Software

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We develop software for specific research needs, from automated data analysis pipelines to data management solutions. Here some examples:

MethylationDB

MethylationDB is the data portal for DNA methylation microarray data produced by the Genomics Unit at the Josep Carreras Institute (IJC). The portal allows users to compare their data with data from collaborators or public data sources, search for samples, download metadata, raw data and processed data. Methylation values can be extracted and visualized genome-wide of for a single gene or list of genes.

EPipe is a bioinformatics pipeline designed for the fully automated (start-to-end) analysis of methylation data from the Illumina Infinium BeadChip microarray platform (450k, EPIC v1/v2). It performs quality control, data normalization and differential analysis, while providing clear, user-friendly result reports. EPipe is highly flexible, with traceable and reproducible execution and can be run locally, in parallel or on a distributed cluster.

Bioforms

BioForms is a web-based application that allows the creation of customizable metadata forms based on predefined templates to collect metadata in a standardized and machine readable way. The forms ensure data accuracy and consistency by using controlled vocabularies, such as ontologies. BioForms integrates with the CEDAR ecosystem and enables data export and access via Office 365 (Excel, SharePoint).