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LipidLynxX v0.4.12-beta preview release

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@ZhixuNi ZhixuNi released this 13 Apr 16:56
· 205 commits to master since this release
v0.4.12-beta
33e276b

This is a preview of LipidLynxX, please use it for test purposes only

Instructions

Sample files:

  • Test input file: LipidLynxX/doc/sample_data/input
  • Test output file: LipidLynxX/doc/sample_data/output

How to install and use LipidLynxX

Please find our user guide in folder doc.

LipidLynx_01_Home

Important Notice

The current LipidLynxX source code was tested using our collection of lipid abbreviations
for major lipid classes from following databases and programs:

  • Databases (4):

    • HMDB, LIPID MAPS, LipidHome, SwissLipids

  • Programs (17):

    • ALEX123 lipid calculator, Greazy, LDA 2, LipidBlast, LipidCreator, LipiDex, LipidFrag, LipidHunter,
      LipidMatch, LipidPro, LipidSearch, Lipostar, LIQUID, LPPtiger, MetFrag, MS-DIAL, MZmine2

  • Common abbreviations (customizable):

    • Abbreviations such as DHA, PAPE, PLPC, POPNC .etc are also included as defined alias.
      detailed settings can be found in lynx\configurations\defined_alias.json

If your database / program is not included in the list above, you can test if any of the configuration files located in lynx\configurations\rules\input would fit to your database / program.
If conversion is not possible, please contact us so that we can help you to generate suitable configuration file.

A robust and accurate converter can only be achieved by community-wide collaborations, thus any issue reports from general users and developers are welcome and will improve LipidLynxX project.

Thus, if you meet any issues during using LipidLynxX, please report your issue
here

Notice to general users

An easy to use .exe version for Windows platform users will be available soon.
For macOS users, a installation pack is under development and will be ready in approximately end of May 2020.
If you really want to have an early access to the exe version, please contact us by email.

Additional notice to developers

Since the code is still changing rapidly, the definitions of API and documentations in the source code may not be updated accordingly.
We kindly ask, if you have any plans to use LipidLynxX API contact us first, or follow this repository to get timely notifications when new changes are introduced.

Key Features

  • Optimized for manual interpretation and computer processing
  • Suitable for both unmodified lipids and modified lipids
  • Unified modification controlled vocabularies
  • Unified position specific annotations
  • Cross level match based on shared levels
  • Extract key information from LipidLynxX ID
  • Strictly controlled format using JSON schema
  • Easy to use Graphic User Interface
  • API access for professional users
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