Services: Access Service

CSC develops and hosts an open source tool REMS to assist a DAC to manage Data Access Applications and access rights to sensitive datasets. REMS is a key component in ELIXIR AAI.

The ELIXIR AAI (Authentication and Authorisation Infrastructure) is the ELIXIR service portfolio for authenticating users and helping relying services to manage users' access rights in the services. 

We provide support and guidance in development of Disease Maps (disease-maps.org), computational and visual repositories of knowledge about mechanisms of human diseases. We offer hosting of open access Disease Maps on the MINERVA Platform (minerva-web.lcsb.uni.lu) on our infrastructure under the elixir-luxembourg.org sub-domain, their backup and conservation. The MINERVA Platform ensures online access, interactive exploration, search for known drug targets and visualisation of omics datasets. We provide training in management of the Disease Maps and guidance to their integration into reproducible computational workflows by using the dedicated API of the hosting platform.

The Ocean Gene Atlas service provides data mining access to three complementary data objects: gene sequence catalogs (ENA), sample environmental context (PANGAEA), and gene abundances estimates in samples (computed by mapping raw sequence reads onto gene catalogs). User queries are composed of either a sequence (nucleic or protein), or a hidden Markov model derived from a multiple sequence alignment. Homologs of the user query in the gene catalogs are identified using standard sequence similarity search tools (eg BLAST or HMMER), and their read based estimated abundance are displayed in interactive world maps and ecological plots. A phylogenetic tree is also inferred in order to situate the user query within its context of marine environmental homologs as well as known homologs from reference sequences.

Open source software underlying the technology for SURF's single sign-on and facilitating national and international online collaboration in education and research.

The REPET package integrates bioinformatics pipelines dedicated to detecte, annotate and analyse transposable elements (TEs) in genomic sequences. The main pipelines are (i) TEdenovo, which search for interspersed repeats, build consensus sequences and classify them according to TE features, and (ii) TEannot, which mines a genome with a library of TE sequences, for instance the one produced by the TEdenovo pipeline, to provide TE annotations exported into GFF3 files.