EMBO Practical Course on Computational Molecular Evolution
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Date:
Sunday 8 - Thursday 19 May 2016Venue:
Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR) - HCMR, 46,7 km, 19013, Heraklion, GreeceApplication deadline:
Friday 30 October 2015Participation:
Open application with selectionContact:
Eftichia MironakiRegistration fee:
€400Registration closed
Course Overview
The need for effective and informed analysis of biological sequence data is increasing with the explosive growth of biological sequence databases. A molecular evolutionary framework is central to many Bioinformatics approaches used in these analyses. To this end, this course will provide graduate and postgraduate researchers with the theoretical knowledge and practical skills to carry out molecular evolutionary analyses on sequence data. The EMBO Practical Course will offer a unique opportunity for direct interaction with some of the world-leading scientists and authors of famous analysis tools in evolutionary Bioinformatics.
Audience
Note that the last three courses in Crete were heavily over-subscribed. The expected participant acceptance rate is below 20%. Experience from previous years has led to preference being given to candidates who:
- Are doctoral candidates in the early to middle stages of their thesis research
- Already have some familiarity (i.e. have already used some of the relevant tools) with phylogenetic methods
- Have already collected/assembled a molecular sequence dataset to analyze in their work
- Have experience working in a Unix/Linux command-line environment
We will also select a small fraction of participants that already work in Bioinformatics labs, to intensify collaboration between early career stage Biologists and Bioinformaticians. Applicants from labs with a strong focus on computational molecular evolution methodology need to carefully outline their motivation for attending the course in this context, since they have ready access to expert supervision and are likely to be very skilled already in the topics we teach, or are in the course of becoming very skilled therein.
Please note that ALL trainees are required to:
- Present a poster during the course
- Be already familiar with using the Linux operating system prior to attending the course or, if not familiar, invest a substantial amount of time prior to the course in getting familiar with Linux (we can provide some help, i.e. a Linux installation on a CD, for those of you with access only to a Windows machine)
We strongly discourage applications of more than one student from the same lab.
Learning outcomes
After this course you should be able to:
- Identify and retrieve molecular sequence data
- Compare methods for molecular evolutionary analyses, and their strengths and weaknesses
- Construct hypotheses and apply appropriate tests to answer evolutionary questions
- Discuss some major challenges and developments in the field
Programme
| Time | Topic | Trainer |
|---|---|---|
| Day 1: Sunday, May 8th 2016 | ||
| 19:00 - 20:00 | Welcome Reception | |
| 20:00 | Dinner at hotel | |
| Day 2: Monday, May 9th 2016 | ||
| 09:30 - 10:30 | Introductions | Antonis Magoulas & Alexandros Stamatakis |
| 10:30 - 11:00 | Interpreting molecular phylogenetic trees (I) | Aidan Budd, Cilia Antoniou and Brian Moore |
| 11:00 - 11:30 | Coffee | |
| 11:30 - 13:00 | Interpreting molecular phylogenetic trees (II) | Aidan Budd, Cilia Antoniou and Brian Moore |
| 13:00 - 15:00 | Lunch | |
| 15:00 - 16:30 | Interpreting molecular phylogenetic trees (III) | Aidan Budd, Cilia Antoniou and Brian Moore |
| 16:30 - 17:00 | Coffee | |
| 17:00 - 18:30 | Optional Linux/Unix Introduction | Aidan Budd, Cilia Antoniou and Brian Moore |
| 18:30 - 20:00 | Interpreting molecular phylogenetic trees (IV) | Alexey Kozlov |
| 20:30 | Dinner at the hotel | |
| Day 3: Tuesday, May 10th 2016 | ||
| 09:00 - 09:30 | Free for analysis of trainees own data | Teaching Assistants (TAs) |
| 09:30 - 11:00 | Dataset Assembly & sequence alignment (I) | Stephen Smith and Ben Redelings |
| 11:00 - 11:30 | Coffee | |
| 11:30 - 13:00 | Dataset Assembly & sequence alignment (II) | Stephen Smith and Ben Redelings |
| 13:00 - 15:00 | Lunch | |
| 15:00 - 16:30 | Dataset Assembly & sequence alignment (III) | Stephen Smith and Ben Redelings |
| 16:30 - 17:00 | Coffee | |
| 17:00 - 18:30 | Dataset Assembly & sequence alignment (IV) | Stephen Smith and Ben Redelings |
| 18:30 - 20:00 | Dataset Assembly & sequence alignment (V) | Stephen Smith and Ben Redelings |
| 20:30 | Dinner at hotel | |
| Day 4: Wednesday, May 11th 2016 | ||
| 09:00 - 09:30 | Free for analysis of trainees own data | Teaching Assistants (TAs) |
| 09:30 - 11:00 | Dataset Assembly & sequence alignment (VI) | Stephen Smith and Ben Redelings |
| 11:00 - 11:30 | Coffee | |
| 11:30 - 13:00 | Phylogeny reconstruction methods (I) | Maria Anisimova, Olivier Gascuel & Brian Moore |
| 13:00-15:00 | Lunch | |
| 15:00 - 16:30 | Optional free tour of the Crete Aquarium | |
| 16:30 - 17:00 | Coffee | |
| 17:00 - 18:30 | Phylogeny reconstruction methods (II) | Maria Anisimova, Olivier Gascuel & Brian Moore |
| 18:30 - 20:00 | Open practical session OR Advanced computing breakout: Pair-wise sequence alignment in R | Teaching Assistants / Benjamin Redelings |
| 20:30 | Dinner at hotel | |
| Day 5: Thursday, May 12th 2016 | ||
| 09:00 - 09:30 | Free for analysis of trainees own data | Teaching Assistants (TAs) |
| 09:30 - 11:00 | Phylogeny reconstruction methods (III) | Maria Anisimova, Olivier Gascuel & Brian Moore |
| 11:00 - 11:30 | Coffee | |
| 11:30 - 13:00 | Phylogeny reconstruction methods (IV) | Maria Anisimova, Olivier Gascuel & Brian Moore |
| 13:00 - 15:00 | Lunch with Poster Session | |
| 15:00 - 16:30 | Phylogeny reconstruction methods (V) | Maria Anisimova, Olivier Gascuel & Brian Moore |
| 16:30 - 17:00 | Coffee | |
| 17:00 - 18:30 | Overview over NGS techniques and methods (I) | Adam Leache and Alexey Kozlov |
| 18:30 - 20:00 | Overview over NGS techniques and methods (II) | Adam Leache and Alexey Kozlov |
| 20:00 | Dinner at hotel | |
| Day 6: Friday, May 13th 2016 | ||
| 09:00 - 09:30 | Free for analysis of trainees own data | Teaching Assistants (TAs) |
| 09:30 - 11:00 | Phylogeny reconstruction methods (VI) | Maria Anisimova, Olivier Gascuel & Brian Moore |
| 11:00 - 11:30 | Coffee | |
| 11:30 - 13:00 | Phylogeny reconstruction methods (VII) | Maria Anisimova, Olivier Gascuel & Brian Moore |
| 13:00 - 15:00 | Lunch together with Poster Session | |
| 15:00 - 16:30 | Phylogeny reconstruction methods (VIII) | Maria Anisimova, Olivier Gascuel & Brian Moore |
| 16:30 - 17:00 | Coffee | |
| 17:00 - 18:30 | Parallel Computing Phylogenetics (I) | Asif Tamuri |
| 18:30 - 20:00 | Parallel Computing Phylogenetics (II) | Asif Tamuri |
| 20:00 | Dinner at hotel | |
| Day 7: Saturday, May 14th 2016 | ||
| 09:00 - 09:30 | Free for analysis of trainees own data | Teaching Assistants (TAs) |
| 09:30 - 11:00 | Hypothesis testing in phylogenetics (I) | Nick Goldman, Asif Tamuri, Maria Anisimova & Ziheng Yang |
| 11:00 - 11:30 | Coffee | |
| 11:30 - 13:00 | Hypothesis testing in phylogenetics (II) | Nick Goldman, Asif Tamuri, Maria Anisimova & Ziheng Yang |
| 13:00 - 15:00 | Lunch | |
| 15:00 - 16:30 | Hypothesis testing in phylogenetics (III) | Nick Goldman, Asif Tamuri, Maria Anisimova & Ziheng Yang |
| 16:30 - 17:00 | Coffee | |
| 17:00 - 18:30 | Hypothesis testing in phylogenetics (IV) | Nick Goldman, Asif Tamuri, Maria Anisimova & Ziheng Yang |
| 20:30 | Dinner at hotel | |
| Day 8: Sunday, May 15th 2016 | ||
| Excursion and hike in the Rouvas gorge | Laura Emery | |
| Day 9: Monday, May 16th 2016 | ||
| 09:00 - 09:30 | Free for analysis of trainees own data | Teaching Assistants (TAs) |
| 09:30 - 11:00 | Hypothesis testing in phylogenetics (V) | Nick Goldman, Asif Tamuri, Maria Anisimova & Ziheng Yang |
| 11:00 - 11:30 | Coffee | |
| 11:30 - 13:00 | Hypothesis testing in phylogenetics (VI) | Nick Goldman, Asif Tamuri, Maria Anisimova & Ziheng Yang |
| 13:00 - 15:00 | Lunch | |
| 15:00 - 16:30 | Estimating divergence times (I) | Jeff Thorne, Tanja Stadler and Tracy Heath |
| 16:30 - 17:00 | Coffee | |
| 17:00 - 18:30 | Estimating divergence times (II) | Jeff Thorne, Tanja Stadler and Tracy Heath |
| 18:30 - 20:00 | Free for analysis of traineeds own data OR Advanced computing breakout session: Markov simulations | Teaching Assistants (TAs) / Brian Moore |
| 20:30 | Dinner at hotel | |
| Day 10: Tuesday, May 17th 2016 | ||
| 09:00 - 09:30 | Free for analysis of trainees own data | Teaching Assistants (TAs) |
| 09:30 - 11:00 | Coalescent model and inference from population data (I) | Bruce Rannala and Adam Leache |
| 11:00 - 11:30 | Coffee | |
| 11:30 - 13:00 | Coalescent model and inference from population data (II) | Bruce Rannala and Adam Leache |
| 13:00 - 15:00 | Lunch | |
| 15:00 - 16:30 | Coalescent model and inference from population data (III) | Bruce Rannala and Adam Leache |
| 16:30 - 17:00 | Coffee | |
| 17:00 - 18:30 | Coalescent model and inference from population data (IV) | Bruce Rannala and Adam Leache |
| 18:30 - 20:00 | Free for analysis of trainees own data | Teaching Assistants (TAs) |
| 20:30 | Dinner at hotel | |
| Day 11: Wednesday May 18th 2016 | ||
| 09:00 - 09:30 | Free for analysis of trainees own data | Teaching Assistants (TAs) |
| 09:30 - 11:00 | Coalescent model and inference from population data (V) | Bruce Rannala and Adam Leache |
| 11:00 - 11:30 | Coffee | |
| 11:30 - 13:00 | Coalescent model and inference from population data (VI) | Bruce Rannala and Adam Leache |
| 13:00 - 15:00 | Lunch | |
| 15:00 - 16:30 | Coalescent model and inference from population data (VI) | Bruce Rannala and Adam Leache |
| 16:30 - 20:30 | Dinner at hotel | |
| Day 12: Thursday, May 19th 2016 | ||
| Departure | ||
In association with
How to apply
Application deadline
30 October 2015
Number of places
30 places
Organisers
Alexandros Stamatakis - Heidelberg Institute for Theoretical Studies, Germany
Laura Emery
Nick Goldman
Ziheng Yang - University College London, UK
Aidan Budd - EMBL, Germany
Trainers
Tanja Stadler - ETH Zurich
Alexey Kozlov - H-ITS, Germany
Antonis Magoulas - ICRE8, Greece
Brian Moore - University of California, Berkeley, USA
Stephen Smith - University of Michigan, Ann Arbor, USA
Adam Leache - Department of Biology & Burke Museum, University of Washington, USA
Maria Anisimova - ETH Zurich, Switzerland
Olivier Gascuel - LIRMM-CNRS, Montpellier, France
Nick Goldman - EMBL-EBI, UK
Asif Tamuri - EMBL-EBI, UK
Ziheng Yang - University College London, UK
Jeff Thorne - Genetics and Statistics Department, North Carolina State University, USA
Tracy Heath - University of California, Berkeley, USA
Bruce Rannala - Genome Center and Department of Evolution and Ecology, University of California, USA
Ben Redelings - National Evolutionary Synthesis Center, North Carolina, USA
Aidan Budd - EMBL, Germany