vaxpress 0.9

Codon Optimizer for mRNA Vaccine Design

VaxPress

VaxPress is a codon optimizer platform tailored for mRNA vaccine development. It refines coding sequences starting from protein or RNA sequences to boost both storage stability and in vivo protein expression. Plus, additional properties can be easily programmed into the optimization process with just a few lines of code via a pluggable interface. For the detailed information about VaxPress, including its options and algorithmic features, please refer to the VaxPress documentation page.

Installation

pip

You can install VaxPress via pip.

Installing

# Create a virtual environment for VaxPress
python -m venv /path/to/vaxpress-env

# Activate the virtual environment
source /path/to/vaxpress-env/bin/activate

# Install VaxPress alone
pip install vaxpress

# Alternatively, install VaxPress with LinearFold (only for non-commercial uses)
pip install 'vaxpress[nonfree]'

Running

# Activate the virtual environment
source /path/to/vaxpress-env/bin/activate

# Run VaxPress
vaxpress -h

iCodon Dependency

If you wish to activate the iCodon predicted stability (--iCodon-weight) in the fitness function, ensure you have working installations of R, rpy2 (version >= 3.0) and iCodon. For detailed installation instructions, visit iCodon's GitHub page.

Conda

Alternatively, you may also install VaxPress via a conda package:

Installation

conda create -n vaxpress -y -c changlabsnu -c bioconda -c conda-forge vaxpress

Running

# Activate the environment
conda activate vaxpress

# Run VaxPress
vaxpress -h

Singularity

To run VaxPress via Singularity, you will need to install the Singularity CE first. Download the container image from the GitHub project page and place it in a directory of your choice.

singularity vaxpress.sif -h

When using the Singularity image, both the input and output must be somewhere inside your home directory for VaxPress to run without complicated directory binding configurations for Singularity.

Usage

Quick Start

Here's a basic command-line instruction to start using VaxPress. Note that -i and -o options are mandatory:

vaxpress -i spike.fa -o output --iterations 1000 -p 32

Input

VaxPress requires a FASTA format input file that contains the CDS (CoDing Sequence) to be optimized. In case the FASTA file holds a protein sequence, the additional --protein switch is required.

Number of Iterations

The --iterations option is set to 10 by default. However, for thorough optimization, it's recommended to use at least 500 iterations. The optimal number of iterations may differ depending on the length, composition of the input, and the selected optimization settings. It's important to note that the optimization process may stop before completing all the specified iterations if no progress is observed over several consecutive cycles. Guidelines for setting the appropriate number of iterations and other optimization parameters can be found in the Tuning Optimization Parameters section.

You can set --iterations to 0 to generate VaxPress's sequence evaluation report without any optimization.

Multi-Core Support

You can use multiple CPU cores for optimization with the -p or --processes option.

More About Options

VaxPress offers the flexibility to adjust optimization strategies in detail and integrate with LinearDesign. It also allows several more convenient functions such as preset parameters, user-defined custom scoring functions, and etc. For comprehensive explanation, please refer to the manual.

Output

Once you've run VaxPress, the specified output directory will contain the following five files:

• report.html: A summary report detailing the result and optimization process.
• best-sequence.fasta: The refined coding sequence.
• checkpoints.tsv: The best sequences and the evaluation results at each iteration.
• log.txt: Contains the logs that were displayed in the console.
• parameters.json: Contains the parameters employed for the optimization. This file can be feeded to VaxPress with the --preset option to duplicate the set-up for other sequence.

Citing VaxPress

If you employed our software in your research, please kindly reference our publication:

Ju, Ku, and Chang (2023) Title. Journal. Volume. (in preparation)

License

VaxPress is distributed under the terms of the MIT License.

LinearFold and LinearDesign are licensed for non-commercial use only. If considering commercial use, be cautious about using options such as --lineardesign and --folding-engine linearfold.