LipidXplorer Installation

Note: The current package of LipidXplorer is mainly compatible with 64bit versions of Microsoft Windows (7,8,10) only. A Linux version is only available from source. If you need help, please contact us.

File conversion

LipidXplorer supports the generic file formats *.mzML and *.mzXML. Raw spectra as they are produced by the mass spectrometer have to be converted into one of those formats before they can be used with LipidXplorer. The recommended converter is MSConvert from the ProteoWizard package. It supports the formats of the main mass spectrometer vendors and is maintained by a team of developers. It comes with an easy-to-use graphical user interface.

Details on how to use msConvert for LipidXplorer can be found here

Binary Distribution for Windows

The binary distribution of LipidXplorer is a zip-Archive containing the LipidXplorer.exe file. You can download the latest release version from here

Requirements: The binary version of LipidXplorer requires a 64bit Windows installation to run. Everything else is already bundled in the .exe file.

In order to run LipidXplorer from the binary distribution, please proceed as follows:

1. unzip the LipidXplorer-X.Y.Z.zip archive to a location of your choice,
2. open the unzipped directory in your Windows Explorer,
3. double-click LipidXplorer.exe to launch the application.

Please see the Tutorial for instructions on how to proceed.

Sourcecode Installation for Windows

Requirements: In order to work with the sourcecode and build LipidXplorer, you will need the following tools on your Windows PC (64 bit)

• Git (TortoiseGit)
• A Python IDE PyCharm CE
• Anaconda2, 64bit

The source code for LipidXplorer has been moved to the ISAS GitLab server. In order to clone it with TortoiseGit, follow these steps:

1. open a folder in your Windows Explorer where you want to keep the sourcecode locally,
2. right-click and select 'Git Clone...',
3. enter the repository URL: https://gitlab.isas.de/lifs-public/lipidxplorer.git ,
4. left-click 'Ok'

The sourcecode should now be cloned into the selected directory within the 'lipidxplorer' folder.

The next step is to import the wx-py27-anaconda.yml environment file, located in the lipidxplorer folder into anaconda. Please follow the instructions here, just replace 'environment.yml' with wx-py27-anaconda.yml

In order to use the dependencies for your project, open a Conda2 shell and navigate to the location where your project was cloned to. Follow the instructions here to activate the environment. You can then run LipidXplorer by typing 'python LipidXplorer.py'.

Using PyCharm

If you use PyCharm as your IDE, the following instructions will help you get started:

1. Use https://gitlab.isas.de/lifs-public/lipidxplorer.git as the Git location: Set up the git repository
2. Use the wx-py27 anaconda environment and the conda Python 2.7 interpreter: [1]
3. For further hints and tutorials, please see the PyCharm Quickstart

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Legacy Sourcecode Instructions (no longer necessary)

Download link

LipidXplorer 1.2.7 can be downloaded here. Unzip it and store the folder at any place you prefer. LipidXplorer is started with a double click on "LipidXplorer.py". In the "mfql" folder you find example queries taken from the LipidXplorer paper[1].

LipidXplorer 32Bit

• Python 2.6 here !Note! Python version has to be >= 2.6.6
• wxPython 2.8 (for Python 2.6) here
• numPy (for Python 2.6) here

LipidXplorer 64Bit

• Python 2.7 here
• wxPython 2.8 (for Python 2.7) here
• install Python 2.7 and wxPython 2.8
• download the lipidxplorer third party dependencies here
  • unzip it to a location of your choice
  • double click on install_dependencies.py
  • after the installation finished you can delete the unzipped folder - it is not needed any longer
  • if this fails, you can manually install the dependencies:
    • download pip: get-pip.py
    • install pip from cmd line with Python get-pip.py
    • download numPy (for Python 2.7 64Bit): Since Numpy is officially not supported for 64Bit there is an unofficial version here which can be used and installed. Please select numpy-<version>+mkl-cp27-none-win_amd64.whl where <version> is the newest.
    • open the command line window:
      • move your mouse cursor over the window in which you saved the numpy[...].whl file
      • do a right mouse click while holding down the SHIFT key
      • in the menu select Open command window here
    • install numPy from command line and type: c:\Python27\scripts\pip.exe install numpy-<version>-win_amd64.whl
    • insert the correct version number for <version>
    • lxml (for Python 2.7 64 Bit): lxml is needed for reading mzML files with Python 2.7. Here is a site where you can download it for your system. Please select lxml‑<version>‑cp27‑none‑win_amd64.whl
    • save it in the same folder as the numpy file
    • install lxml from command line: c:\Python27\scripts\pip.exe install lxml-<version>-win_amd64.whl

The requirements for Linux are the same. However, the links above are only for the Windows version. For Linux, please check out the repositories of your distribution. Further, the Python C extensions have to be build separately on Linux. Please contact us for further information.

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[1] Herzog, R., Schwudke, D., Schuhmann, K., Sampaio, J.L., Bornstein, S.R., Schroeder, M., and Shevchenko, A. 2011. A novel informatics concept for high-throughput shotgun lipidomics based on the molecular fragmentation query language. Genome Biol 12(1): R8.