iCFree

iCFree is a Python-based program designed to automate the process of generating and running a Snakemake workflow for sampling and preparing instructions for laboratory experiments. The program includes components for generating samples, creating plates, and instructing the handling of these plates.

Table of Contents

• iCFree
  • Table of Contents
  • Installation
  • Usage
    • Basic Command
    • Components
      • Sampler
        • Usage
        • Arguments
      • Plate Generator
        • Usage
        • Options
      • Instructor
        • Usage
        • Options
    • Example
  • License
  • Authors

Installation

1. Install Conda:

   • Download the installer for your operating system from the Conda Installation page.
   • Follow the instructions on the page to install Conda. For example, on Windows, you would download the installer and run it. On macOS and Linux, you might use a command like:

     bash ~/Downloads/Miniconda3-latest-Linux-x86_64.sh

   • Follow the prompts on the installer to complete the installation.

2. Install iCFree from conda-forge:

   conda install -c conda-forge icfree

Usage

The main entry point of the program is the __main__.py file. You can run the program from the command line by providing the necessary arguments for each step of the workflow.

Basic Command

python -m icfree --sampler_input_filename <input_file> --sampler_nb_samples <number_of_samples> --sampler_seed <seed> --sampler_output_filename <output_file> --plate_generator_input_filename <input_file> --plate_generator_sample_volume <volume> --plate_generator_default_dead_volume <dead_volume> --plate_generator_num_replicates <replicates> --plate_generator_well_capacity <capacity> --plate_generator_start_well_src_plt <start_well_src> --plate_generator_start_well_dst_plt <start_well_dst> --plate_generat...

Components

Sampler

The sampler.py script generates Latin Hypercube Samples (LHS) for given components.

Usage

python icfree/sampler.py <input_file> <output_file> <num_samples> [--step <step_size>] [--seed <seed>]

Arguments

• input_file: Input file path with components and their max values.
• output_file: Output CSV file path for the samples.
• num_samples: Number of samples to generate.
• --step: Step size for creating discrete ranges (default: 2.5).
• --seed: Seed for random number generation for reproducibility (optional).

Plate Generator

The plate_generator.py script generates plates based on the sampled data.

Usage

python icfree/plate_generator.py <input_file> <sample_volume> [options]

Options

• --default_dead_volume: Default dead volume.
• --dead_volumes: Dead volumes for specific wells.
• --num_replicates: Number of replicates.
• --well_capacity: Well capacity.
• --start_well_src_plt: Starting well for the source plate.
• --start_well_dst_plt: Starting well for the destination plate.
• --output_folder: Folder to save the output files.

Instructor

The instructor.py script generates instructions for handling the generated plates.

Usage

python icfree/instructor.py <source_plate> <destination_plate> <output_instructions> [options]

Options

• --max_transfer_volume: Maximum transfer volume.
• --split_threshold: Threshold for splitting components.
• --source_plate_type: Type of the source plate.
• --split_components: Components to split.

Example

Here is an example of how to run the program with sample data:

python -m icfree --sampler_input_filename data/components.csv --sampler_nb_samples 100 --sampler_seed 42 --sampler_output_filename results/samples.csv --plate_generator_input_filename results/samples.csv --plate_generator_sample_volume 10 --plate_generator_default_dead_volume 2 --plate_generator_num_replicates 3 --plate_generator_well_capacity 200 --plate_generator_start_well_src_plt A1 --plate_generator_start_well_dst_plt B1 --plate_generator_output_folder results/plates --instructor_max_transfer_volume...

License

This project is licensed under the MIT License. See the LICENSE file for details.

Authors

ChatGPT, OpenAI