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 or pipenv:

$ pip install vimms

or

$ pipenv 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 However, note that this version may be outdated.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 can be managed using either Pipenv or Anaconda Python. After installing your chosen tool and cloning the repo, create a new virtual environment and install all required packages:

For Pipenv:

$ pipenv install
$ pipenv shell

For Anaconda:

$ conda env create --file environment.yml
$ conda activate vimms

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