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Welcome to ViMMS

Welcome to the Virtual Metabolomics Mass Spectrometer (VIMMS), a comprehensive and modular framework for the simulation of fragmentation strategies in tandem mass spectrometry-based metabolomics.

ViMMS allows you to simulate fragmentation strategies, generate virtual chemicals through various methods, and evaluate the performance of different strategies or controllers in either single or multi-sample settings. ViMMS is designed to serve as a unified platform for the development, testing, and optimization of fragmentation strategies in LC-MS metabolomics.

We also offer an extension that allows ViMMS controllers to operate directly on the Thermo Orbitrap Fusion Tribrid instrument. Please note that you'll need a license for IAPI to use this feature.

Installation

ViMMS is compatible with Python 3+. You can install the current release of ViMMS using pip:

$ pip install vimms

Find the current version on our Release page or on PyPi.

To use an older version like ViMMS 1.0, used in our original paper, download it here. However, note that this version may be outdated.

To access the latest, unreleased ViMMS code, clone our repository:

git clone https://github.com/glasgowcompbio/vimms.git

ViMMS dependencies are managed with Poetry. After cloning the repository, create a new virtual environment and install all required packages: 

$ poetry install
$ poetry shell

Within the virtual environment, you can develop new controllers, run notebooks ($ jupyter lab), and more.

Building the Documentation

ViMMS uses MkDocs to build its documentation, which is hosted at vimms.readthedocs.io. You can preview the docs locally by running:

poetry run mkdocs serve

This command launches a local webserver so you can view the site at http://127.0.0.1:8000/.

Running the Test Suite

If you plan on contributing, make sure all tests pass. Execute the following from the project root:

./run_tests.sh

On Windows, use run_tests.bat instead. The test suite requires the development dependencies installed via poetry install.

More Information

Additional usage notes and installation instructions are available in our Installation guide, while example notebooks can be found in the demo directory.

Running on a Real Instrument

Controllers written for ViMMS are compatible with the Thermo Orbitrap Fusion Tribrid when used with the vimms_fusion extension. You must have a licensed copy of Thermo Fisher's IAPI installed. See Running on a Real Instrument for a minimal example.

Where to Go Next