Program completed. On Sunday, we finished our EuroEPINOMICS next generation sequencing (NGS) bioinformatics meeting. After working through the command line, running scripts, and staring at black screens with white cursors, we completed our four day course by looking at the more user friendly, web-based tools that the NGS world has to offer, including Galaxy, Varbank, and Ingenuity. I think it was the general consensus among the participants that this was the bioinformatics meeting that we needed in order to understand the data that we generate and deal with on day-to-day basis. These were my favorite sound bites of our meeting. Continue reading
Lessons. Today was the first day of our bioinformatics workshop in Leuven, Belgium. We started out with some basic command line programming and eventually moved on to working with R Studio. What is this all about? It’s about getting some basic understanding of what your computer does and how your computer handles files. It’s about good data and bad data and losing the fear of the command line. We collected responses from the participants today about today’s take home messages. Continue reading
Join the genome hacking league. We are preparing a EuroEPINOMICS bioinformatics workshop in Leuven and I really, really encourage you to join us, as there are handful of place left. This will be the workshop that I always wanted to attend, but never got a chance to take part in. And yes, there is a final exam, but there is a chance that you might pass it. If you’re worried, skip ahead two paragraphs.
Desert Dessert. Cold temperatures, streets closed because of snow – this is not what you expect when traveling to Israel. You also do not expect to have the chance to taste traditional Bedouin food and to see a beautiful canyon every morning. The biggest surprise is that you do not expect this during a workshop. From Dec 12-15th, the European epilepsy genetic community gathered in Be’er Sheva and Sde Boker, Israel for a combined epilepsy genetics workshop and a Young Researcher Meeting. This is a brief attempt to capture the atmosphere of this workshop for everybody who could not attend. By the way, “desert dessert” is a port wine produced in the Negev desert.
Variations on Copy Numbers. In the third issue of our series on the papers of the week I will focus on the detection and annotation of the most common form of structural variation encountered in genomes. Deletions, duplications and inversions are frequent events, which are surprisingly hard to deal with using sequencing-based tools. Hence, this is an area of active development.
Heathrow. Dark social? Threat? I’ll get back to that. I am writing this wrap-up post for the SpotOn 2013 meeting overlooking the British Airways planes on their way to take-off. In the last two days, we caught a glimpse of what online science communication is about. On Saturday, we had our own session #solo13blogs on using blogs for peer-to-peer science communication. As a science communication newbie, I am happy that our session was well received and stimulated quite some discussion. I have taken away three things from this meeting – a new understanding of our readership, an appreciation for Open Access and data sharing, and finally, a fear of the destructive power of dark social that also applies to epilepsy genetics research. But first things first. Continue reading
#solo13. Some strange symbols that made it onto our blog originate on Twitter. The “#” (hash) precedes a hashtag, which indicates a Twitter topic. “@” (at) is called a handle, a possibility to contact people. As you might remember from our previous announcements, Roland and me are currently participating in SpotOn 2013, a conference for online science communication. The meeting is held at the British Library in London. This is just a brief update on what #solo13 was about today. Continue reading
Climate change. In the era of exome and genome sequencing, it might be worthwhile revisiting the merit of family studies in epilepsy research. Seizure disorders are known to have a highly diverse genetic architecture. When singleton studies identify a single, unique gene finding, this discovery usually does not provide much information about the potential causal role of the variant given the high degree of genomic noise. In contrast, family studies are usually considered more robust, as segregation of variants can be traced. Here is the inconvenient truth: unless the family is very large, segregation of possibly monogenic variants adds little information given the vast amount of variants present in our genomes. Continue reading
2D. I am writing this post during our EuroEPINOMICS meeting in Tübingen listening to presentation from CoGIE, the EuroEPINOMICS project working on IGE/GGE and Rolandic Epilepsies and RES, the project on rare epilepsies. At some point during the afternoon, I made my selection for the best graph during the presentations today – an overview of the conservation space of epilepsy genes. Continue reading
Outreach. SpotOn is a series of community events for the discussion of how science is carried out and communicated online. SpotOn London (November 7-9, 2013) is organized by the Nature Publishing Group and represents the flagship conference of the SpotOn series. SpotOn discussions fall into three broad topic areas – policy, outreach, and tools – and this site collates the conversations and other archive material around all of the events. Within the outreach track, Roland and I will contribute to the session about scientist-to-scientist communication using blogs and other online tools. Here is why this pertains to you: in a semi-strategic last-minute move, we managed to reserve one extra ticket that we would like to give to a young scientist who would like to join us in London. Short notice? Spontaneous ideas are sometimes the best ideas. Also, for everybody else, there is one last chance on Friday at 12:00 London time to get tickets. Continue reading