EMBO Practical Course on Computational Molecular Evolution (Heraklion, Greece)
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, e.g., de novo gene finding from genomic sequences.
Additionally, explicit use of molecular evolutionary and phylogenetic analyses provide important insights in their own right, e.g., analysis of adaptive evolution in viruses providing clues of their interaction with host immune systems.
To this end, we aim to provide graduate and postgraduate researchers with the theoretical knowledge and practical skills to carry out molecular evolutionary analyses on sequence data.
Preference is given to applicants 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
The course will offer a unique opportunity for direct interaction with some of the world-leading scientists and authors of famous analysis tools (John Huelsebeck, Olivier Gascuel, Nick Goldman, Bruce Rannala, Alexandros Stamantakis, Ziheng Yang, etc.) in evolutionary Bioinformatics.
The course will entail data retrieval and assembly, alignment techniques, phylogeny reconstruction, hypothesis testing, and population genetic approaches. The course will cover sessions on analysis of both protein and nucleotide sequences, including NGS data.
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| Day 0 (Sunday May 4th, 2014) | |
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| Participants arrive at the hotel Dinner at hotel (20.00 - ) |
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| Day 1 (Monday May 5th, 2014) | |
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Introductions (09.30 - 10.00): Antonis Magoulas & Alexandros Stamatakis: Introduction to course and venue Introductory Computational Practical Session (10.00 - 11.00): Aidan Budd and Brian Moore "Interpreting molecular phylogenetic trees (I)" Coffee (11.00 – 11.30) Introductory Computational Practical Session (11.30 - 13.00): Aidan Budd and Brian Moore "Interpreting molecular phylogenetic trees (II)" Lunch (13.00 - 15.00) Presentations and Practical Sessions (15.00 - 16.30): Aidan Budd and Brian Moore "Interpreting molecular phylogenetic trees (III)" Coffee (16.30 - 17.00) Presentations and Practical Sessions (17.00 - 18.30): Aidan Budd and Brian Moore "Interpreting molecular phylogenetic trees (IV)" Further free exercises (18.30 - 20.00) Dinner at hotel (20.30 - ) |
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| Day 2 (Tuesday May 6th 2014) | |
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Open practical session (09.00 - 09.30): Teaching Assistants (TAs) - Free for analysis of trainees own data Presentations and Practical Sessions (09.30 - 11.00): Stephen Smith and Ben Redlings - "Dataset Assembly & sequence alignment (I)" Coffee (11.00 - 11.30) Presentations and Practical Sessions (11.30 - 13.00): Stephen Smith and Ben Redlings - "Dataset Assembly & sequence alignment (II)" Lunch (13.00 - 15.00) Presentations and Practical Sessions (15.00 - 16.30): Stephen Smith and Ben Redlings - "Dataset Assembly & sequence alignment (III)" Coffee (16.30 - 17.00) Presentations and Practical Sessions (17.00 - 18.30): Stephen Smith and Ben Redlings - "Dataset Assembly & sequence alignment (IV)" Presentation (19.00 - 20.00): Martin Embley "The Tree of Life" Dinner at hotel (20.30 - ) |
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| Day 3 (Wednesday May 7th 2014) | |
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Open practical session (09.00 - 09.30): Teaching Assistants (TAs) - Free for analysis of trainees own data Presentations and Practical Sessions (09.30 - 11.00): Stephen Smith and Ben Redlings - "Dataset Assembly & sequence alignment (V)" Coffee (11.00 - 11.30) Presentations and Practical Sessions (11.30 - 13.00): Stephen Smith and Ben Redlings - "DatasetAssembly & sequence alignment (VI)" Lunch (13.00 - 15.00) Short Excursion: (15.00 - 16.30): Optional free tour of the CreteAquarium Coffee (16.30 - 17.00) Open practical session (17.00 - 20.00): Teaching Assistants (TAs) - Free for analysis of trainees own data Dinner at hotel (20.30 - ) |
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| Day 4 (Thursday May 8th 2014) | |
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Open practical session (09.00 - 09.30): Teaching Assistants (TAs) - Free for analysis of trainees own data Presentations and Practical Sessions (09.30 - 11.00): Maria Anisimova, Olivier Gascuel & Brian Moore - "Phylogeny reconstruction methods (I)" Coffee (11.00 - 11.30) Presentations and Practical Sessions (11.30 - 13.00): Maria Anisimova, Olivier Gascuel & Brian Moore - "Phylogeny reconstruction methods (II)" Lunch (13.00 - 15.00) together with Poster Session Presentations and Practical Sessions (15.00 - 16.30): Maria Anisimova, Olivier Gascuel & Brian Moore - "Phylogeny reconstruction methods (III)" Coffee (16.30 - 17.00) Presentations and Practical Sessions (17.00 - 18.30): Maria Anisimova, Olivier Gascuel & Brian Moore - "Phylogeny reconstruction methods (IV)" Presentation (19.00 - 20.00): Antonis Rokas "Experimental molecular evolution" Dinner at hotel (20.30 - ) |
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| Day 5 (Friday May 9th 2014) | |
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Open practical session (09.00 - 09.30): Teaching Assistants (TAs) - Free for analysis of trainees own data Presentations and Practical Sessions (09.30 - 11.00): Maria Anisimova, Olivier Gascuel & Brian Moore - "Phylogeny reconstruction methods (V)" Coffee (11.00 - 11.30) Presentations and Practical Sessions (11.30 - 13.00 Maria Anisimova, Olivier Gascuel & Brian Moore - "Phylogeny reconstruction methods (VI)" Lunch (13.00 - 15.00) together with Poster Session Presentations and Practical Sessions (15.00 - 16.30): Alexandros Stamantakis - "Parallel Computing Phylogenetics (I)" Coffee (16.30 - 17.00) Presentations and Practical Sessions (17.00 - 18.30): Alexandros Stamantakis - "Parallel Computing Phylogenetics (II)" Presentation (19.00 - 20.00): John Huelsenbeck "Bayesian Phylogenetic Analysis" Dinner at hotel (20.30 - ) |
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| Day 6 (Saturday May 10th 2014) | |
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Open practical session (09.00 - 09.30): Teaching Assistants (TAs) - Free for analysis of trainees own data Presentations and Practical Sessions (09.30 - 11.00): Nick Goldman & Ziheng Yang - "Hypothesis testing in phylogenetics (I) Coffee (11.00 – 11.30) Presentations and Practical Sessions (11.30 - 13.00): Nick Goldman & Ziheng Yang - "Hypothesis testing in phylogenetics (II) Lunch (13.00 - 15.00) Presentations and Practical Sessions (15.00 - 16.30): Nick Goldman & Ziheng Yang - "Hypothesis testing in phylogenetics (III) Coffee (16.30 - 17.00) Presentations and Practical Sessions (17.00 - 18.30): Nick Goldman & Ziheng Yang - "Hypothesis testing in phylogenetics (IV)" Open practical session (18.30 - 20.00): Teaching Assistants (TAs) - Free for analysis of trainees own data Dinner at hotel (20.30 - ) |
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| Day 7 (Sunday May 11th 2014) | |
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| Excursion and hike in the Rouvas gorge | |
| Day 8 (Monday May 12th 2014) | |
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Open practical session (09.00 - 09.30): Teaching Assistants (TAs) - Free for analysis of trainees own data Presentations and Practical Sessions (09.30 - 11.00): Nick Goldman & Ziheng Yang - "Hypothesis testing in phylogenetics (V) Coffee (11.00 – 11.30) Presentations and Practical Sessions (11.30 - 13.00): Nick Goldman & Ziheng Yang - "Hypothesis testing in phylogenetics (VI) Lunch (13.00 - 15.00) Presentations and Practical Sessions (15.00 - 16.30): Jeff Thorne and Tracy Heath – "Estimating divergence times" (I) Coffee (16.30 - 17.00) Presentations and Practical Sessions (17.00 - 18.30): Jeff Thorne and Tracy Heath - "Estimating divergence times" (II) Presentation (19.00 - 20.00): Tanja Stadler "Estimating speciation and extinction rates" Dinner at hotel (20.30 - ) |
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| Day 9 (Tuesday May 13th 2014) | |
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Open practical session (09.00 - 09.30): Teaching Assistants (TAs) - Free for analysis of trainees own data Presentations and Practical Sessions (09.30 - 11.00): Bruce Rannala and Adam Leache - "Coalescent model and inference from population data (I)" Coffee (11.00 – 11.30) Presentations and Practical Sessions (11.30 - 13.00): Bruce Rannala and Adam Leache - "Coalescent model and inference from population data (II)" Lunch (13.00 - 15.00) Presentations and Practical Sessions (15.00 - 16.30): Bruce Rannala and Adam Leache - "Coalescent model and inference from population data (III)" Coffee (16.30 - 17.00) Presentations and Practical Sessions (17.00 - 18.30): Bruce Rannala and Adam Leache - "Coalescent model and inference from population data (IV)" Open practical session (18.30 - 20.00): Teaching Assistants (TAs) - Free for analysis of trainees own data |
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| Day 10 (Wednesday May 14th 2014) | |
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Open practical session (09.00 - 09.30): Teaching Assistants (TAs) - Free for analysis of trainees own data Presentations and Practical Sessions (09.30 - 11.00): Bruce Rannala and Adam Leache - "Coalescent model and inference from population data (V)" Coffee (11.00 - 11.30) Presentations and Practical Sessions (11.30 - 13.00): Bruce Rannala and Adam Leache - "Coalescent model and inference from population data (VI)" Lunch (13.00 - 15.00) Practical Session (15.00 - 16.30) Final discussion session, trainee feedback, additional issues raised during the course Dinner at hotel (20.30 - ) |
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| Day 11 (Thursday May 15th 2014) | |
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| Departure | |
Registration fees:
i) Non-local students: 400 Euro (includes breakfast, lunch, dinner and accommodation)
ii) Local students from Crete only: 75 Euro (excluding accommodation and dinner)
NB: Participants are responsible for their own travel arrangements and need to make reservations directly with the hotel themselves.
Further details regariding this event and how to register can be found here: http://events.embo.org/14-computational-evolution/index.html