sopsim 0.2.4

SOPSim simulation library

SOPSim

SOPSim is a Python simulation package for investigating SOP pattern formation. You can choose to use it in one of four ways:

1. The official SOPSim website
2. As a Command line tool
3. As a website, local to your computer
4. As a Python API

Each method is explained in detail below.

1. The official SOPSim website

The official SOPSim website is available at (link coming soon).

2. As a Command line tool

Inside your command line, type:

pip install sopsim

to install the package.

Use this command below to run a single simulation:

sopsim run --nc 4 --filopodia-type A --filopodia-life-time 10 --out-dir output

In this specific example, this command will also generate plots and metadata to a folder called output.

For help, run:

sopsim run -h

3. As a website, local to your computer

After installing SOPSim with pip install, you can start the local web app with:

sopsim serve

Once you run this, copy the link and paste it into your browser. The link will show up in your terminal and will start with:

http://...

For help, run:

sopsim serve -h

4. As a Python API

Assuming you have Python and the sopsim library installed, create a new Python script and add the following code:

from sopsim import sopsim

if __name__ == '__main__':
    results = sopsim(Nc=4, filopodia_type="A", filopodia_life_time=10)
    print(results["FData"])

Note: In its current version, using the API does not allow users to view plots.

• results["FData"][0] → Convergence time
• results["FData"][1] → Relative Sensory Area (RSA)
• results["FData"][2] → Mean Local Sensory Area (LSA)

Input Values

The repo enforces these input rules:

Input	Allowed values
Nc (Number of cells per row in final square tissue*)	Integer >= 1
filopodia_type	One of A, B, C, D. Default = A
filopodia_life_time	Integer >= 1. Default = 10

Important:

• *Nc = 4 implies a 4x4 tissue
• Nc>=10 can take many hours to run, so start smaller when testing

Bug fixes:

• 0.2.4: Made an update to better describe FData in the README.md file
• 0.2.3: Backend works. Front end changes now applied so cards do not overlap. Slight rewording of help command
• 0.2.2: Broken. Issue: default values for filopodia type and lifetime come from a single source
• 0.2.1: Broken. Issue: default values for filopodia type and lifetime come from a single source