This repository contains the python notebooks and in vitro and in vivo data used in the workflow to produce the figures & results in our paper “Cell-autonomous timing drives the vertebrate segmentation clock’s wave pattern” (Rohde et al. 2023). Please use the subject titles of the notebook to find data & code & results of interest. Note, the data folder is not organized according to Rohde et la. 2023 figure number. Enjoy!
To run the notebooks, please install the following conda enviroment:
conda env create -f wsc.yml- PSM4 Dynamics in culture Part 1
- PSM4 Dynamics in the embryo Part 1
- PSM4 Dynamics in culture Part 2
- PSM4 Dynamics in the embryo Part 2
- AP Dynamics in culture Part 1
- AP Dynamics in culture Part 2
- Dynamics by cycle in culture
- Dynamics by cycle in embryo
- Backtracked somites
- TB dynamics in embryo
- FGF in culture Mesp analysis
- FGF in culture Her1 analysis
All the Jupyter Notebooks can be found in the "notebooks" folder and all the data can be found in the "Data" folder. As long as the repository directory structure is kept after download, the notebooks will run without any problem. All the resulting .pdf plots are saved in a "Results" folder inside the "Data" folder.