Node Service

Dodona

Dodona is an e-learning environment containing thousands of programming exercises that can be used to master several programming languages. Currently, we support Python, Java, JavaScript, R, Haskell, Prolog and Bash. 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 few years, the platform provided automated feedback on more than five 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. In addition, ELIXIR AAI accounts can be used to access the platform. Currently, the platform is under active development.

Get a glimpse of Dodona by these examples:

Follow Dodona on Twitter: @DodonaEdu

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.

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).

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.

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.

WiNGS

WiNGS is being developed to succeed NGS-Logistics, the genomics data sharing platform established at KULeuven. The NGS-Logistics platform is currently deployed at 6 of the 8 genetic centres in Belgium and lets users identify clinically relevant mutations at other genetic centres. Its scope is similar but broader than the more recent Beacon project of the Global Alliance for Genomics and Health (GA4GH) and ELIXIR Europe, which provides a framework for public web services for variant discovery against distributed genomic data collections. The ELIXIR Belgium Human Data consortium, led by KULeuven, has been participating in the ELIXIR Beacon project and maintains a Belgian Beacon node.

The WiNGS (Widely integrated NGS) platform holds significant scalability improvements to tackle the complexity of analysing of Whole-Genome Sequencing (WGS) data. Because of the sensitivity of patient genomes and GDPR requirements, enhanced access control and privacy protection for this integrated platform will be developed. The first manuscript of the platform can be downloaded here.

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.  

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).