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MVsim

A toolset for quantifying and designing multivalent interactions

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/.


MVsim v1.0

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: csarkar@umn.edu

Code related questions: bruncsics@mit.bme.hu

Requirements:

Available App version

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 desctop app:

Option 1:

  1. Downloading and installing MATLAB Runtime for windows, linux, mac
  2. Running the MyAppInstaller_web.exe executable file and follow the installation instractions
  3. Run the installd version of MVsim.

Option 2:

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

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

Usage:

Web App:

  1. After installing the web app, the page is accessible via: : /webapps/home/
  2. 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.

MATLAB App:

  1. Install MATLAB MVsim app
  2. Input parameters and press initiate and run button

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 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.

Troubleshooting: