Unipept

The Unipept web application supports biodiversity and functional analysis of large and complex metaproteome samples and the analysis of peptidomes.

The 6.0 release of Unipept brings support for non-tryptic peptides and the novel Peptonizer analysis pipeline to the tool.

An API and command line tool are available for integration in other programs.

Contributing

Found a bug or have an idea for an awesome new feature? File an issue using the github issue tracker or drop us a line at unipept@ugent.be.

If you're willing to get your hands dirty, you might of course also send us a pull request!

Installation

This repository contains the source code for the Unipept web application.

To run this application locally, you need to have Node.js and Yarn installed.

1. Clone the repository:

   git clone https://github.com/unipept/unipept.git
   cd unipept

2. Install dependencies:

   yarn install

3. Start the development server:

   yarn dev

The application will be available at http://localhost:3000.

Custom Unipept Instance

This repository only contains the code for the web application of Unipept. To run a fully functional custom version of Unipept (with your own data), you also need to set up:

• The Unipept Database
• The Unipept API

We have detailed guides on how to set up all of these components on our Wiki: https://github.com/unipept/unipept/wiki

Adding custom icons

The application uses a small custom icon font (unipept-icons) for icons not available in Material Design Icons. The SVG sources live in custom-icons/ and the font is generated automatically by fantasticon when you run yarn dev or yarn build. You can also regenerate it manually:

yarn generate-icons

Adding a new icon

1. Export your icon as an SVG (24x24 px viewBox, filled paths — no strokes) and place it in custom-icons/.

2. Regenerate the font:

   yarn generate-icons

3. Check the assigned codepoint in the generated src/styles/unipept-icons.css and add it to .fantasticonrc.json to lock it in permanently:

   "codepoints": {
     "your-new-icon": 59395
   }

4. To make the icon available as a Vuetify alias, add an entry to src/plugins/unipept-icons.ts:

   const unipeptIconsAliases = {
       yourNewIcon: 'unipept-your-new-icon'
   }

5. Use it in a component:

   <VIcon icon="unipept:your-new-icon" />

Who made this app?

Unipept is a research project of the computational biology group at Ghent University. If you use this application, please cite:

• Vande Moortele et al. (2025) J. Proteome Res. doi.org:10.1021/acs.jproteome.4c00848
• Verschaffelt et al. (2023) J. Proteome Res. doi:10.1021/acs.jproteome.3c00091
• Verschaffelt et al. (2021) J. Proteome Res. doi:10.1021/acs.jproteome.0c00855
• Verschaffelt et al. (2020) Bioinformatics doi:10.1093/bioinformatics/btaa553
• Gurdeep Singh et al. (2019) J. Proteome Res. doi:10.1021/acs.jproteome.8b00716
• Mesuere et al. (2018) J. Proteomics doi:10.1016/j.jprot.2017.05.022
• Mesuere et al. (2016) Proteomics doi:10.1002/pmic.201600023
• Mesuere et al. (2016) Bioinformatics doi:10.1093/bioinformatics/btw039
• Mesuere et al. (2015) Proteomics doi:10.1002/pmic.201400361
• Mesuere et al. (2012) J. Proteome Res. doi:10.1021/pr300576s

Current team:

• Bart Mesuere (@bmesuere): Group leader and PhD supervisor, Unipept founder
• Pieter Verschaffelt (@pverscha): Postdoc and lead developer
• Tibo Vande Moortele (@tibvdm): PhD student
• Simon Van de Vyver (@SimonVandeVyver): PhD student
• Ben-Björn Binke (@benbnk): PhD student
• Peter Dawyndt (@pdawyndt): Group leader and PhD supervisor

Other contributions from:

• Felix Van der Jeugt (@ninewise): Master's student 2014 - 2016 and PhD student 2016 - 2022
• Robbert Gurdeep Singh (@beardhatcode): Developer 2017-2018
• Tom Naessens (@silox): Master's student 2014-2015
• Toon Willems (@nudded): Master's student 2013-2014
• Ewan Higgs (@ehiggs): Ghent University HPC team
• Peter Vandamme: PhD co-supervisor of Bart
• Bart Devreese: PhD co-supervisor of Bart

For code contributions, the contributors graph is the place to be.