Computational phenotypes. Clinical epilepsy research requires the capturing of complex information in a way that then can be subjected to statistical analysis. For the analysis on the phenotype level, new standards are emerging that are heavily informed by genetic studies. In fact, in addition to the known domain-specific classifications such as the ILAE classification for epilepsy, interdisciplinary action is often required to improve the classification of neurological syndromes for a larger analysis. During the upcoming EMBO Practical phenotyping course in Luxembourg, we will introduce trainees in the field to concepts like the Human Phenotype Ontology (HPO), a controlled vocabulary to characterize syndromes and one of pillars of research in complex syndromes such as epilepsy and how to address aspects not covered in HPO. The course will be held in Luxembourg from Oct 4 to Oct 10, 2018. There has already been a strong interest in this course, but we have a few spots left if you would like to register!
Retreat. Part of the Kingdom of Denmark, the Faroe Islands are an archipelago between the Norwegian Sea and the North Atlantic halfway between Norway and Iceland. From May 24 to 26, 2017, the international epilepsy community will retreat to the Faroe Islands for a conference on the mechanisms of focal epilepsies. With this post, I am inviting clinicians and scientists who typically read our blog to this meeting. Take a quick glance at the program and you will understand why I think that this meeting is interesting. In 2017, a conference on the mechanisms of focal epilepsy has become a conference with a main focus on genetic mechanisms. Here is how our perception of the genetics of focal epilepsies changed over the last 18 years and why a trip to the middle of the North Atlantic may be worthwhile for you. Continue reading
There is no escape from big data – it haunts you on the web, in social media, enables self-driving cars and supposedly revolutionizes health care. Big Data in Healthcare is a meeting in Luxembourg today and tomorrow which brings together a colorful mix of people from all domains and should convince the last of us that this is not at all an IT specialist issue.
YESTI. On behalf of the ILAE Genetics Commission, we are looking for young clinician scientists who would like to help us build the Epilepsiome – a comprehensive, up-to-date database on epilepsy and genes. We are looking for YESTI’s – “young experts with sufficient time and interest”. Read more about what we would expect from you. Continue reading
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