Courses in Biology and Environmental Sciences

Courses in Biology and Environmental Sciences in the 28th Jyväskylä Summer School. The University of Jyväskylä reserves the right to make changes to the course programme.

BIO1: Designing recirculating aquaculture systems

Time: 6.-10.8.2018, 8 - 16 
Participants: 12
Lecturer(s): Prof. Michael Ben Timmons (Cornell University, USA)
Coordinator(s):  Juhani Pirhonen
Code: BENS7001
Modes of study: Pre-course assignment, lectures (online?), reading assignments, self-check quizzes, practical exercises, visit to a fish farm
Pre-course assignment: Before the beginning of the course participants are required to read designated chapters (TBA, about 400 pages) from the book Timmons M.B. & Ebeling J.M. 2013: Recirculating aquaculture. Third edition. 
Credits: 5 ECTS
Evaluation: final exam

Contents: Overview of recirculating aquaculture systems (RAS) engineering; Water quality objectives, monitoring and measurement; Fish growth and system staging; Engineering design of individual unit processes; System management; Fish health management; Economic and risk evaluation

Learning outcomes: 
The course will equip you to examine how to design a recirculating aquaculture system, component, or process to meet production objectives; Determine how to best select appropriate water quality targets; Develop a capability to design pumping systems; Build an analytical capability to quantify costs of production; Identify the critical factors for managing a fish farm

Prerequisites: Any student in an aquaculture, engineering, or biology curriculum. Familiarity with Excel is considered an asset. 

BIO2: Bioinformatics for microbial ecologists - sequence processing made easy

Time: 6.-8.8.2018
Participants: max. 25
Lecturer(s):  Prof. Marja Tiirola (University of Jyväskylä, Finland), Dr. Anu Mikkonen (University of Jyväskylä), PhD Student Ville Hoikkala (University of Jyväskylä), Dr. Antti Rissanen (Tampere University of Technology, Finland), NN (Qiagen), Dr. Eija Korpelainen (CSC - IT Center for Science Ltd.)
Coordinator(s):  Sanni Aalto
Code: BENJ7001
Modes of study: Lectures (20%) and hands-on exercises (80%) at the computer class
Credits: 1 ECTS
Evaluation: pass/fail - presence and active participation required
Contents: Processing of barcoded Ion Torrent and MiSeq NGS data from multiple samples; NGS 16S rRNA gene sequence (“microbiome”) data analysis, functional gene sequence data analysis, CRISPR sequence data analysis; running mothur commands on PC and on CSC superclusters (Chipster); NGS data analysis on CLC Genomics Workbench (16S rRNA genes - also functional genes/metagenomes and transcriptome analysis possible if requested)

Learning outcomes: TBA/see above

Prerequisites: This is a graduate course meant for PhD students & postdocs, also senior scientists and advanced MSc students. Intermediate knowledge of environmental microbiology/microbial ecology is required, 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. Basic understanding about the generation of NGS data (for example use of barcodes) is required, but can be accomplished by specified preliminary reading.

If we receive more applications than there are seats, 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.