Please see the original research associated with MVsim at https://www.nature.com/articles/s41467-022-32496-6.

The installation files for MVsim can be found at https://github.com/sarkarlab/MVsim/.

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MVsim v1.1

Bence Bruncsics, Wesley J. Errington, Casim A. Sarkar

University of Minnesota

July 22, 2022

MVsim is licensed under the MIT License.

Questions related to licensing: csarkar@umn.edu

Code related questions: bruncsics@mit.bme.hu

Requirements:

• MATLAB R2019b or newer
  • Packages:
    • Image visualization toolbox
    • Curve fitting toolbox
    • (MATLAB compiler for modifying MVsim)
• For hosting the webserver:
  • MATLAB Runtime
  • MATLAB WebAppServer

Available app versions

• MATLAB app: app installation file for MATLAB users
• Standalone desktop app: desktop application compiled by MATLAB
• Web app: deployable web app file for closed networks

Installation and setup for the Web App:

1. Setting up the webserver by following the instructions
2. Staring the Webserver following the instructions
3. Copying the ctf file to the default /local/MathWorks/webapps/R2019b/apps/ location

Installation and setup for standalone desktop app:

Option 1:

1. Download and install MATLAB Runtime for windows, linux, or mac
2. Run the executable MVsim_standalone_win.exe for windows, MVsim_standalone_linux.install for linux, or MVsim_standalone_mac.app for mac and follow the installation instractions
3. Run the installed version of MVsim

Option 2:

1. Download the MVsim version v1.1 packaged with runtime for windows, linux, or mac
2. Follow the installation guide and launch the program

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The directory MVsim contains the following uncompiled files and folders for the model:

• [Images] Containing the png files in the Images folder for the GUI
• [Diffs] Containing the 189 automatically generates .m files with the ODE system for the MATLAB ODE solver
• MVsim_GUI_V1_1.mlapp – the code for the GUI interface in the MATLAB App Designer
• GUI_Manual_input3x3x3.m – The code for plotting and for initial information for the model
• diff_time_series_calculation_3x3x3.m - Calls and process the output of the ode15s solver with apropriate time and ligand concentrations
• EffC_Calculator_polar.m - Used for the effective concentration calculation using polar coordinate integration in the GUI
• [Support_Scripts] - A collection of scripts used for state and ODE system genration used for the .m files generation is the Diffs folder (not required for the GUI)
• copyUIAxes.m and copyUIAxes.ReadMe.txt - used for saving the images and figures in the GUI (license information at the end of the script)

Usage:

Web app:

1. After installing the web app, the page is accessible via: : /webapps/home/
2. After choosing the desired version, input parameters on the Main and Parameters tabs and click the initiate button to produce the desired plots

MATLAB app:

1. Install MATLAB MVsim app
2. Input parameters and press the initiate and run button. For more details, see the “MVsim user tutorial.pdf” file

Installation and run times:

1. Typical installation time is ~1 min.
2. Run time varies based on the complexity of the simulation. For the included bivalent-bivalent demo with default parameters, the typical run time should be < 30 s. More involved simulations can take up to 10 min; a progress bar is included in the app for the user to monitor the calculations and ensure that the app has not stalled.

Troubleshooting:

• Undefined function error:
  • Check for all required MATLAB packages
  • Check MATLAB version (2019b required; 2021a preferred)
  • Add the Diff_Equations folder to the path
• Missing images:
  • Add State_images folder to the path