NSCPHD1171 Molecular Community Analysis
Recent years have seen an enormous increase in publications based on NGS amplicon data and much emphasis has been put into the bioinformatic treatment of data i.e. de-noising and OTU assignment. Extracting the community signal from the obtained OTU matrix is next important step in the process, and the focus of this course. The modern community ecological tool box includes many advanced tools and great developments have been achieved in recent years within this field - now often termed ecoinfomatics. This course mainly addresses PhD students who already have generated sequence-based OTU data.
The course focuses on hands-on data analysis. Therefore the bulk of the course time is allocated to participants’ work on their own data under expert guidance. We will supply accompanying “standard datasets” if participants would like to explore types of analysis that their own data are not suited for.
- Data types, input and transformation. Ways to explore species/OTU richness and diversity (α-diversity)
- Rank-abundance patterns and models
- Comparisons across communities (β-diversity). Distance measures, ordination and correlation with meta-data
- Permutation tests
- Variation partitioning
- GLS models and use of AICs
- Functional groups and analysis in trait space, trait dispersion
- Phylogenetic dispersion
- Ways to analyze spatial community turnover, optimization of sampling protocols
- Complementary lectures on Design of ecological studies sampling communities, Sampling and processing different types of substrate for molecular analysis, OTU assignment and Current state of next generation sequencing techniques
Sunday | Monday | Tuesday | Wednesday | Thursday | Friday | Saturday |
Arrival | Lecture: Computerlab: | Lecture: Computerlab: | Lecture: Computerlab: | Lecture: Computerlab: | Lecture: Computerlab: | Departure |
Lunch | Lunch | Lunch | Lunch | Lunch | ||
Lecture: Computerlab: | Lecture: Computerlab: | Lecture: Computerlab: | Lecture: Computerlab: | Student presentations of results: | ||
Evening mixer | Diner and student presentations | Evening free | Evening free | Evening free | Course diner |
Participants are, after the course, expected to be able to thoroughly analyze their own datasets and think critically on published and own data and data analysis.
Participants sought: The students we seek for to this course are students working with meta-barcoding of eukaryote communities. We strongly recommend that you bring your own NGS-generated community dataset. Note that this course will not directly include how to define OTUs from sequence data i.e. the bioinformatics tools for this.
Lunch is included all days. Dinner/snacks is included the first (Sunday), second (Tuesday) and last evening (Friday).
Travel, accommodation and reimbursement
Accommodation in Copenhagen are self-organized. Cheaper possibilities are International House (https://adobeformscentral.com/?f=obplZ-NE-GelHW7mK3-Hfg) which offers special rates for UCPH guests (use link). Otherwise, the cheapest hotel possibilities are CABINN (https://www.cabinn.com/en/). Three main hostels in Copenhagen (http://www.danhostel.dk/en) and B&Bs ( http://www.copenhagenbedandbreakfast.dk/CopenhagenKortGB.htm)
Up to 10 students from outside the Copenhagen/Lund area can be reimbursed for some travel expenses (max 1500 DKK) and accommodation expenses (max 1500 DKK).
- Category
- Hours
- Lectures
- 10
- Practical Training
- 45
- Preparation
- 30
- Total
- 85
Potential participants should apply for course admission by sending a max 1-page motivational letter to course responsible Rasmus Kjøller (rasmusk@bio.ku.dk) not later than April 17, 2015. Admission to course will be announced shortly after.
- Credit
- 3 ECTS
- Type of assessment
- Course participation under invigilation
Course information
- Language
- English
- Course code
- NSCPHD1171
- Credit
- 3 ECTS
- Level
- Ph.D.
- Duration
- Placement
- Spring
- Schedule
- 18-22 May 2015, 17th and 23th for arrival and departure of external participants
- Course capacity
- 20 participants
- Study board
- Natural Sciences PhD Committee
Contracting department
- Department of Biology
Course responsibles
- Rasmus Kjøller (7-7b6a7c767e7c74496b727837747e376d74)
Lecturers
Rasmus Kjøller (coarse organizer), Hans Henrik Bruun, Knud Brian Nielsen (all UCPH-BIO) & Mohamed Bahram (University of Tartu, Estonia)