Services

ELIXIR Belgium

  • offers specialized bioinformatics resources accelerating research in life-science. These include databases, data resources, tools, workflows, …that have applications in plant sciences, human health and proteomics. We aim to extend the functionality and compatibility of the resources developed by different Belgian research groups.
  • focusses on data management, data analysis platforms and training. We provide an ELIXIR template and guidance to fill in data management plans in DMPonline.be. The research data management tool, Fairdomhub.be is in full development and enables researchers to manage their research data and produce FAIR data by design. Recommended best practises and guidelines for research data management are available in our Data Management Hub. To facilitate reproducible analysis, we have set up the centrally managed Galaxy instance UseGalaxy.be. Our training portfolio can be consulted on the Training page.
  • supports COVID-19 research. To encourage and assist researchers to make scientific data available, we implemented a tool to simplify the submission of SARS-CoV-2 sequencing data to the European Nucleotide Archive (ENA). This video illustrates how to use the tool. A complete overview of our COVID-19 related activities can be found on the dedicated ELIXIR interactive map.

A call for Node Services is launched every two years. Services that are positively evaluated by the Scientific Advisory Board are added to ELIXIR Belgium’s Service Delivery Plan. Node Services are labelled as important resources produced by the Belgian bioinformatics community. Below, an overview of all ELIXIR Belgium services is given - Node Services have the respective tag. The next call for Node Services is scheduled for April 2022. A complete service list of all ELIXIR Nodes can be found on this link.  


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Logo MS2PIP

The MS2PIP Server is a tool to accurately predict peptide fragment ion intensities for mass spectrometry-based proteomics data. It employs the XGBoost machine learning algorithm and is accessible through a RESTful API.

The MS²PIP Server enables any interested researcher to make use of MS²PIP, regardless of their computational experience. It is the only peak intensity prediction server that can predict peak intensities for multiple fragmentation methods, instruments and labelling techniques. The MS2PIP Server has been used as the benchmark for comparison of other recently published tools for the prediction of MS² peak intensities.

The MS2PIP Server was developed at Ghent University and published in Bioinformatics (original server) and Nucleic Acids Research (update 2015update 2019).

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Logo MutaFrame

MutaFrame enables you to explore the likely effect of amino acid variants (mutations) on human proteins. It provides predictions of the ‘deleteriousness’ of mutations in human proteins, with interpretation of the underlying machine learning decisions, access to other resources (EXaC, dbSNP), and the connection to protein structure information from the Protein Data Bank (PDB). MutaFrame aims to visualise these data to make them understandable for non-expert users, and serves as a knowledge base by providing information for all possible mutations in all human proteins.

MutaFrame is developed at the Interuniversity Institute of Bioinformatics in Brussels (IB)², the manuscript can be accessed here. Follow MutaFrame on Twitter: @MutaFrame.

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Logo ORCAE

ORCAE (Online Resource for Community Annotation of Eukaryotes) is a wiki style genome annotation and curation portal for eukaryotic species which offers the community the opportunity and means to improve genome annotations and to keep gene annotations up-to-date.

ORCAE was developed at the Ghent University and published in Nature Methods (manuscript - method). ORCAE-AOCC is a branch that is dedicated to the genomes of African orphan crops (resource - manuscript).

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Logo PIPPA

PIPPA is a central web interface and database that provides the tools for the management of different types of WIWAM plant phenotyping robots and for the analysis of images and data.

Due to significant advancements in imaging sensors and automation, digital phenotyping is becoming a routine tool in plant sciences requiring tools to manage and analyse the huge datasets produced. PIPPA is being developed at the Ghent University and the VIB-UGent Center for Plant Systems Biology. The website provides detailed information, demo’s and an illustrating flowchart.

Logo PLAZA

PLAZA is a plant-oriented online resource for comparative, evolutionary and functional genomics. It allows querying and visualising structural and functional annotations, gene families, protein domains, phylogenetic trees, and genome organization. PLAZA 4.0 is the latest iteration of the PLAZA framework. This version provides a large increase in newly available species, and offers access to updated and newly implemented tools and visualisations, helping users with the ever-increasing demands for complex and in-depth analyses.

PLAZA was developed at the Ghent University. Core publications and training material can be found here. The latest training on PLAZA took place in October 2019.  

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Logo QCQuan

QCQuan is a webtool for automated quality control and statistical analysis of protein expression following labelled mass spectrometry experiments. The tool is focused on differential expression analysis generated by isobaric labelling experiments. Flat text files from maxQuant, Proteome Discoverer or any other tools can be uploaded for a post-identification analysis. In this process, the user is offered very few options to modify the workflow in order to enhance comparable outcomes from different proteomic experiments

QCQuan was developed at the University of Hasselt in collaboration with VITO, the manuscript published in the Journal of Proteome Research can be accessed here.

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Logo Scop3P

Scop3P provides a unique and powerful resource to explore and understand the impact of phospho-sites on human protein structure and function, and can thus serve as a springboard for researchers seeking to analyse and interpret a given phosphosite or phosphoprotein in a structural, biophysical, and biological context.

The resource re-uses public domain data from a variety of leading international resources, including UniProtKB and PDB, but also uses reprocessed mass spectrometry-based phospho-proteomics data from PRIDE/ProteomExchange, which is in turn globally collected and thus wholly international-driven.

Scop3P was developed at Ghent University and is online since June 2019. The manuscript describing Scop3P is available as a preprint in BioRXiv.

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Logo Tabloid Proteome

The online Tabloid Proteome is a database of protein association network generated using publically available mass spectrometry based experiments in PRIDE. These associations represent a broad scala of biological associations between pairs of proteins that goes well beyond mere binary protein interactions. As such, the provided information is almost completely complementary to traditional direct protein interaction studies.

In addition to the collection of co-occurring protein pairs, Tabloid Proteome also links to their biological relation in existing knowledgebases. Moreover, pathway links from Reactome, protein-protein interactions from IntAct and BioGRID, protein complexes from CORUM, and paralog information from Ensembl are also superimposed. Functional annotation is provided by disease information from DisGeNET, and Gene Ontology annotations.

Tabloid Proteome was developed at the Ghent university in 2017 and published in Nucleid Acids Research (manuscript). In October 2018, the first training on Tabloid Proteome took place in Gent.

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Logo TCRex

The TCRex webtool allows functional interpretation of full human T-cell repertoire data derived from next generation sequencing.

TCRex is the first tool of its kind and is able to link T-cell receptor sequences to a rapidly expanding list of 49 different important immunogenic epitopes, consisting of 44 viral and 5 cancer epitopes. Additional epitopes can be added by users for their own use. The tool is able to calculate enrichment statistics and baseline prediction rates to evaluate full repertoires. It is unique among TCR-epitope prediction tools in that it allows processing of full human repertoires. It has also brought together the largest database on TCR-epitope data to train the underlying machine learning models through manual curation of various online resources and scientific literature.

TCRex was developed at the University of Antwerp and has been released for public use in 2018. The manuscript describing the webtool is available as a preprint in BioRXiv.  TCRex can also be followed on Twitter: @TCRexTool.

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Logo Unipept

Unipept is an open source web application developed at Ghent University that is designed for metaproteomics data analysis with a focus on interactive data visualizations. Unipept is powered by an index containing all UniProt entries, a tweaked version of the NCBI taxonomy and a custom lowest common ancestor algorithm. This combination enables a blazingly fast biodiversity analysis of large and complex metaproteome samples. Next to these core functions, Unipept also has a tool for selecting unique peptides for targeted proteomics and for comparing genomes based on peptide similarity.

A tutorial on Unipept has been published in 2018. All Unipept journal articles can be found on this page. Unipept can be followed on Twitter: @unipept.

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