master's thesis, Ohio State University, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=osu1430011382

    Chicago Manual of Style (17th edition)

osu1430011382
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This open access ETD is published by The Ohio State University and OhioLINK.