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/.
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)
- Packages:
- 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:
- Setting up the webserver by following the instructions
- Staring the Webserver following the instructions
- Copying the ctf file to the default /local/MathWorks/webapps/R2019b/apps/ location
Installation and setup for standalone desktop app:
Option 1:
- Download and install MATLAB Runtime for windows, linux, or mac
- 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
- Run the installed version of MVsim
Option 2:
- Download the MVsim version v1.1 packaged with runtime for windows, linux, or mac
- Follow the installation guide and launch the program
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:
- After installing the web app, the page is accessible via:
: /webapps/home/ - 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:
- Install MATLAB MVsim app
- Input parameters and press the initiate and run button. For more details, see the “MVsim user tutorial.pdf” file
Installation and run times:
- Typical installation time is ~1 min.
- 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