Date on Master's Thesis/Doctoral Dissertation

5-2021

Document Type

Master's Thesis

Degree Name

M. Eng.

Department

Bioengineering

Committee Chair

Frieboes, Hermann

Committee Member

Chen, Joseph

Committee Member

Altiparmak, Nihat

Author's Keywords

Python; XML; Text File; PhysiCell; Biological Simulation

Abstract

Biological simulation tools are a valuable asset to bridge the gap between biological experimentation and biological theory. As systems thinking has become more regularly applied to biological materials and processes, these materials and processes have been characterized in multi-disciplinary, computational manners. This characterization has yielded an ability to create more realistic simulation tools that can provide in silico experiments for a wider range of scenarios. One prominent simulation tool is PhysiCell, an open-source physics-based multicellular simulation program which utilizes input Digital Cell Lines or Digital Snapshots from the MultiCellular Data Standard (MCDS) project.

This project aims to allow data exchange between MCDS Digital Cell Lines and ISA-Tab file sets to bring benefits of online editing and searching held by ISA-Tab files to Digital Cell Lines, which are useful for biological simulation. Additionally, conversion of ISA-Tab file sets to Digital Cell Lines allows a vast increase in the number of cell lines that can be used for simulation within PhysiCell.

This project allows data exchange between the two file types by using Python scripts to convert between the Digital Cell Line (XML) and ISA-Tab (text) file formats. The scripts produced in this project are validated for file format and verified for file contents for the Digital Cell Lines which exist at time of writing (up to DCL #242). All tools and outputs created in this project are open-source and provided on GitHub in order to facilitate cooperation in biological research to increase the knowledge of the scientific community.

In this project, the scope of inputs for ISA-Tab to Digital Cell Line conversion are limited to those which are derivatives of Digital Cell Lines due to limited ability of the conversion script to match ISA-Tab labels to MCDS Digital Cell Line elements. While limited, the created ISA-Tab to MCDS-DCL script provides an accepted ISA-Tab formatting framework for automated conversion rather than requiring file conversion “by hand”. The products of this project should be expanded in the future to allow a greater range of ISA-Tab input formats for conversion to Digital Cell Lines.

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