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Please read this file to run the simulations 

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Methodology:
We use Multi-scale 3D-0D closed-loops of the systemic and pulmonary circulation, together with patient-specific MRI data on two hemodynamic conditions (stress and pharmacologically-induced stress) to study potential complications during liver transplantation.
For more information on methods, abbreviations, MRI parameters and model design, please see the related paper (citation below) and accompanying technical note.


Data overview: 
The CRIMSON (www.crimson.software) MITK file containing the Rest case is Condition_1.mitk. Stress and PRS are identical in terms of CRIMSON MITK file set-up; these settings are all contained in Conditions_2&3.mitk. The remaining files are ready-to-run simulation file sets, which can be used to reproduce the results demonstrated in the associated paper (https://doi.org/10.1371/journal.pone.0205829). These files can be used as-is, or you can replace the geombc.dat.1 and restart.0.1 files with new ones that you generate using the .mitk scenes, adjusted according to your preferences; for example, you might adjust the vessel wall properties.


Required software:
CRIMSON (CARDIOVASCULAR INTEGRATED MODELLING & SIMULATION) - a prototype simulation environment developed under the support of the European Research Counci ((http://www.crimson.software/)


Instructions for running simulations:
This file provides the key commands to manually setup the computational simulations used in the PLOS ONE paper 'Patient-specific modeling of right coronary circulation vulnerability post-liver transplant in Alagille’s syndrome' using CRIMSON.

Note that a Windows version of the CRIMSON flowsolver is provided as part of the CRIMSON Windows installer, but you will need a very powerful Windows computer to run these simulations, as the models used in the present work are extremely computationally-demanding. It is recommended that you use a Linux version of the CRIMSON flowsolver on a high-performance computer.



Option 1 (ready-to-use files to immediately start the simulation):
1. Please unzip the Ready-to-use files.
2. Copy the folders of each of the three conditions to the high performance computer.
3. In addition to different codes used, each folder provides the boundary conditions applied in the simulations described in the manuscript (e.g. LPN parameters). To run the 3D simulations for each condition simply launch the it using the CRIMSON flowsolver. In addition, the solver.inp file can be modified to run a 0D Ôreal-time simulationÕ (please open solver.inp with a text editor and modify line 4 "Simulate in Purely Zero Dimensions:"" to "True").
  



Option 2 (using the MITK files):
1. Please download and install Crimson software (http://www.crimson.software/).
2. Please unzip the MITK files and the Ready-to-use files.
3. From amongst the provided MITK files, load the MITK file of interest to CRIMSON (using the MITK files, additional changes can be made to the computational model in case the user wants to explore different settings/boundary conditions e.g. change the vascular wall properties, introducing a change in the geometry to create a virtual stenosis).
4. Navigate to the tree in the "Data Manager" panel and select the "Pulmonaries", "CRIMSON SOLVER" and then "Solver study 3D" items, in the described order.
5. In the right hand panel select the "CRIMSON Solver setup" tab and scroll down the right hand bar until to find the "Setup Solver" box; click to output the simulation files (faceInfo.dat, geombc.dat.1, multidomain.dat, netlist_surface.dat,numstart.dat, presolver folder, solver.inp, restart.0.1).
6. Copy and replace the geombc.dat.1 and restart.0.1 generated by CRIMSON for each individual condition to the respective unziped folder in the Ready-to-use file (discard the remaining files that were output by CRIMSON). Note that if you have not changed anything about the model (e.g. vascular wall properties), then doing this will produce restart.0.1 and geombc.dat.1 files which are identical to the ready-to-use versions.
7. Finally copy each Condition folder to the high performance computer and simply launch the simulation using the CRIMSON flowsolver.



For technical queries please contact crimson-users@googlegroups.com.


Citation to related material: 
Silva Vieira M, Arthurs CJ, Hussain T, Razavi R, Figueroa CA (2018) Patient-specific modeling of right coronary circulation vulnerability post-liver transplant in AlagilleÕs syndrome. PLOS ONE 13(11): e0205829. https://doi.org/10.1371/journal.pone.0205829


When referencing these data, please use the citation:
Figueroa, C.A. (2018). Patient-specific modeling of right coronary circulation vulnerability post-liver transplant in AlagilleÕs syndrome [Data set]. University of Michigan Deep Blue Data Repository. https://doi.org/10.7302/Z2N58JM4

October 2018.