OpenEBench (https://openebench.bsc.es) is the ELIXIR benchmarking and technical monitoring platform for bioinformatics tools, web servers, and workflows. OpenEBench is part of the ELIXIR Tools platform and its development is led by the Barcelona Supercomputing Center (BSC) in collaboration with partners within ELIXIR and beyond.

Within the ELIXIR project, OpenEBench is being developed under the Tools Platform at the Work Package 2 (WP2: Benchmarking) (https://elixir-europe.org/platforms/tools). ...

TransBioNet is the Translational Bioinformatics Network impulsed and coordinated by the Spanish National Bioinformatics Institute (INB) as a reference network of 35+ bioinformatics support units working at health care settings including Health Research Institutes (IIS) certified by the Carlos III Health Institute (ISCIII), and bioinformatics core facilities from biomedical research institutions. TransBioNet is an Excellence Thematic Network (Red de Excelencia Temática) recognized by the Spanish ...

An integrative analysis pipeline of genomic and transcriptomic human data for disentangling the genetic origin of a rare-disease in the context of the European Open Science Cloud.

EJPRD WP13 case-studies workflows from phase 1.

Description

The workflow takes an input file with Cancer Driver Genes predictions (i.e. the results provided by a participant), computes a set of metrics, and compares them against the data currently stored in OpenEBench within the TCGA community. Two assessment metrics are provided for that predictions. Also, some plots (which are optional) that allow to visualize the performance of the tool are generated. The workflow consists in three standard steps, defined by OpenEBench. The tools needed ...

Exome SAMtools Workflow

Exome Alignment Workflow

Rare disease researchers workflow is that they submit their raw data (fastq), run the mapping and variant calling RD-Connect pipeline and obtain unannotated gvcf files to further submit to the RD-Connect GPAP or analyse on their own.

This demonstrator focuses on the variant calling pipeline. The raw genomic data is processed using the RD-Connect pipeline (Laurie et al., 2016) running on the standards (GA4GH) compliant, interoperable container ...

COnSensus Interaction Network InFErence Service

Inference framework for reconstructing networks using a consensus approach between multiple methods and data sources.

Reference

[Manica, Matteo, Charlotte, Bunne, Roland, Mathis, Joris, Cadow, Mehmet Eren, Ahsen, Gustavo A, Stolovitzky, and María Rodríguez, Martínez. "COSIFER: a python package for the consensus inference of molecular ...