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pverscha committed Apr 15, 2024
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25 changes: 25 additions & 0 deletions src/components/pages/PublicationsPage.vue
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This page lists all Unipept peer-reviewed journal articles in reverse-chronological order.
</h3>

<publication-card
class="mt-5"
title="Unipept Desktop 2.0: Construction of Targeted Reference Protein Databases for Metaproteogenomics Analyses"
:authors='["Pieter Verschaffelt", "Alessandro Tanca", "Marcello Abbondio", "Tim Van Den Bossche", "Tibo Vande Moortele", "Peter Dawyndt", "Lennart Martens", "Bart Mesuere"]'
journal="Journal of Proteome Research"
year="2023"
doi="doi.org/10.1021/acs.jproteome.3c00091"
google-scholar="https://scholar.google.com/scholar?hl=en&as_sdt=0%2C5&as_ylo=2023&q=Unipept+Desktop+2.0%3A+construction+of+targeted+reference+protein+databases+for+proteogenomics+analyses&btnG="
:image="Publication2023Image"
>
<template #abstract>
Unipept Desktop 2.0 is the most recent iteration of the Unipept Desktop tool that adds support for the analysis
of proteogenomics datasets. Unipept Desktop now supports the automatic construction of targeted protein reference
databases that only contain proteins associated with a predetermined list of taxa. This improves both the
taxonomic and functional resolution of a metaproteomic analysis and yields several technical advantages. By
limiting the proteins present in a reference database, it is now also possible to perform (meta)proteogenomics
analyses. Since the protein reference database now lives on the user's local machine, they have complete control
over the database used during an analysis. Data does no longer need to be transmitted over the internet,
decreasing the time required for an analysis and better safeguarding privacy sensitive data. As a proof of
concept, we present a case study in which a human gut metaproteome dataset is analyzed with Unipept Desktop 2.0
using different targeted databases based on matched 16S rRNA gene sequencing data.
</template>
</publication-card>

<publication-card
class="mt-5"
title="Unipept Desktop: a faster, more powerful metaproteomics results analysis tool"
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import PublicationCard from '../cards/PublicationCard.vue';
import Initialism from '../highlights/Initialism.vue';
import RLink from '../highlights/ResourceLink.vue';
import Publication2023Image from '@/assets/publications-2023.jpg';
import Publication2021Image from '@/assets/publications-2021.jpg';
import Publication2020Image from '@/assets/publications-2020.jpg';
import Publication2019Image from '@/assets/publications-2019.jpg';
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from the previous one to the one. Doing so is, however, quite technical and is not recommended for
non-technical users. Instead, we recommend to use a Linux system (such as Ubuntu) or a Mac in this case.
If you do want to move the virtual hard drive on Windows, you can follow the steps in
<a class="link" href="https://learn.microsoft.com/en-us/windows/wsl/vhd-size">this guide</a>.
<a class="link" href="https://verschaffelt.be/increase-maximum-size-of-docker-volume-on-windows/">this guide</a>.
</p>
<h3 class="font-weight-bold">
Q: Is Docker always required when using the Unipept Desktop application?
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