Please see the original research associated with MVsim at https://www.biorxiv.org/content/10.1101/2021.08.01.454686v1.
The installation files for MVsim can be found at https://github.com/sarkarlab/MVsim/.
Bence Bruncsics, Wesley J. Errington, Casim A. Sarkar
University of Minnesota
May 13, 2022
MVsim is licensed under the MIT License.
Questions related to licensing: email@example.com
Code related questions: firstname.lastname@example.org
- MATLAB R2019b or newer
- Packages: Image visualization toolbox
- For hosting the webserver:
Available App version
- MATLAB app: App installation file for MATLAB users
- Standalone Desktop App: Desktop application compiled by MATLAB
- Web App: deployable web app file
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 desctop app:
- Downloading and installing MATLAB Runtime for windows, linux, mac
- Running the MyAppInstaller_web.exe executable file and follow the installation instractions
- Run the installd version of MVsim.
- Download the MVsim version packaged with runtime for windows, linux or for 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_9.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
- 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)
- After installing the web app, the page is accessible via:
- After choosing the desired version the filling up the parameters in the Main and Parameters tabs and pushing the Initiate button the app droves the desired plots.
- Install MATLAB MVsim app
- Input parameters and press initiate and run button
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 30 min; a progress bar is included in the app for the user to monitor the calculations and ensure that the app has not stalled.
- 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