Package: vaxpress
VaxPressVaxPress 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 andin vivoprotein
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 theVaxPress documentation page.InstallationpipYou can install VaxPress via pip.Installing# Create a virtual environment for VaxPresspython-mvenv/path/to/vaxpress-env# Activate the virtual environmentsource/path/to/vaxpress-env/bin/activate# Install VaxPress alonepipinstallvaxpress# Alternatively, install VaxPress with LinearFold (only for non-commercial uses)pipinstall'vaxpress[nonfree]'Running# Activate the virtual environmentsource/path/to/vaxpress-env/bin/activate# Run VaxPressvaxpress-hiCodon DependencyIf you wish to activate the iCodon predicted stability
(--iCodon-weight) in the fitness function, ensure you have
working installations ofR,rpy2(version >= 3.0) andiCodon.For detailed installation instructions, visitiCodon's GitHub page.CondaAlternatively, you may also install VaxPress via a conda package:Installationcondacreate-nvaxpress-y-cchanglabsnu-cbioconda-cconda-forgevaxpressRunning# Activate the environmentcondaactivatevaxpress# Run VaxPressvaxpress-hSingularityTo run VaxPress via Singularity, you will need to install theSingularity CEfirst.
Download the container image fromthe GitHub project pageand place it in a directory of your choice.singularityvaxpress.sif-hWhen 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.UsageQuick StartHere's a basic command-line instruction to start using VaxPress.
Note that-iand-ooptions are mandatory:vaxpress-ispike.fa-ooutput--iterations1000-p32InputVaxPress 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--proteinswitch is required.Number of IterationsThe--iterationsoption is set to10by default. However,
for thorough optimization, it's recommended to use at least500iterations. 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 theTuning Optimization Parameterssection.You can set--iterationsto0to generate VaxPress's sequence
evaluation report without any optimization.Multi-Core SupportYou can use multiple CPU cores for optimization with the-por--processesoption.More About OptionsVaxPress 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 tothe manual.OutputOnce 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--presetoption to duplicate
the set-up for other sequence.Citing VaxPressIf you employed our software in your research, please
kindly reference our publication:Ju, Ku, and Chang (2023) Title. Journal. Volume. (in preparation)LicenseVaxPress is distributed under the terms of theMIT License.LinearFold and LinearDesign are licensed for non-commercial use
only. If considering commercial use, be cautious about using options
such as--lineardesignand--folding-engine linearfold.