Release 2.6 (final)

Final update before paper re-submission. This is be the version associated with the 2019 paper - any potential future changes will extend the software beyond what is described in the 2019 paper.

Major changes:

• Implemented fix boundaries. Choosing periodic boundary conditions becomes an option.

Minor changes:

• Changed app window name to MultiCellSim.

Release 2.5 (pre-print)

Final version of MultiCellSim, accompanying the Dang et al., 2019 bioRxiv pre-print.

Release of standalone application: MultiCellSim can finally be used for users without MATLAB! Download the file "MultiCellSim_R2_5_Setup.zip" (Windows) or "MultiCellSim_setup_macOS.zip" (macOS) and see the main page for detailed instructions on how to install MultiCellSim.

For MATLAB R2019a users: directly download "MultiCellSim_R2_5_R2019a.mlappinstall" and run it. Note that this installer is for MATLAB R2019a. The raw code contains (untested) applications for R2017b, R2017a and R2016b.

Changes from previous version:

• Implemented OR-logic for integrating two signals. Previously the two signals were always integrated using and AND-gate, now the user has the choice between AND and OR logic.
• Simplified the saving and loading scheme.
• Various minor bugs from previous versions fixed.
• Application name changed into MultiCellSim.
  *Added short descriptions for each of the fields and buttons that will pop up if you hover your mouse over for some time

Release 2.4

Major changes:

• New interface: unessential features have been discarded and the two signalling molecules with additive interaction has been removed.
• Initiate the system with custom input state (loaded from excel file). Save snapshots of a simulation as excel files that can be reloaded with this function.
• New plot feature: plot a kymograph (space-time plot) of the states over time.

Release 2.3

Major changes:

• Plots cells on a different lattice (still triangular, but overall shaped like a rectangle rather than a trapezoid shape).
• Allows for randomizing cell positions.
• Allows for controlling cell size.
• Plot cross-correlation function between different genes (preliminary).

Release 2.2

Major changes:

• Simultaneous plotting of two genes through multiple colors.
• Visualise gene circuit, phase diagram and state diagrams for chosen parameter set.
• Export movies (.avi) of the simulated tracjectories.

Release 2.1

Release 2.1 has a few minor updates from release 2.0:

• Plotting the lattice is now significantly faster, allowing playback at a faster rate. This also resolves a previous issue where the simulation skips time steps.
• Added slider for controlling playback speed.
• Added "Skip to time" menu to skip to any time in the simulation.

Release 2.0

Version 2.0 is out! Major modifications in the new version include:

• Simulations with two types of signalling molecules. The two molecules can interact additively or multiplicatively to turn ON and OFF cells.
• Improved simulation control through the use of press and play buttons reminiscent of media playback. Added replay mode for skipping through paused or terminated simulations.
• I/O features allow users to easily save and load interesting simulated trajectory data and figures.
• Plotting options give the user the option to plot features of the simulations and save the plots, which can be useful in identifying periodic dynamics and spatial organisation.
• Options enable handling of the spatial index as an input variable (for the initial state) and display during simulations.
• Several back-end improvements speed up the simulations and facilitate addition of more features in the future.
  Enjoy playing with our cells!

Note: download "Multicellularity-2.0.release.zip" to obtain the source files. The sources files named "Source code (zip)" and "Source code (tar.gz)", which GitHub automatically adds, are not correct!

Release 1.1

Mostly the same as 1.0, with a few minor changes:

• Added a "Pause" button that halts the simulation until the "Run" button is pressed again.
• Fixed initial window issue (thanks @MarcelBrusius).
• Clicking the slide to change the cell state from binary to continuous or vice versa now also stops the simulation.

Initial release

To install the app in MATLAB, downloading and executing "Multicellularity.R1.0.mlappinstall" should be sufficient. To view the full source code, download the package (which also contains the installation file).

Multicellular model MATLAB application

• Created MATLAB-based application for visualising simulations.
• Installation as a MATLAB app through executable file.
• Initial documentation provided on GitHub.