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Published: 10 June 2021

Please visit the new version of LipiOne 2.0 at lipidone.eu.

Description

GENERAL DESCRIPTION

LipidOne, a freely available software that processes lipidomics data to help researchers to find new relationships between lipid profile and the activity of enzymes/genes involved.

LipidOne, automatically highlights all qualitative and quantitative changes in lipid building blocks both among all detected lipid classes and among experimental groups.  Thanks to LipiOne, the discovered differences in lipid building blocks can be easily linked to the activity of specific enzyme classes and or gene expression.

CITATION

Please, cite our work as:

Roberto Maria Pellegrino, Matteo Giulietti, Husam B R Alabed, Sandra Buratta, Lorena Urbanelli, Francesco Piva, Carla Emiliani, LipidOne: user-friendly lipidomic data analysis tool for a deeper interpretation in a systems biology scenario, Bioinformatics, 2021; btab867, https://doi.org/10.1093/bioinformatics/btab867

CONTACT

For general questions concerning the use of the software please contact Roberto Maria Pellegrino (This email address is being protected from spambots. You need JavaScript enabled to view it.)

For problems with installation, operation, software compatibility contact Matteo Giulietti (This email address is being protected from spambots. You need JavaScript enabled to view it.)

Download

Click here to download

LipidOne is an executable file that does not require installation. Follow the instructions below and try working with our example datasets.

Instruction:

a) For the first time only, the user must install the Gnuplot graphics libraries. They can be downloaded free of charge from: https://sourceforge.net/projects/gnuplot/files/gnuplot/5.4.2;

b) Download LipidOne and place it in a folder of the user's choice.

c) Double click on the icon to start LipidOne.

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*) We would like to thank Dmitry Karasik and colleagues for the development of the Perl Prima library (http://www.prima.eu.org/), which we used for the development of the Graphical User Interface of LipidOne.

**) We also thank Thomas Williams and colleagues for their GNUPLOT graphical library (http://www.gnuplot.info/), useful for the creation of the LipidOne bar graphs.

Dataset

Try and explore some example datasets with LipidOne.

RETINA: Trzeciecka, A. et al. (2019) Comparative lipid profiling dataset of the inflammation-induced optic nerve regeneration. Data in Brief, 2352-3409.

FUNGUS: Lipid profiling of fungus (our internal, unpublished results).

ALGAE: Lipid profiling of algae from Riken Demonstration Files (http://prime.psc.riken.jp/compms/msdial/main.html).

Note: If the lipid annotation of your dataset does not comply with the LSI guidelines*, you can convert your data with LipidLynxX Converter.

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*) Liebisch,G. et al. (2020) Update on LIPID MAPS classification, nomenclature, and shorthand notation for MS-derived lipid structures. Journal of Lipid Research, 61, 1539-1555.

How to use

Three-step LipidOne workflow

1) Data upload: the user must select a data matrix (txt or csv tab delimited file) containing the names and concentrations in each lipid sample detected (see example dataset). The accepted lipid nomenclature is the "molecular species level" or "sn-position level" as reported by the Lipidomics Standards Initiative (LSI) Guidelines.

2) Query selection: The user starts to explore the dataset using seven types of analysis and dynamic context-dependent menus.

3) Get results: all graphs and tables can be exported.

Click here to download the quick guide 

License

GENERAL STATEMENT

LipidOne is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

DISCLAIMER

LipidOne is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

CONTACT

For general questions concerning the use of the software please contact Roberto Maria Pellegrino (This email address is being protected from spambots. You need JavaScript enabled to view it.)

For problems with installation, operation, software compatibility contact Matteo Giulietti (This email address is being protected from spambots. You need JavaScript enabled to view it.)

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Published: 08 February 2018

Biodiversity and Ecology (Prof. Roberto Venanzoni)

Biochemical and Biotechnological Sciences (Prof. Carla Emiliani)

Bio-Molecular Diversity & Evolutionary Biology (Prof. Ines Di Rosa)

Molecular Physiology (Prof. Luigi Catacuzzeno)

Computing, Theory and Experiments of Dynamics and Kinetics Studies for Chemical Processes (Prof. Fernando Pirani)

Molecular Spectroscopy (Prof. Assunta Morresi)

Environmental Chemistry and Technologies (Prof. David Cappelletti)

Catalysis for Energy (Prof. Alceo Macchioni)

Green S.O.C. (Prof. Luigi Vaccaro)

Materials for Artworks' Conservation (Prof. Aldo Romani)

Photophysics and Photochemistry (Prof. Fausto Elisei)

Plant Physiology Lab (Prof. Stefania Pasqualini)

Design, Synthesis and Properties of Compounds with Potential Pharmaceutical Interest (Prof. Gabriele Cruciani)

Theoretical and Computational Inorganic Chemistry (Prof. Filippo De Angelis)

Integrated Physiology and Preclinic (Prof. Bernard Fioretti)

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Published: 21 April 2020

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Published: 27 June 2022

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