Date on Master's Thesis/Doctoral Dissertation


Document Type

Master's Thesis

Degree Name

M. Eng.



Degree Program

JB Speed School of Engineering

Committee Chair

Frieboes, Hermann

Committee Co-Chair (if applicable)

Chen, Joseph

Committee Member

Chen, Joseph

Committee Member

Altiparmak, Nihat

Author's Keywords

MultiCellDS; PhysiCell; XML; Python; Biological simulation


In the field of multicellular biology, it is currently very difficult for researchers to share digital data, due to a lack of standards for said data. Each laboratory will collect data from a particular project, which will describe only the features relevant to their research, and then present that data using written descriptions, charts, graphs, and images. This makes it difficult for the data produced by these studies be leveraged in other research efforts by scientists studying similar phenomena. An open-source, universal standard that attempts to meet this need is the MultiCellular Data Standard (MultiCellDS). MultiCellDS is described as a “a community-developed standard to functionally describe cell phenotypes with contextual information from the microenvironment”. A program called PhysiCell utilizes a modified, compact version of the MultiCellularData Standard through use of “custom” data tags that bypass validation. The goal of this project is to update MultiCellDS to reflect the data format utilized by PhysiCell so that PhysiCell files can be successfully validated by the standard. Additionally, a script is required to update PhysiCell files to remove the “custom” data tags, which are discouraged in the standard.