NGS Chipster workshop in Thessaloniki
I’m really happy to report that the “NGS Analysis Training Workshop: cross-domain data exploration” in Thessaloniki was a resounding success.
As an educational event, it was co-organized by the Institute of Applied Biosciences (INAB/CERTH) and the Information Processing Lab (IPL/AUTH). However, particular mention should be made to the effort and help from Diego Scardaci (EGI.eu/INFN) and Kimmo Mattila (CSC). Many thanks!
The main goal of this workshop was to attract researchers from different fields in life sciences who are
- (a) actively using Next Generation Sequencing (NGS) data analysis workflows in their research, and
- (b) have limited experience in employing large scale computer systems or specifically EGI resources.
The workshop lasted for a whole day (09:30 – 17:00) and it attracted 23 participants, mostly from the Aristotle University and the Institute of Applied Biosciences here in Thessaloniki, but we also had three participants coming in from Athens as well.
Their background was mainly from wet-lab research but with some experience in handling NGS data. However, almost none of them had any experience either with a Unix environment, nor with the command-line tools required for NGS data analysis. Despite that, they were able to follow the process of logging in to a UI and launching a Chipster instance with little difficulty (in fact, all problems stemmed from their lack of experience in using a terminal).
Beyond that, and using some preset Chipster exercises, we spent about 5 hours exploring the capabilities of Chipster and running some simple pipelines (such as quality control, alignments, mapping of reads and visualization). Needless to say, the general response was really positive on Chipster, to the point of asking how they can set this environment up for their own use (either at their organizations’ local infrastructure or through EGI resources).
Blog posted on behalf of Fotis Psomopoulos, who organised the workshop in Thessaloniki.