Better together. The advance of (omics) data integration at VIB

20 March 2019

To remain competitive in the era of big data, VIB seeks to strengthen its position in the field of data integration. As such, the VIB BioInformatics Core Facility – one of the VIB cores – develops reproducible analysis workflows to identify correlations between various ‘omics’ data sets.
‘Omics’ is an umbrella term covering genomics, transcriptomics, proteomics and metabolomics, among others. At the initiative of Lennart Martens (VIB-UGent Center for Medical Biotechnology) and Alexander Botzki (VIB BioInformatics Core), VIB hired the first ‘omics data integration specialist’ at the institute: Oren Tzfadia. We asked him how this new position took shape and which services the VIB BioInformatics Core precisely offers in this field.

Oren’s job goes beyond simply data integration. “Of course, I help VIB scientists discover and understand state-of-the-art tools to analyze omics data from different sources in their labs. With the help of Alex, I render the installations user friendly and make sure they run smoothly by wrapping tools in a Docker container,” Oren explains. “However, since plenty of the data at VIB remains unused, it is also my task to expand the concept of data integration to the entire institute – that is to say, beyond the usual scope of omics. As such, I seek to integrate post translation modifications, copy number variations and single cell data.”

To complete this task successfully, the VIB BioInformatics Core offers customized methodology services for data integration. Oren: “In some projects, we take the lead on data integration, while in others, we serve as a bridge between research question and methodology. We also provide consultancy on data preprocessing and experimental design.” Training programs serve the same purpose. “In early November, we organized our first workshop. On day 1, 10 expert trainers from all around the world welcomed 50 to 70 participants – both VIB scientists and external researchers. 25 of them also attended the hands-on course the next day.”

By integrating information from different research groups, the VIB BioInformatics Core boosts the VIB data ecosystem. “After meeting the heads of the Metabolomics Core and the Proteomics Core in Leuven and Ghent, for example, we set up a plan to streamline omics data flowing to various core facilities, allowing for optimized meta-information to enhance biological discoveries,” Oren elaborates.

The aim for the future is to bring this ecosystem to the next level. Oren: “We will not only collaborate more closely with other core facilities to design tools that meet their specific demands, but we will also stimulate data reproducibility efforts across all research groups.” To realize this plan, the VIB BioInformatics Core is developing a Nextflow pipeline to analyze various omics data in the same set, using different tools, like MOFA and WGCNA. What is more, VIB recently recruited Vid as ‘data steward’ – a brand-new function at the institute.

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Oren Tzfadia   ©VIB_IneDeHandschutter