CyLaKS

The Cytoskeleton Lattice-based Kinetic Simulator

Installation

If you plan on compiling or instally CyLaKS locally, clone the repo:

git clone https://github.com/Betterton-Lab/CyLaKS
cd CyLaKS

Using pre-built Docker image

A pre-built image of CyLaKS is available as a Docker image. To download this image, run

docker pull shfiorenza/cylaks

Depending your local Docker permissions, you may need to add sudo to the command above. If this is the your first time using Docker, you may have to initialize the Docker Daemon. On Linux distributions, you can simply run

dockerd

On Windows and MacOS, you can use Docker Desktop.

Once you have the CyLaKS image, you can launch a Docker container named cylaks in the background via the provided script:

./launch_docker.sh

Again, you may need to add 'sudo' depending on your local Docker permissions.

Once the container is running, you can select from available CyLaKS demos to run by using the -d flag:

./launch_docker.sh -d

You can also launch custom CyLaKS simulations via Docker while the container is running:

docker exec -it cylaks cylaks.exe [parameter-file] [sim-name] [optional-flags]

To close the cylaks container, use the stop command:

docker stop cylaks

If the Dockerhub image does not work for whatever reason, try building the environment and simulation images on your machine:

./launch_docker.sh -e
./launch_docker.sh -b

Building from source

CyLaKS requires the following libraries:

• gsl
• yaml-cpp

On most Linux distributions, you can install these dependences as follows:

sudo apt-get install libgsl-dev
sudo apt-get install libyaml-cpp-dev

In order to use most of the included bash scripts found in scripts/, yq is also required. There are a variety of ways to install this utility, so consult the documentation to find the most convenient means for your local environment.

To use the provided installation script, you must have CMake (version 3.13+) installed. On most Linux distributions, CMake can be installed via:

sudo apt-get install cmake

Once CMake is installed, call the installation script to compile CyLaKS. An executable will be added to the main folder.

./install.sh 

There are additional flags to build CyLaKS in debug mode or clean the build directory. To view these options, add the '-h' flag:

./install.sh -h

Once compiled, you can observe CyLaKS run options by calling the executable:

./cylaks.exe

Running simulations

To run CyLaKS, use the cylaks.exe executable as follows:

./cylaks.exe [parameter-file] [sim-name] [optional-flags]

The parameter file must be a YAML file. See the files included in params/ for an example of proper formatting.

The sim name sets the prefix of all output files and can be whatever you'd like.

Demos

To select from currently available demos, use the run_demos.sh script.

Test modes

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Analyzing output

CyLaKS has two types of output files:

• .log: plain-text record of simulation output
• .file: raw data collected during simulation Log files can be viewed in any text editor, e.g., notepad. Data files must be parsed using the MATLAB scripts found in analysis/

To use the included analysis scripts, simply change the sim_name variable to the name of the simulation you wish to analyze. Note that this should be the raw sim name without directory or file suffixes, e.g., identical to the name of the log file without the .log suffix.