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Releases: SysMedOs/LipidLynxX

LipidLynxX version 0.9.24 for ELM2020

01 Oct 15:48
@ZhixuNi ZhixuNi
v0.9.24
4166a04
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LipidLynxX version 0.9.24 for ELM2020 Latest
Latest

Description

After intensive development, the LipidLynxX is switched to FastAPI based web oriented package and finally first phase of the Linker module.

LipidLynxX_Start_Firefox

!For test use only, not for production!
Please send use feedback to help us improve our software, thanks!

Main Modules

  • LipidLynxX Converter

    • Convert different abbreviations to uniformed LipidLynxX ID

  • LipidLynxX Equalizer

    • Cross compare different level of LipidLynxX ID on selected level

  • LipidLynxX Linker

    • Link lipid abbreviations to available resources

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
  • Command line tools for professional users

Install

For general Windows users:

  • Download LipidLynxX_v0-9-24.zip ~125MB
  • Unzip it to a folder
  • Find the LipidLynxX.exe and double click
  • LipidLynxX backend will pop-up a webpage in your default web browser e.g. Chrome, and a command line window for debug information.
  • Please allow LipidLynxX to pass firewall for the Linker module to access databases
  • Just close the command line debug window to quit LipidLynxX
  • Due to limitations of packaging, please run max 3 tasks at the same time.
  • Known issues: if Linker runs more than 300s or more than 30s/per ID, please restart LipidLynxX and try again.

For developers:

  • Please use python 3.8.5 and run from source code.
  • Recommend to use "pip install -r requirements.txt" in an virtual env to install the dependencies
  • run python LipidLynxX.py to start.
  • please check lib\lynx\config.ini for more settings of ports and max clients/workers

Type of change

  • Bug fix (non-breaking change which fixes an issue)
  • New feature (non-breaking change which adds functionality)
  • Breaking change (fix or feature that would cause existing functionality to not work as expected)
  • This change requires a documentation update

LipidLynxX Linker in v0.9.24

LipidLynxX-Linker

Assets 3

LipidLynxX v0.4.12-beta preview release

13 Apr 16:56
@ZhixuNi ZhixuNi
v0.4.12-beta
33e276b
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LipidLynxX v0.4.12-beta preview release Pre-release
Pre-release

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
Assets 4