Scientific Staff (Postdoc/Research Software Engineer)
Web Developer SILVA DB
Backend developer Java, Maven, Spring Boot (SILVA DB)
Bioinformatician Natural Language Processing
Visit to prepare & coordinate genomic data infrastructure project in Europe
This project is to improve the coordination between the Beyond 1 Million Genomes project and the Federated Human Data / ELIXIR CONVERGE projects. All three projects are based around Federated EGA, or its technology, to support cross border access to human controlled access genetic and phenotypic data.
Development of the PROCOGNATE database
The functional annotation of enzymes is an interesting but nontrivial task requiring experimental data and scientists' manual revision for optimal results. Due to the increasing amount of structural and sequence data, it is more difficult to do the case- by-case analysis, and there is a high demand for automated solutions.
Strategic Development of DOME Recommendation for Machine learning Focus Group
Machine Learning (ML) enables computers to assist humans in making sense of large and complex data sets. With the fall in the cost of high-throughput technologies, large amounts of omics data are being generated and made accessible to researchers. Analysing these complex high-volume data is not trivial, and the use of classical statistics cannot explore their full potential.
Tools integration under Galaxy and tools development for the integration and querying of heterogeneous QTL data
This collaborative project focuses on two issues related to bioinformatics.
The first issue concerns the availability of the virAnnot pipeline (doi:10.1094/PBIOMES-07-19-0037-A) that was developed in the Virology team (INRAE UMR 1332) for the CATI BARIC community and the collaborators of the Virology team. This pipeline, intended for everyone, is however only used by bioinformaticians as it can only be used on command line.
ELIXIR Portugal as a case-study for the deployment of Local EGA/Beacon v2 instances
The European Genome-phenome Archive (EGA) is a repository for all types of sequence and genotype
experiments, including case-control, population, and family studies. The EGA will serve as a permanent archive
that will archive several levels of data including the raw data (which could, for example, be re-analysed in the
future by other algorithms) as well as the genotype calls provided by the submitters. In spite of EGA accepting
data from all Europe, due to regulations over data and other constraints, it is desirable that ELIXIR Nodes deploy