Workshop – Getting your hands-on data management

The First Hands-on Workshop on Data Management of Digital Life Norway was held at the University of Bergen on 8th and 9th of May 2017. The Two-day workshop provided researchers with practical skills about the data management tools SEEK (https://fairdomhub.org/) and NeLS (https://nels.bioinfo.no/) platforms, which are adapted towards systems biology and omics data, respectively.

Each day of the workshop was arranged in two parts, with presentations and introductions about a particular data management tool in the morning and practical and hands-on session about that tool in the afternoon.

SEEK training

On the first day of the workshop, the SEEK session started by Natalie Stanford from the University of Manchester. She gave an introduction to the FAIR concept, FAIRDOMHub and the ISA structure inside SEEK. Olga Krebs, from Heidelberg Institute for Theoretical Studies (HITS), gave a short introduction afterwards to RightField, a tool for annotating spreadsheets to create semantically aware Excel spreadsheet templates.

The afternoon hands-on session was split into basic and advanced level and researchers could choose between two levels.

Basic training was organized for researchers who had either never encountered FAIRDOMHub, or who had very little experience of using FAIRDOMHub.

The basic level including, how to create and interlink ISA elements, browsing and downloading information/data from FAIRDOMHub, uploading/registering assets in FAIRDOMHub, linking assets to the ISA and registering publications and linking to other assets, was taught by Olga.

At the advanced level, there were three different tutorial options that researchers could choose to follow.

Model management in FAIRDOMHub, including creating modeling assays, reproducing simulation experiments registered in FAIRDOMHub, creating SEDML and COMBINE archives and tracking model evolution. Ron Henkel taught this part from the University of Rostock, Germany. Researchers with (mathematical) modeling background participated in this tutorial.

Natalie Stanford taught publishing using FAIRDOMHub. This training included setting up the ISA structure and assigning DOIs for linking to within publications.

Some new features on samples in FAIRDOMHub were also included at the training. In this part, learning about the samples, how to use Metadata sheets to describe samples and how to generate samples using forms and templates in FAIRDOMHub were the main core of this part of training.

NeLS and Galaxy training

The second day of the workshop started by an introduction to NeLS (Norwegian e-infrastructure for Life Sciences) and Galaxy by Kjell Petersen, from the university of Bergen, Computational Biology Unit (CBU).

Kjell gave an overview of NeLS, an infrastructure providing storage, data sharing and analysis tools. He also mentioned NorStore platform for long-term storage and Galaxy for data analysis and computing. Using Galaxy in NeLS makes it easy to document the processing and analysis of research data.

Charitra Kumar Mishra and Tomasz Furmanek were assisting the hands-on session for NeLS and Galaxy with the training project and data. At this section, how to login to NeLS (either by NeLS portal or SSH command), how to organize data in NeLS and how to transfer data to Galaxy and applying workflows and pipelines in Galaxy were covered. Practical information about StoreBioinfo projects and Data Manager’s responsibility was also given.


Conclusions

This workshop was a nice example of a collaborative effort between Centre for Digital Life Norway (DLN), ELIXIR Norway and the FAIRDOM association. It was also a combined arrangement for DLN projects, participants in the DLN Research School and environments outside DLN that are eager to learn more about digital biotechnology and specifically data management. The workshop had a good combination of participants with different backgrounds such as modeler, experimentalist, bioinformaticians and RRI showed that researchers in different areas are interested in applying Data Management. Attendees expressed that the workshop was useful and the volume of content delivered by SEEK and NeLS training was well adapted. The valuable comments will help the competence and infrastructure work group for organizing the next Data Management workshop.

Author

Fatemeh Zamanzad Ghavidel

E-mail: Fatemeh.Ghavidel@uib.no

Topic
Workshop Forskerskolen

Published: 26. May 2017 - kl. 09:43
Last updated: 20. Jun 2017 - kl. 12:42