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LipidXplorer

LipidXplorer is a software that is designed to support bottom-up and top-down shotgun lipidomics experiments performed on all types of tandem mass spectrometers. Lipid identification does not rely on a database resource of reference or simulated mass spectra but uses user-defined molecular fragment queries. It supports accurate, isotope-corrected quantification based on the identified MS1 or MS2 level fragments.

Downloading LipidXplorer

The latest (binary) release version of LipidXplorer is available from the LIFS Portal. You can obtain the source code for LipidXplorer from our GitLab server and release version archives from here.

Running LipidXplorer on Windows

For Windows, we provide a single executable for LipidXplorer for download from the LIFS Portal. Please download the zip-archive to a location of your choice and extract (unzip) the contents. Change to the unzipped LipidXplorer archive directory and simply double-click on LipidXplorer.exe to start it.

Installation and Tutorials

Please see more detailed installation instructions on our Wiki. These also cover the case of working with the source code.

The Wiki also offers an overview of the concepts behind LipidXplorer, as well as tutorial and reference materials.

Working with the LipidXplorer Source Code

We recommend PyCharm for development of the LipidXplorer codebase and Anaconda 3 to manage a stable, versioned Python environment. Any other Python IDE will also work just as well. Please see the environment.yml file in the project's source root folder for reference of an exported Anaconda environment. You can import it in your local Anaconda installation, call

conda env create -f environment.yml 

Creating a Windows Executable

We use pyinstaller (part of the Anaconda environment) to create a Python executable of LipidXplorer that can be easily run on Windows. To create the exe in the LipidXplorer-1.2.8 folder, please run the following command:

pyinstaller --distpath="LipidXplorer-1.2.8" LipidXplorer.spec

This will also create a zip archive of the distpath folder in the root directory of the project: LipidXplorer-1.2.8.zip.

Creating a Linux Executable

The same instructions for creation of a standalone executable also apply under Linux. Please make sure, that you have a proper Anaconda environment installed and activated. Then run the following command:

pyinstaller --distpath="LipidXplorer-1.2.8" LipidXplorer.spec

This will also create a zip archive of the distpath folder in the root directory of the project: LipidXplorer-1.2.8.zip.

Versioning

We use Semantic Versioning for versioning of the software.

To browse available versions and releases, please see the tags on this repository.

Authors

  • Ronny Herzog - Initial work
  • Jacobo Miranda Ackermann - Current Developer
  • Fadi Al Machot - Contributor
  • Nils Hoffmann - Contributor

License

This project is licensed under the GNU GPL License, version 2 - see the COPYRIGHT.txt file for details

Help and Support

Please check our Wiki on details on how to contact us to receive help and report errors.

known issues

to run it in a virtual environment in on macOS use pythonw instead of python

Citing the Software

Herzog R, Schwudke D, Shevchenko A: LipidXplorer: Software for Quantitative Shotgun Lipidomics Compatible with Multiple Mass Spectrometry Platforms. Current Protocols in Bioinformatics 2013 Oct 15 PUBMED