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 (qiime.org). 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 day 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. An extra day, targeted mostly for researchers in Finnish universities with free access to CSC computing resources, is planned to educate the course participants and anyone else interested on how to efficiently utilize these superclusters for processes run on QIIME. 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: Dr. Antonio Gonzlez Pea (University of Colorado, United States), and prof. Greg Caporaso (the lead developers of QIIME, Northern Arizona University, United States), QIIME Application specialist Kimmo Mattila (CSC - IT Center for Science Ltd.,

Target group
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, 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.

Credits info
2 ECTS Passing: Obligatory attendance at lectures, and completing the exercises.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 Jyvskyl.

Scholarships
The 25th Jyvskyl Summer School is not able to grant any Summer School students financial support. In order to ensure your participation, we recommend that you take steps to secure your own funding, for example, by turning first to your home institution



University of Jyv%C3%A4skyl%C3%A4
Address: Faculty of Mathematics and Science and Faculty of Information Technology, Jyv%C3%A4skyl%C3%A4 Summer School, Faculty of Mathematics and Science P.O.Box 35 (YK312), FIN-40014 University of Jyv%C3%A4skyl%C3%A4, Finland
Postal code: FIN-40014
City: Jyv%C3%A4skyl%C3%A4
Country: Finland
Website: http://www.jyu.fi/summerschool
E-mail: jss@jyu.fi
Phone: +358505818351