Development of algorithm simulating spatial fold change of cell signaling for pattern formation in zebrafish
Embryos develop robust spatiotemporal patterns by encoding and interpreting biological signals in real time. Developmental patterns often scale with body or tissue size even when total cell number, cell size or growth rate are changed. A striking example of patterning is the segmentation of somites — the precursors of vertebral column. Despite decade-long efforts, how positional information for segmentation is encoded by cell signaling remained elusive. To address this fundamental question, we studied a novel zebrafish tail explant model that recapitulated the scaling of somite sizes with the length of unsegmented tissue in growing intact embryos. This paper provides an algorithm written in MATLAB as well as Python and finally finding a way to write an efficient algorithm to be able to answer the question described above. Information encoding by spatial fold-change of cell signaling is a remarkable strategy that could be utilized for engineering precisely patterned tissues or organs. We also discuss the limitations of simulations performed using MATLAB with performance decreasing with the large data sets. So, we tried to analyze the factors that impacted the performance of the algorithm. Finally, we tried to answer questions regarding the language selection in which a simulation method can be written efficiently.