LORA

LORA is the Lipid Over-Representation Analysis tool based on GOSLIN grammars

LORA online webapplication

Requirements

• Python 3.10+
• Java 17+

Installation

Linux

$ git clone https://github.com/IPHYS-Bioinformatics/LORA.git
$ cd LORA

Set up a Python virtual environment to isolate dependencies:

$ python -m venv .LORA-venv

Enter the virtual environment:

$ source .LORA-venv/bin/activate

Install LORA dependencies:

$ pip install -r requirements-linux.txt

Change into the main source directory to run LORA:

$ cd src/
$ python index.py

and visit https://localhost:8050

Windows

git clone https://github.com/IPHYS-Bioinformatics/LORA.git
cd LORA

Set up a Python virtual environment to isolate dependencies:

python -m venv LORA-venv

Enter the virtual environment:

LORA-venv\Scripts\activate

Install LORA dependencies:

pip install -r requirements.txt

Change into the main source directory to run LORA:

cd src
python index.py

and visit https://localhost:8050

Test data

1. DEMO 1: src/data/demo_janovska_query.csv & demo_janovska_universe.csv - Janovska et al. 2020, Figure 5D
2. DEMO 2: src/data/adipoatlas_query.csv & adipotlas_universe.csv - Lange et al. 2021, Figure 4A
3. DEMO 3: src/data/Query_Human_Lung_Endothelial_Cells.txt & Universe_Human_Lung_Endothelial_Cells.txt - Clair et al. 2019, LipidMiniOn test data
4. DEMO 4: src/data/Goslin_oxPE.txt & Goslin_oxPEq.txt - Kopczynski et al. 2020, Goslin test file and Lauder et al. 2017, Figure 7A

Using Docker

You can build the LORA Docker container by running

$ docker build . -t lora

The container exposes port 8050 for the webapplication, you can run it as follows:

$ docker run -it --rm --name lora -p 8050:8050 lora

Once the container has started, open your browser and open it at http://127.0.0.1:8050

You can stop the container with CTRL+c from the command line where you started it.

Citation

LORA, Lipid Over-Representation Analysis Based on Structural Information. Michaela Vondrackova, Dominik Kopczynski, Nils Hoffmann, Ondrej Kuda Analytical Chemistry 2023 [https://doi.org/10.1021/acs.analchem.3c02039]

Related Projects

• GOSLIN, (Goslin paper, Goslin 2.0 paper)
• GOSLIN Webapplication and REST API
• LipidMiniOn
• LION
• LipidLynxX, lipid ID converter and equalizer
• LINEX2
• lipidr
• LipidSig

License

• LORA is licensed under the terms of the MIT license (see LICENSE).
• The Goslin grammars are licensed under the terms of the MIT license (see licenses).
• jgoslin Java Implementation is licensed under the terms of the Apache License v2 (see licenses).