Finland, Jyväskylä

Bioinformatics for Microbial Ecologists

when 15 August 2016 - 19 August 2016
language English
duration 1 week
credits 2 ECTS

Are you drowning in high-throughput amplicon (marker gene) sequence data? How to filter it, cluster it, classify it and extract some ecological information from those hundreds of thousands of reads of variable quality? More and more microbial ecologists and environmental scientists now have economic and logistic access to high-throughput amplicon sequencing by MiSeq, Ion Torrent and 454, but the real trick is what you do with the data, with or without supercluster computers. This course will introduce the participants with one of the most used amplicon analysis pipelines with the open-source software QIIME - Quantitative Insights Into Microbial Ecology ( Besides hands-on computer class exercises familiarizing the participants with the technical details and finesses of QIIME, the course will discuss the theory behind the methods and pipelines used by some of the most successful groups on the field. One afternoon is dedicated to an open and broadcasted panel discussion where were top scientists describe and defend their debated analytical decisions from primer choice to filtering parameters to statistical standards. The last day will focus on possibilities to speed up the time-consuming bioinformatics computations. The tree cases presented are centralized computing resources (CSC, enabling free use of superclusters for Finnish institutes,, efficiency-optimized commercial analysis platforms (CLC, and the servers of in-house high-throughput sequencers. To compensate for the long hours in the computer class, there will be plenty of chances for networking and discussing your own research - during poster walks as well as canoeing trips.

Course leader

Lecturers: Two of the lead developers of QIIME (“QIIME Masters”), Senior Field Application Specialist Holger Karas (CLC bio), QIIME Application specialist Kimmo Mattila (CSC - IT Center for Science Ltd.), Prof. Marja Tiirola (University of Jyväskylä) and

Target group

The Summer School annually offers courses for advanced master’s students, graduate students, and post-docs in the various fields of science and information technology.

Intermediate knowledge of environmental microbiology/microbial ecology, especially nucleic-acid based methods. This course is especially suitable for those more familiar with the lab than the command line programs, as no previous coding experience is required. Participants will be selected based on a max. 1-page motivation letter where affiliation, background, current and future research plans are briefly stated, with special focus on why you need this course right now (CV may be attached). Please note that even shorter QIIME workshops often cost hundreds of US dollars, so a high number of applications is expected on this free course. We hope to have a diverse, balanced selection of participants.

Course aim

The most important aims of the Summer School are to develop post-graduates scientific readiness and to offer students the possibility to study in a modern, scientific environment and to create connections to the international science community. The Summer School offers an excellent pathway to develop international collaboration in post-graduate research.

Credits info

Passing: Obligatory attendance at lectures and exercises, active participation is required. In addition participants will present their own microbiological or environmental research with a poster or a 5 min oral presentation prepared beforehand. Each participant filling the above-stated requirements will receive a diploma of participation to the workshop, but to receive a course diploma with credit statement (2 ECTS) the student must also return a 1-2 page report (evaluate what you have learned and how can/will you use it in your future research).

Grading: Pass/fail

Fee info

EUR 0: Participating the Summer School is free of charge, but student have to cover the costs of own travel, accommodation and meals at Jyväskylä.


The 26th Jyväskylä Summer School is not able to grant any Summer School students financial support.