BIG 4 Fall Workshop 2016
Phylogenetics, phylogenomics, citizen science and entrepreneurship
The BIG4 fall workshop 2016 has two main themes. One theme is focused on phylogenetics, phylogenomics and bioinformatics, and is intended to provide students with an introduction to these topics, focused on skills that will be useful in their PhD research projects. There will be a mixture of lectures and practicals; students are encouraged to bring their own datasets and analysis problems. The other theme is citizen science and entrepreneurship, and this part of the course will provide broad introductions, exercises, and inspiration for students interested in pursuing these subjects as part of their current or future activities.
The workshop is primarily aimed at BIG 4 students but (except for the Friday morning session) is open to outside participants as well. We have room for up to 10 additional outside participants on a first come first served basis. Outside participants may choose to come for only part of the course, if they wish.
The workshop is primarily aimed at BIG 4 students but (except for the Friday morning session) is open to outside participants as well. We have room for up to 10 additional outside participants on a first come first served basis. Outside participants may choose to come for only part of the course, if they wish.
Venue and practical information
The Tovetorp research station (http://www.zoologi.su.se/tovetorp/) belongs to Stockholm University and was founded in 1969. It hosts courses and research projects, primarily in ecology and ethology. It is situated about 95 km southwest of Stockholm. For driving directions and maps that will help you get there, see http://www.zoologi.su.se/tovetorp/hitta.php [in Swedish]. In English: Take E4 south from Stockholm. Between Järna and Nyköping, you take the "Lästringe" exit and follow signs to Nyköping. After about 10 km, take a right towards Aspa and Öster-Malma. Follow signs towards Öster-Malma until you get to a yellow sign pointing to Tovetorp to your left, close to Öster-Malma. If you need more detailed instructions, you should have no problems finding "Tovetorp forskningsstation" on Google Maps.
Students should be prepared to share rooms. Please note that outdoor shoes are not allowed inside the station. We recommend you to bring slippers for indoor use. There is a hot tub and an indoor recreation area with a floorball court (complete with goals, balls and sticks) and a sauna (unisex). We recommend that you bring indoor sport shoes, gym clothes, swimsuit, and a big towel for sauna use.
Students should be prepared to share rooms. Please note that outdoor shoes are not allowed inside the station. We recommend you to bring slippers for indoor use. There is a hot tub and an indoor recreation area with a floorball court (complete with goals, balls and sticks) and a sauna (unisex). We recommend that you bring indoor sport shoes, gym clothes, swimsuit, and a big towel for sauna use.
Transportation
The most convenient option coming from abroad is probably to fly to Stockholm Arlanda airport. From there you can choose express train (Arlanda Express) bus to downtown Stockholm (or taxi if you prefer). There is also the regional commuter train, but it is the slowest option and is not recommended unless you have the time to spare. You can enquire about details and buy tickets at Arlanda airport.
An alternative option is to fly into Stockholm Skavsta airport south of Stockholm (used by Ryan air). From there, you can take the bus to downtown Stockholm. Skavsta airport is actually fairly close to Tovetorp field station, so if you are adventurous there is also the possibility of taking public transport (bus) from Skavsta to the vicinity of Tovetorp (expect a 2 km walk from nearest bus stop). Alternatively, you can rent a car at Skavsta and drive (about 30–40 min. drive from there to Tovetorp).
For those students and teachers who will only participate in part of the course, you may want to take the train to Gnesta Station (36 min. from Stockholm central station with regional trains). We will organize transports between Gnesta railway station and Tovetorp, as needed.
We have arranged common transportation for BIG 4 students. Bus to Tovetorp will leave Stockholm central station (?) on Sunday, October 9th at 7:30 PM. Bus from Tovetorp to Stockholm central station (?) will leave Tovetorp on October 19th 8:30 AM (after breakfast). The bus drive will take approximately an hour and a half. Outside students are encouraged to use these buses if they plan to participate in the entire course, or in the starting or ending part of the course.
An alternative option is to fly into Stockholm Skavsta airport south of Stockholm (used by Ryan air). From there, you can take the bus to downtown Stockholm. Skavsta airport is actually fairly close to Tovetorp field station, so if you are adventurous there is also the possibility of taking public transport (bus) from Skavsta to the vicinity of Tovetorp (expect a 2 km walk from nearest bus stop). Alternatively, you can rent a car at Skavsta and drive (about 30–40 min. drive from there to Tovetorp).
For those students and teachers who will only participate in part of the course, you may want to take the train to Gnesta Station (36 min. from Stockholm central station with regional trains). We will organize transports between Gnesta railway station and Tovetorp, as needed.
We have arranged common transportation for BIG 4 students. Bus to Tovetorp will leave Stockholm central station (?) on Sunday, October 9th at 7:30 PM. Bus from Tovetorp to Stockholm central station (?) will leave Tovetorp on October 19th 8:30 AM (after breakfast). The bus drive will take approximately an hour and a half. Outside students are encouraged to use these buses if they plan to participate in the entire course, or in the starting or ending part of the course.
Preparations
Bring your own computer with wireless access and an ssh client. For Windows machines we recommend MobaXTerm (http://mobaxterm.mobatek.net/). For Mac computers, simply make sure you know where to find the Terminal application.
Some basic familiarity with Unix will be highly beneficial for the first week. This is one of many unix tutorials for beginners on the web: http://www.ee.surrey.ac.uk/Teaching/Unix/. It includes eight short tutorials that cover all the necessary basics, and more.
Some basic familiarity with Unix will be highly beneficial for the first week. This is one of many unix tutorials for beginners on the web: http://www.ee.surrey.ac.uk/Teaching/Unix/. It includes eight short tutorials that cover all the necessary basics, and more.
Teachers
Fredrik Ronquist (Professor, Swedish Museum of Natural History), Chris Wheat (Professor, Stockholm University), Rodrigo Esparza-Salas (PhD, Technician at the DNA-lab, Swedish Museum of Natural History), Johan Nylander (Bioinformatician, Swedish Museum of Natural History), Erik Gobbo (PhD student, Swedish Museum of Natural History), Daniel Marquina (PhD student, Swedish Museum of Natural History); Karin Carlsson (Business Developer, Savantic AB), Miroslav Valan (PhD student, Savantic AB/Swedish Museum of Natural History). [Miroslav and Karin to complement this list with teachers/discussion participants for the part on citizen science and entrepreneurship].
Pre- or post-course activities
Students interested in sightseeing in Stockholm or visits to the Swedish Museum of Natural History before or after the course, please contact a member of the local organizing committee (Erik, Daniel, Miroslav, Fredrik).
Course registration and fee
Register for the course no later than September 28 using the form at this web site: http://bit.ly/2c6i6v0. Outside student participation will be confirmed on September 29. If you cancel past that date, we may very well have to charge you the course fee anyway.
There will be a fee for course, accommodation and food. We expect the total cost to be approximately 2,000 SEK/day for students participating for part of the course, and approximately 15,000 SEK in total for those students taking the entire workshop. Students will receive an invoice after the course is finished.
There will be a fee for course, accommodation and food. We expect the total cost to be approximately 2,000 SEK/day for students participating for part of the course, and approximately 15,000 SEK in total for those students taking the entire workshop. Students will receive an invoice after the course is finished.
Schedule
Coffee breaks are scheduled all days at 10:15-10:45 and 14:30-15:00.Sunday October 9
19:30 Bus to Tovetorp leaving from Stockholm Central Station
21:00 (appr.) Arrival at Tovetorp Field Station
Monday October 10
07:30–08:30 BREAKFAST
09:00–12:00 Fredrik Ronquist. Introduction to statistical inference. Bayesian phylogenetic inference and Markov chain Monte Carlo simulation.
12:00–13:00 LUNCH
13:00–17:00 Fredrik Ronquist. Stochastic models of evolution. Introduction to MrBayes. Exercises using MrBayes.
18:00–19:00 DINNER
19:30–21:00 Continued exercises. Questions. Discussion.
Tuesday October 11
07:30–08:30 BREAKFAST
09:00–12:00 Fredrik Ronquist. Divergence time estimation: node dating and total-evidence dating. Statistical biogeography. Model testing, model averaging and other special topics.
12:00–13:00 LUNCH
13:00–17:00 Fredrik Ronquist. Phylogenetic graphical models. Introduction to RevBayes. Exercises using MrBayes and RevBayes.
18:00–19:00 DINNER
19:30–21:00 Continued exercises. Questions. Discussion.
Wednesday October 12
07:30–08:30 BREAKFAST
09:00–12:00 Erik Gobbo. De novo genome sequencing: next generation sequencing and genome assembly.
12:00–13:00 LUNCH
13:00–17:00 Chris Wheat. Gene finding, genome annotation and phylogenomic inference.
18:00–19:00 DINNER
19:30–21:00 Questions. Discussion.
Thursday October 13
07:30–08:30 BREAKFAST
09:00–12:00 Chris Wheat, Erik Gobbo. Genome assembly, gene finding, genome annotation and phylogenomics exercises.
12:00–13:00 LUNCH
13:00–17:00 Rodrigo Esparza-Salas. Introduction to metabarcoding.
Daniel Marquina. Metabarcoding: special topics.
18:00–19:00 DINNER
19:30–21:00 Continued exercises. Questions. Discussion.
Friday October 14
07:30–08:30 BREAKFAST
08:30–12:30 BIG 4 Midterm Review [Only BIG 4 participants].
12:30–13:30 LUNCH
13:30–17:00 Daniel Lundin, Daniel Marquina. Metabarcoding exercises.
18:00–19:00 DINNER
19:30–21:00 Continued exercises. Questions. Discussion.
Saturday October 15
07:30–08:30 BREAKFAST
09:00–12:00 Johan Nylander. Handling bioinformatics data in a unix environment. Bioinformatics exercises. Bring your own data and questions!
12:00–13:00 LUNCH
13:30–17:00 Continued exercises. Questions. Discussion.
18:00–19:00 BANQUET DINNER
Sunday October 16
Free day for social activities. Food will be served as usual.
07:30–08:30 BREAKFAST
12:00–13:00 LUNCH
18:00–19:00 DINNER
Monday October 17
07:30–08:30 BREAKFAST
09:00–10:15 TBA. Why you should become an entrepreneur.
10:45–12:00 Several contributors. Round table discussion: insights from experienced entrepreneurs in biosystematics, informatics and genetics.
12:00–13:00 LUNCH
13:30–17:00 Karin Karlsson (Savantic AB). Training session: Steps in the entrepreneurship process.
18:00–19:00 DINNER
Tuesday October 18
07:30–08:30 BREAKFAST
09:00–10:15 Karoly Makonyi. A personal view on citizen science.
Karin Carlsson. Gamification and viral effects: a case study.
10:45–12:00 Jakob Jönsson. Citizen science in cosmology.
12:00–13:00 LUNCH
13:30–17:00 TBA. [Contribution from Chalmers].
Emma Lundberg. [Title TBA].
Miroslav Valan. [Title TBA].
18:00–19:00 DINNER
Wednesday October 19
07:30–08:30 BREAKFAST
08:30 Bus to Stockholm from Tovetorp
10:00 (appr.) Arrival at Stockholm Central Station