Quantitative analysis of MinDE patterns

Cees Dekker Lab, Bionanoscience department, TU Delft, 03/2022, developed by Jacob Kerssemakers and Sabrina Meindlhumer

Publication available at: https://www.frontiersin.org/articles/10.3389/fphy.2022.930811/full?field=&journalName=Frontiers_in_Physics&id=930811

In the following, we provide instructions on how to set up a Python environment 'min_analysis' and install a package 'min_analysis_tools'. These tools can be used to perform analysis on Min protein surface pattern data. The folder 'min_analysis_scripts' contains scripts that use the provided tools to perform analysis on single stacks or perform batch processing of all stacks within a given folder.

This repository contains three main notebooks:

• DEMO_MinDE_global_analysis.ipynb: demonstration of global analysis
• DEMO_MinDE_local_analysis.ipynb: demonstration of local analysis
• Quickstart_Min_analysis.ipynb: quick analysis tool for single-stack Min pattern analysis

Further, a series of "Supplementary" notebooks, which provide accuracy tests and controls for the provided methods.

Jupyter notebooks can be accessed in the following binder:

The second release can be found at Zenodo:

Installation

• Install miniconda from https://docs.conda.io/en/latest/miniconda.html
• Open terminal (on Windows, search for 'Anaconda prompt')
• Install Git from https://git-scm.com/book/en/v2/Getting-Started-Installing-Git
• Clone this repository with git clone
• Within a terminal, change directory into this repository (cd mypath, replace mypath with the directory in which environment.yml is located)
• Create the environment by executing conda env create -f environment.yml
• Install the Python package by executing pip install -e .

Execute Python files

• Activate the environment by executing conda activate min_analysis in a terminal
• Can now run python file by executing python NAME_OF_FILE.py

Alternatively, change the interpreter path of your IDE to the min_analysis environment. For Spyder, that can be done as follows:

• Go to Preferences
• Go to tab 'Python interpreter'
• Select 'Use the following Python interpreter'
• With Miniconda and on Windows, the path to the Python interpreter will be as follows: C:/Users/USERNAME/Miniconda3/envs/min_analysis/python.exe (change USERNAME to your user)

Execute Jupyter notebook

• Activate the environment by executing conda activate min_analysis in a terminal
• Execute jupyter lab
• Open the notebook (.ipynb extension) within Jupyter

Remove environment

If you want to remove the environment (because you don't need it anymore or you want to recreate it), execute conda env remove -n min_analysis from the base environment.