BIG 4 Fall Workshop 2016

Phylogenetics, Phylogenomics, Citizen science and Entrepreneurship

Dates: Mon Oct 10 – Tue Oct 18, 2016

Venue: Tovetorp research station (http://www.zoologi.su.se/tovetorp/)

Description

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.

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.

Schedule Overview

Monday October 10
Fredrik Ronquist. Introduction to statistical inference. Bayesian phylogenetic inference and Markov chain Monte Carlo simulation.
Fredrik Ronquist. Stochastic models of evolution. Introduction to MrBayes. Exercises using MrBayes.

Tuesday October 11
Fredrik Ronquist. Divergence time estimation: node dating and total-evidence dating. Statistical biogeography. Model testing, model averaging and other special topics.
Fredrik Ronquist. Phylogenetic graphical models. Introduction to RevBayes. Exercises using MrBayes and RevBayes.

Wednesday October 12
Erik Gobbo. De novo genome sequencing: next generation sequencing and genome assembly.
Chris Wheat. Gene finding, genome annotation and phylogenomic inference.
Chris Wheat, Erik Gobbo. Genome assembly, gene finding, genome annotation and phylogenomics exercises. Questions, discussion.

Thursday October 13
Rodrigo Esparza-Salas. Introduction to metabarcoding.
Daniel Marquina. Metabarcoding: special topics.
Rodrigo Esparza-Salas, Daniel Marquina. Metabarcoding exercises.

Friday October 14
BIG 4 Midterm Review [Only BIG 4 participants].
BIG 4 Midterm Review [Only BIG 4 participants].

Saturday October 15
Johan Nylander. Handling bioinformatics data in a unix environment. Bioinformatics exercises. Bring your own data and questions!

Sunday October 16
Free day for social activities. Food will be served as usual.

Monday October 17
Inga von Sydow. Why you should become an entrepreneur.
Inga von Sydow, Lyubomir Penev, Eduardo Pareja, Karin Carlsson. Round table discussion on entrepreneurship in biosystematics, informatics and genetics.
Karin Karlsson (Savantic AB). Training session: Steps in the entrepreneurship process.

Tuesday October 18
Karoly Makonyi. A personal view on citizen science.
Karin Carlsson. Gamification and viral effects: a case study.
Jakob Jönsson. Citizen science in cosmology.
Devin Sullivan. [Title TBA].
Erik Thorelli. Bionote – A citizen science platform for logging and sharing species sightings
Miroslav Valan. A brief history of citizen science and its potential in the era of big data.
Miroslav Valan, Karoly Makonyi. Roundtable discussion on citizen

SIU and ForBio course: Biodiversity data management and Open data

Nov 2-5, Tartu, Estonia

What are the modern, efficient, mistake-proof ways to collect and manage field and lab data, identifiers, traits, and environmental variables? How can you store your data to easily integrate with external databases?
This hands-on SIU and ForBio course on Biodiversity data management and Open data covers the basics of data collecting, data management, and publishing Open Data.

Last chance to apply, deadline 22 August!

http://www.forbio.uio.no/events/courses/2016/Open%20data

SIU and ForBio course: Polypores as tools in forest conservation

Sep 19-23, Lammi Biological Station, Finland

Polypores are dominant wood decomposers in boreal forests, and the basis of the saprobic wood web. Polypores are used as indicators of high conservation value forests in Nordic countries, and during this course one will learn how to identify polypores and selected corticioid fungi, focusing on indicator species. Also you will be familiarized with the concept of indicator species and indexes in practical use. The course includes lectures and daily field work in different types of forests, including old-growth forests.

Last chance to apply, deadline 22 August!

http://www.forbio.uio.no/events/courses/2016/Polypores

The ForBio course: Phylogenomics has an extended application deadline: September 1st!

ForBio course: Phylogenomics
http://www.forbio.uio.no/events/courses/2016/phylogenomics.html

Time and place: Nov 14, 2016 – Nov 18, 2016, Natural History Museum, University of Oslo, Norway.
Teachers: Torsten Hugo Struck, NHM, UiO and Patrick Kück, NHM London.

Objectives: Advances in high-throughput sequencing and genomics have revolutionized research in evolutionary biology and systematics. The use of genomics data in phylogenetic analyses has brought new challenges in terms of data handling and analysis. This course aims to help those that have basic experience in bioinformatics and molecular phylogenetics, and have projects focused on high-throughput sequencing data and phylogenetics, to become acquainted with tools, programs and pipelines for phylogenomics and want to contact phylogenomic studies beyond the standard also addressing potentially confunding biases in their datasets.

Prerequisites: Basic knowledge of command line interaction, regular expressions, UNIX, sequence data and alignments, model-based phylogenetic analyses, model testing, Bayesian inference, is a prerequisite for participation. Pre-course exercises on command line, regex and UNIX will need to done, submitted and passed to ensure that all participants have an equal minimum level at start.

NB: This course consists of two parts, week I (14-18 Nov 2016) and week II (in March or April 2017). We will provide the exact dates as soon as possible. The first week covers the basic foundation of phylogenomic studies. Lectures and labs in week II will build upon this and focus on dissecting the phylogenetic signal in the dataset and detecting possible misleading biases such as long branches and compositional heteroegenities. Strategies for thorough sensitivity analyses in phylogenomic studies will be part of this week.

Maximum number of participants is 26.

Application deadline is September 1, 2016.

For more information and application go to the website: http://www.forbio.uio.no/events/courses/2016/phylogenomics.html

Contact Hugo de Boer (hugo.deboer@nhm.uio.no) or Torsten Hugo Struck (t.h.struck@nhm.uio.no) for more information.
All the best,

ForBio/Hugo

The evolution of life on Earth is inevitably linked with the geological and climatic history that has dramatically changed available habitats and resources over time. In this course we will explore how geological and paleoclimatic evidence and paleontological and neontological data can be combined to better understand the interplay between Earth history and the evolution and biogeography of organisms. We will provide key concepts about biostratigraphy and fossil preservation and their crucial role in dating events in deep time. We will touch upon several major events of climate changes and landmass dynamics in different part of the world and at different geological times, such as the formation of the Himalayan mountain range, the Paleocene–Eocene Thermal Maximum (PETM; ~ 55 Ma), and the formation of a land bridge connecting the North and South American continents. A special focus will be given to the effects of these events on local and global biodiversity and its spatial distribution. Further, we will demonstrate computational methods that can help us investigating the dynamics of origination, dispersal, and extinction of organisms using fossil occurrence data. This course will also include practicals providing training in computational (paleo)biology to infer macroevolutionary dynamics and instill or reinforce skills in python and R computing.

Course content
The course includes: 1) formal lectures on earth history and its links to biodiversity dynamics; 2) workshops on the use of computational methods to infer macroevolutionary processes from fossil data with hands-on practicals; 3) visiting the “The history of life and its teeming diversity” exhibition at the Natural History Museum of Gothenburg.

Outcomes
After completion of the course the PhD student will have gained insights on important geological and climatic events that have characterized Earth history and inevitably impacted biodiversity and evolution. They will also have a better understanding of the paleontological and geological evidence that these events left and how they can be used to understand the origin and history of life on Earth, at different geographic and temporal scales. Finally, participants will learn how to setup and carry out macroevolutionary analyses using the software PyRate (https://github.com/dsilvestro/PyRate) to infer origination, extinction and preservation rates from fossil occurrence data.

Required reading
A list of scientific publications required for the course will be distributed among confirmed students two weeks before the start of the course.

Assessment
Preparation of a short research proposal (powerpoint presentation and two page executive summary) to be presented and submitted 10 days after course completion.

Course teachers
Christine D. Bacon, Carina Hoorn, Carlos Jaramillo, Daniele Silvestro

The University of Gothenburg course plan can be found here.

Application deadline is August 12^th, 2016. Apply here. Plan to book travel arrangements that weekend.

A 1.5 ECTS course certificate will be given to students that pass the course, either by GU or ForBio depending on registration.

Contact the course leaders Daniele Silvestro or Christine D. Bacon, or ForBio leader Hugo de Boer for more information.