Tag Archives: training

Teaching my first Software Carpentry Workshop

Group Photo at the finish of the AUTH SWC workshop (Oct 2016)
Group Photo at the finish of the AUTH SWC workshop (Oct 2016)

My first Software Carpentry workshop“. Sounds a bit like a first-grader’s essay. But in all honesty, it was a brand new experience for me. Sure, I have been teaching University lectures and seminars for quite some time, but doing a live-coding session was an experience of its own

All things considered, the workshop was a success (evident also in the group photo here); participants were engaged throughout the two-day workshop, there was continuous feedback and discussions on tough points in the lesson, so everyone left quite happy and (hopefully) more knowledgeable than before.

For me, two things have become even more clear:

  1. Better organization of the workshop in terms of the participants’ level of experience. Sure, very few actually complained for the pace, but I have the impression that we could do a better job if we had focused only on beginner level (for example) or intermediate.
  2. Two days may be convenient in terms of time allocated for any person (given the rather busy schedule of most people now), but it’s a very short time to cover R, Shell and Git. So maybe next time (because there will definitely be a next time) we will aim for three days.

Oh, and a final piece of advice: if you intend to have food or catering at a SWC workshop, ordering pizza may be the best solution…. 🙂

Training for NGS data analysis using Chipster

The story is rather simple. Yesterday, my lab together with the Institute of Applied Biosciences co-organized a training workshop for NGS data analysis. For anyone even remotely engaged in NGS data, the biggest problem in NGS data is usually the computational complexity. In simple words, analyzing tons of data takes a very very long time. Which means that essentially the analysis in performed by people that are familiar with the tools (and their command-line interfaces) that can be used in high end computational systems.
However, this workshop went slightly off the treaded path by (mostly) skipping the command line interface and going directly to the graphical interface of Chipster, developed, maintained and kindly provided by CSC. This “deviation” allowed the participants, who had mainly wet-lab research background, to easily follow the established workflows and pipelines used in NGS data analysis. Moreover, instead of using local computational resources, we launched several Chipster servers through the EGI Federated Cloud. So in one training session, the participants were exposed both to the computational capabilities and infrastructure of EGI, as well as the pipelines used in NGS data analysis. All in all, a very dense 8-hour workshop!
The level of the participants’ experience was also quite diverse, ranging from undergraduate students to faculty members and staff scientists. Despite that though, the workshop was very engaging to all members, a fact clearly seen in the happy faces all around, even when the workshop extended a full hour beyond the expected wrap-up time!
So, the take home message; there is clearly a need (some might consider it a desperate one) for training events in bioinformatics, and especially in Big Data studies such as NGS data analysis. However, such events should not necessarily focus on the tech-savvy user. Or at least, actively encourage the non technical-expert researchers to attend by providing (a) user friendly interfaces, (b) hands-on exercises that feel close to the actual work of the participants, and (c) the time necessary for everyone to keep their own pace.
Finally, I would be remiss if I didn’t thank enough the two people that really supported this workshop: Diego Scardaci from EGI.eu and Kimmo Mattila from CSC, whom I constantly pestered with questions and issues in the past few weeks, and they always had the time and patience to lend me their experience.
Hopefully, there will be follow-up and more specialized workshops. However, if you are interested, the next one will take place at the EGI Community Forum in Bari. So, hope to see you there!