Technology Transfer

Open-source tools for cancer genomics researchers, clinicians, geneticists, molecular biologists

GenoSurf ( multi-ontology semantic search system providing access to a consolidated collection of human genome datasets for bioinformatic tertiary analysis.

OpenGDC ( extraction and integration tool for cancer genomics data.

GeMI ( interactive interface to annotate genomic samples exploiting a deep-learning-based prediction model, accelerating genomic metadata extraction into structured formats.

VarSum API ( API computing summary statistics on user-defined populations and their variants, using a large genomic data repository.

META-BASE ( tool that integrates and enriches heterogeneous biological and clinical data sources, exploiting several configurations to build a repository.

Open-source tools for experts in virology, phylogenetics, epidemiology, pathogenesis, immunology, focusing on SARS-CoV-2 and other viral species

ViruSurf ( search system for public viral sequences described by their metadata and exhibiting nucleotide and amino acid mutational patterns.

EpiViruSurf ( search system for evaluating the impact of viral mutational patterns on epitopes, i.e., areas of the virus recognized by the human immune system.

VirusViz ( visualization tool for the comparison of the mutational distributions of user-selected viral populations.

ViruClust ( data analysis tool to perform temporal and spatial comparison of mutational patterns of SARS-CoV-2 sequences.

VariantHunter ( tool for fast detection of emerging SARS-CoV-2 variants and sub-variants.

CoV2K API ( knowledge base of SARS-CoV-2 sequence mutations, variants, and their effects.

CoVEffect ( interactive web interface for deep learning-assisted scientific text annotation with effects of SARS-CoV-2 mutations and variants.

Open-source tools for the exploration of COVID-19-related research literature

GRAPH-SEARCH ( explorer of COIVD-19-related literature using graph-based queries with shortest paths and sophisticated ranking.

CORToViz ( user-friendly visualizer for trends of topics extracted from COVID-19 scientific research abstracts, with easy-to-drive statistical testing. This is the first prototype developed in the context of the NGI Search Program (TETYS project), aiming to build the next-generation open-source Web topics explorer (applicable to many other text document corpora).

Participation in standardization initiatives

Participation in the COVID-19 Host Genetics Initiative for designing the COVID-19 clinical data dictionary for describing COVID-19 patients’ phenotype; our work was used in the publication on Nature and adopted within ELIXIR-CONVERGE, as deemed appropriate as standardization guidelines (

Participation in the FAIRification of Genomic Annotations RDA Working Group, for the standardization of Genomic Annotations and FAIRification data processing pipelines (