Looking back at recent BioSB courses

Recently three BioSB courses were organised successfully: the 4th edition of the ‘Pattern Recognition’ course in March 2015, the ‘Kick of R’ course in April 2015 and the ‘Advanced de novo assembly’ course in June 2015. The courses received very good reviews and below you can read a short update about each of the courses.

Pattern Recognition course – March 2015

The 4th edition of the Pattern Recognition course took place at the VU University, from March 23-27, 2015. Thirteen participants from the Netherlands and abroad were submerged for five days in the theory and practice of pattern recognition and machine learning. Morning sessions consisted of three-hour lectures on parametric and non-parametric classifiers, feature selection, dimensionality reduction, clustering, hidden Markov models, neural networks, and support vector machines. In the afternoon the participants applied what they learned in hands-on computer labs using Matlab. Fun parts were the Bio-Pantomime organized by the RSG on Monday and the 2-hour power outage on Friday, that gave Marcel Reinders the opportunity to give an old school blackboard lecture. After the course about half of the participants worked on a final assignment and successfully applied pattern recognition techniques to their own datasets. The course was highly appreciated by the participants, to quote just a few of them: “… it caters for students with diverse backgrounds”, “Many subjects were covered in quite some detail, which is worth a compliment”, and “… most importantly I can see the big picture now”.

Kick start R course – April 2015

This one-day BioSB Introductory course: ‘Kick start R’ took place in Amsterdam at the VU University on April 24, 2015. The course was organized by Douwe Molenaar (VU University) in collaboration with BioSB. The course offered an introduction to the possibilities of the statistical calculation environment R. 18 Highly motivated researchers (half of them PhD students) participated in the course, most of them already having some programming experience, some already working with R. Both during the lecture and the practical sessions there was a lot of discussion about subjects in R. After the course several participants indicated that they would be interested in a more extensive course on R. The course day started with a lecture about the philosophy behind the R-language. Most of the day was further devoted to a computer tutorial where participants could start learning to work with R or, start exploring more advanced topics in R. Topics discussed during the course: R language basics, installing R and R-packages, finding help, using R-studio, making dynamic reports, model fitting, reading/writing data from/to files, making modern publication-ready graphs, books and tutorials on the use of R.

Advanced de novo assembly course – June 2015

The Advanced course on “de novo assembly and resolving complex genomic regions” took place in Leiden where over 35 attendees from 7 countries gathered at Leiden University Medical Center on June 1-3, 2015. The course was organized by Seyed Yahya Anvar and Johan den Dunnen (LUMC, Netherlands), in collaboration with BioSB, and generously supported by Generade and 3Gb-Test. In this course, distinguished speakers from 6 countries and 10 different prestigious institutes shared their expertise and novel insights on genome assembly and resolving genomic dark matter. Invited speakers shared highlights of state-of-the-art tools and technologies that could facilitate a reliable and comprehensive interpretation of the genetic makeup of a full spectrum of different species (from single bacteria to complex metagenomes, plants and animals). Keynote lectures by Alexandre de Kochko (Centre IRD de Montpellier, France) and Mark Chaisson (University of Washington, USA) were made available to a larger audience beyond those attending the course and were very well received. For the first time, organizers provided other means such as twitter (#leidenovo) for the audience to interact with the speakers and discuss topics that are of interest to them. Overall, the course received high ratings from the audience as well as positive and constructive feedback that will certainly improve the future edition of the course.