Description
===========
This is a finite element simulation package specifically designed to model morphogenesis and deformaion of 
biological material. 

The package have been used to model morphogenesis of real tissues inside the fly embryo,
providing mechanical basis of tissue shape formation and sucessfully predicting the emergent shape of tissues with
mutations. The predictive power has long term high impact in wound healing, regeneration, and tissue engineering.
Details of the thory and methodology can be found in https://www.biorxiv.org/content/10.1101/515528v1. 
One example for morphogeneis is provided for 36 hour development of the wing of the fly, see EXAMPLE sections below.

Additional to modelling morphogenesis, this simulation platform has been used to model a series of experimental 
setups used to determine physcal properties of biological samples. As these samples have highly complex structures,
and noise in their physical properties, it is not trivial to use analytical approaches to interpret the 
experiments and deduce physical properties. The simulations allow for fitting of the experimental result to provide
quantitatave outputs for physical property measurement form the experiments. One example is provided for stiffness 
measurement from micro-pipette aspiration, see EXAMPLE sections below.


Compilation
===========
The package has relatively standard library dependencies. Of note, it requires OpenMP, OpenGL, Boost, 
GLM and PARDISO solver (see below). The .pro files for compilation in linux environment is available for
both the user interface and server versions, and can be adjusted for the setup of the user. The 
recommended compilation is with a modern c++ compiler, through qmake. 

qmake -o Makefile TissueFolding.pro OR qmake -o Makefile TissueFoldingUI.pro
make 

Which will generate the executable under Release folder for both UserInterface and Tissuefolding folders. The .pro 
files can be found under {Mainpath}/UserInterface and {Mainpath}/TissueFolding, respectively.

** IMPORTANT **
This package requires PARDISO sparse matrix solver. If this library is not available in the test machine,
it can be downloaded and an academic license obtained freely through https://pardiso-project.org - this 
does not require an academic email address.

For purely test purposes, a copy of the library for unix environment is available in {MainPath}/Pardiso, and a 
PLACEHOLDER license file pardiso.lic is included. Having the library in an accessable path will allow for 
compilation, and placing a pardico.lic file either in the home directory OR where the executable is called 
from will allow for running the simulation without error termination, but the solver WILL NOT SOLVE THE SYSTEM.
Please feel free to use this method for saved simulation displays and testing the compilation of the code. 
For a functioning solver, the contents of the pardiso.lic should be replaced with an actual license, that can be 
freely obtained from https://pardiso-project.org.


DOCUMENTATION
=============
Documentation can be found in {Mainpath}/Documentation
It is suggested that the html version is viewed through {Mainpath}/Documentation/html/index.html


EXAMPLE Saved simulations and videos
====================================
There are two sample simulations saved for demonstrating some of the capabilities of the TissueFolding package.
1) Morphogenesis
2) Pipette

Saved under {Mainpath}/ExampleSimulations/

Each sample simulation contains a one-page summary of the setup, a pre-rendered video of the simulation and
the saved data files for displaying the simulations results with the TissueFolding package. 

The script to demonstrate each saved simulation can be found in:
{Mainpath}/ExampleSimulations/displaySave.sh 

Please modify the main path and the simulation you would like to display accordingly.

** IMPORTANT **
The provided script will inflate some archived files. If running without the displaySave.sh script,
please unzip the SaveFile.zip and GrowthFile.zip in {Mainpath}/ExampleSimulations/morphogenesis before attempting to display.


EXAMPLE Simulations to run
==========================
There are three sample simulations to demonstrate the TissueFolding package in action, in parallel with the 
saved simulations. In each scenario, the parameter set used to generate the saved simulation is used. 
Simulations can be started from scratch, or can be continued from saved files. 

A script to inititate simulations can be found in:
Saved under {Mainpath}/ExampleSimulationToRun/runSimulation.sh

The results can be displayed via:
Saved under {Mainpath}/ExampleScriptsToRun/displaySave.sh

Folder naming is self-explanatory, it is recommended the script provided is used to 
initiate the simulations. 

The morphogesis script here is set up for 10 hours, wherease the provided exapmle is a longer simulation of 
36 hours (under {Mainpath}/ExampleSimulations/morphogenesis, see "EXAMPLE Saved simulations and videos" above). 
The examples simulations to run can be set up for longer, by modifying the modelinput file under each example directory.
The length of simulation is set in parameter "SimulationLength(sec):" It is recommended to keep the time step shorter 
for morphogenesis simulations longer than 24 hours (parameter "TimeStep(sec):") as the geometry becomes challenging 
with increasing self-contacts.