This README.txt file was generated on <20210413> by <Yao Jiaxing>


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GENERAL INFORMATION
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1. Title of Dataset:
Simulation of Cell Migration and Oscillation


2. Author Information
<create a new entry for each additional author>

First Author Contact Information
    Name: Yao Jiaxing
    Faculty: Engineering
    Email: yaojx@connect.hku.hk



Corresponding Author Contact Information
    Name: Dr. Yuan Lin
    Faculty: Engineering
    Email: ylin@hku.hk


Author Contact Information (if applicable)
    Name: N/A
    Faculty: N/A
    Email: N/A


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DATA & FILE OVERVIEW
---------------------


Directory of Files:
   A. Filename: Migration Simulation       
      Short description: simulations of collective cell migration.       


       
   B. Filename: Oscillation Simulation
      Short description: simulations of collective cell oscillation.


        
   C. Filename: N/A       
      Short description: N/A


Additional Notes on File Relationships, Context, or Content 
(for example, if a user wants to reuse and/or cite your data, 
what information would you want them to know?): N/A


File Naming Convention:
  folders:
    results3/simulation3: a different simulation result named 3.

  files:
    SPV_Oscillation.m: main function of oscillation simulation.
    simulation.info: simulation parameters.
    results_123.vtu: cell sheet configuration at timestep 123.
    T2SwapLocations.dat: locations where T2 swaps happen.



-----------------------------------------
DATA DESCRIPTION FOR: T3SwapLocations.dat
-----------------------------------------
<create sections for each dataset included>


1. Number of variables: 4


2. Number of cases/rows: Determined by the simulation time.


3. Missing data codes: N/A
        Code/symbol        Definition
        Code/symbol        Definition


4. Variable List

    A. Name: Time
       Description: Time when T3 swaps happen
                    Value labels if appropriate

    B. Name: Num
       Description: Number of T3 swaps happened at this timestep
                    Value labels if appropriate

    C. Name: X_coordinate
       Description: X coordinate of T3 swap location
                    Value labels if appropriate

    D. Name: Y_coordinate
       Description: T coordinate of T3 swap location
                    Value labels if appropriate


--------------------------
METHODOLOGICAL INFORMATION
--------------------------

1. Software-specific information:
<create a new entry for each qualifying software program>

Name: Matlab
Version: 18a
System Requirements: Windows 10
Open Source? (Y/N): No

(if available and applicable)
Executable URL: N/A
Source Repository URL: N/A
Developer: MathWorks
Product URL: https://www.mathworks.com/company.html
Software source components: N/A

Additional Notes(such as, will this software not run on 
certain operating systems?): N/A


Name: Chaste
Version: Develop branch
System Requirements: Ubuntu
Open Source? (Y/N): Yes

(if available and applicable)
Executable URL: N/A
Source Repository URL: https://github.com/Chaste/Chaste.git
Developer: the University of Oxford
Product URL: http://www.cs.ox.ac.uk/chaste/
Software source components: N/A

Additional Notes(such as, will this software not run on 
certain operating systems?):
This work is done by developing our own codes on the basic framework of the CHASTE project of the University of Oxford. Many thanks to them. Some of the simulation output files are uploaded to the dateset. The codes are mainly written in C++. To repeat the results, you need to install, configure, make, and run the CHASTE source code package (refer to https://chaste.cs.ox.ac.uk/trac/wiki/ChasteGuides).



2. Equipment-specific information: N/A
<create a new entry for each qualifying piece of equipment>

Manufacturer: N/A
Model: N/A

(if applicable)
Embedded Software / Firmware Name: N/A
Embedded Software / Firmware Version: N/A
Additional Notes: N/A