Services

The Belgian ELIXIR node offers specialized data resources and tools for the European user community. These include databases, data resources and bioinformatics infrastructure that have applications in Plant Sciences, Proteomics and Human Data.

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Logo DIDA

DIDA (DIgenic diseases DAtabase) is a database that provides detailed information on genes and associated genetic variants involved in digenic diseases, the simplest form of oligogenic inheritance. The database was developed at the Interuniversity Institute of Bioinformatics in Brussels (IB)² and currently includes 258 digenic combinations involved in 54 different digenic diseases. These combinations are composed of 448 distinct variants, which are distributed over 169 distinct genes. The web interface provides browsing, exploration and search functionalities, as well as documentation and help pages, general database statistics and references to the original publications from which the data have been collected. The possibility to submit novel digenic data to DIDA is also provided.

DIDA is published in the Nucleic Acids Research Database issue 2016 and has been selected as a NAR 2016 Breakthrough paper. The manuscript can be accessed here and an in-depth analysis of the different types of digenic diseases, i.e. true digenic and composite, in DIDA can be found here.

Logo Dodona

Dodona is an e-learning environment containing hundreds of programming exercises that can be used to master several programming languages. All exercises come with automatic feedback on correctness, execution time and/or programming style.

The Dodona platform has been developed at Ghent University and was launched in September 2016. Over the last two years, the platform provided automated feedback on more than two million submissions from Ghent University students. Dodona is registered as a service provider with Belnet to enable access to a wide range of international research and education institutions that have been registered as identity providers in the eduGAIN project. Currently, the platform is under active development.

Get a glimpse of Dodona by these examples:

Logo DynaMine

DynaMine is a fast predictor of protein backbone dynamics using only sequence information as input. DynaMine is able to accurately distinguish regions of different structural organization within proteins, such as folded domains and disordered linkers of different sizes. Additionally, it can identify disordered regions within proteins with an accuracy comparable to the most sophisticated existing disorder predictors. DynaMine achieves this high performance without depending on prior disorder knowledge or three-dimensional structural information, which makes it a unique approach on the field as well as providing independent proof of the relationship between dynamics and structural disorder in protein regions.

DynaMine was developed at the Interuniversity Institute of Bioinformatics in Brussels (IB)² and published in Nature Communications (the method) and Nucleic Acids Research (the web-server).

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Logo iMONdb

iMonDB (Instrument MONitoring DataBase) is a unique tool and resource for online, longitudinal quality control monitoring of mass spectrometry instruments and the data they produce. The advantage of instrument information at the lowest level is the high sensitivity to detect emerging defects in a timely fashion. To this end, iMonDB allows to automatically extract, store, and manage the instrument parameters from raw-data objects into a highly efficient database structure. iMONdb was developed at the University of Antwerp, the manuscript can be accessed here.

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Logo MS DataConnect

The MSDataConnect consortium (UHasselt) connects partners involved in Multiple Sclerosis (MS) care, rehabilitation, and research, with partners involved in IT development, database management, data sharing procedures, statistics, machine learning and prediction modelling.

MS DataConnect focuses on developing (1) data collection procedures and tools to create data that is FAIR, (2) IT solutions to allow (temporarily) pooling and linking of FAIR data sets, (3) statistical methods to define minimal requirements for data sets, and (4) new analytical methods for optimal mining of connected and pooled FAIR data sets.

The MS DataConnect consortium is the project coordinator of the international project Multiple Sclerosis Data Alliance (MSDA), which brings together registry holders, patients, medical societies, academia, industry, the European Medicine Agency (EMA), and Health Technology Assessment (HTA) bodies. One of the first goals of the MSDA is the development of the MSDA cohort explorer. This tool will enable searching aggregated data across different MS registries and cohorts after data is mapped to a harmonized data template. The subject and variable selection tools in the MSDA cohort explorer will allow end-users to identify MS data cohorts suitable for their (research-)question, and will facilitate the initiation of (new) collaborations with these MS cohorts.

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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).

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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 September 2017.  

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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 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.

Unipept 4.0 is the latest release of the Unipept framework and includes a completely new functional analysis tool and an updated database based on UniProt 2018.06. A tutorial on Unipept has been published in 2018. All Unipept journal articles can be found on this page.