oOo

oOo is a High-Performance Parallel Magnetic Tweezer program for real-time monitoring of protein folding and unfolding under force.

Usual Method [Sequential and single threaded]

Our Method [Concurrent]

System and Hardware Requirements

• Windows
• Ximea camera (xiQ USB 3.0 SuperSpeed)
• Piezo Controller (P-725.xDDPIFOC adnd PI-E-709) ( We tested on AMD threadripper Pro 3975wx 32 core 3.5Ghz 64GB RAM 64Bit Windows 10 Pro 20H2 )

Installation

To get started with this project, you'll need to have Python 3.8 and its dependencies installed on your machine. Here's how you can do it:

1. Python 3.8: Visit the official Python website at python.org and download the Python 3.8 installer for your operating system.

2. Ximea Drivers : Visit Ximea and install the camera drivers then install the xiAPI. ( We have used https://www.ximea.com/support/attachments/37/XIMEA_API_Installer.exe with all API option ticked while installing and the used this guide to install ximea python API https://www.ximea.com/support/wiki/apis/Python_inst_win )

   python camtest.py

   if this return no error we good to go!

3. Dependencies: Once Python 3.8 is installed, open a terminal or command prompt and run the following command to install the required dependencies:

   pip install -r requirements.txt

   This command will install all the necessary dependencies listed in the requirements.txt file.

Usage

To run the program, use the following command:

python oOo.py [arg1] [arg2]

Usage: [arg1] can be 
    fresh       ->     To take fresh stack.
    start       ->     Start data aquisition.
    plot        ->     Plot the collected data with [arg2] as bead number.
    stackplot   ->     Plot stack graph.

Modification

You can modify specific settings in the config.py the default settings are:

stack_size = 200        # Size of the stack
exposure = 1000         # Exposure time in milliseconds
resolution = 256        # Resolution of the image
workers = 20            # Number of workers for processing
driftworkers = 2        # Number of workers for drift correction
qu_limit = 100          # Queue limit for processing
driftworker = 4         # Number of workers for drift calculation

Cite

Pritam Saha, Vishavdeep Vashisht, Ojas Singh, Amin Sagar, Gaurav Bhati, Surbhi Garg, Sabyasachi Rakshi. Exploring Force-Driven Stochastic Folding Dynamics in Mechano-Responsive Proteins and Implications in Phenotypic Variation. (In press)

Please feel free to contact the corresponding author ([email protected]) through mail in case of any difficulty in installation and running the codes.