Skip to content

Latest commit

 

History

History
132 lines (92 loc) · 4.47 KB

summerschool.md

File metadata and controls

132 lines (92 loc) · 4.47 KB
layout title nav
page
Summer School 2016
summerschool

We are organizing a computational ecology summer school in May 2016, near Montréal. Apply now, or read more about the program and venue below.

Goals

The goal of this summer school is to give graduate students and early-career scientists in ecology a basic training in computational skills. Over the course of 40 hours of lessons, including students-led research projects, we will cover:

  • good practices for data management and scientific software
  • useful tools from applied mathematics and statistics
  • notions of parallel computing and tips for efficient code
  • interaction with web-based data through APIs

General informations

Instructors

The summer school will be led by Timothée Poisot (Université de Montréal) and Dominique Gravel (Université de Sherbrooke).

Timothée is an assistant professor in Quantitative and Computational Ecology. He is a certified Software Carpentry instructor, and serves on the editorial board of Methods in Ecology & Evolution and PLOS Computational Biology. His research focuses on the spatio-temporal dynamics of species interactions, and the applications of graph theory to a variety of ecological questions.

Dominique is a professor of biogeography at the Université de Sherbrooke, and holds a Tier I Canada Research Chair. His research focuses on theoretical ecosystem ecology, and notably the interactions between community structure, ecosystem functioning, and species distributions.

Venue

The summer school will take place at the Station de Biologie des Laurentides (SBL), operated by the Université de Montréal. Situated in the middle of a series of lakes, in the Laurentians, it is a very pleasant and stimulating place to work and relax.

Dates

The summer school will take place during the first week of May, 2016 (from May 2, to May 8).

Pre-requisites

It is expected that attendees will be familiar with programming, and have a working knowledge of at least one programming language (R, python, perl, ...). We will provide training in how to use the command line, and how to work on remote machines, on day 1. We will provide one high-performance computing server to work on, but students will have to bring their own laptops.

Program

All days will follow the same template. Starting from an ecological problem, we will discuss ways to solve it using computational tools, and in so doing explore different programming approaches and practices.

At the end of the week, attendees will work on a series of projects, based on empirical data. We do hope that these analyses will be continued when the summer school is over, and eventually turn into new papers.

Day 1: Best practices for scientific computing

  • Introduction to the command line (shell, bash .... )
  • Version control
  • Unit testing, continuous integration

Day 2: Code optimization

  • Profiling
  • Parallel and distributed computing
  • Genetic Algorithms

Day 3: Data management and analysis

  • Introduction to databases
  • Maximum Likelihood, Simulated Annealing

Day 4: Computational statistics

  • Bayesian statistics
  • Approximate Bayesian Computation and inference from tiny data
  • Computational macro-ecology and automated data synthesis

Day 5: Open data

  • Open data on the web, API, JSON
  • Student-led projects on a dataset

Day 6

  • Student-led projects
  • Presentations in the evening

Day 7

  • Students are welcome to stay at the Station de Biologie des Laurentides for an additional day, to hike, canoe, or work.

Registration

The registration fees are 60 CAD a day. This includes transportation, three meals a day, and hosting. Please do indicate if you intend to stay on day 7. We will organize transportation to and from Montréal (exact location to be announced).

Attendance is limited to 12 students. To apply, please fill in the following form: http://goo.gl/forms/wyoScdU2Ia. Applications begin immediately and selected applicants will be notified by the first week of March 2016 at the latest.

Applicants that have completed a Software Carpentry or Data Carpentry workshop will be given priority to attend.

If your application is selected, we ask that you pay in advance the first two-days of the summer school, as a non-refundable deposit. Students affiliated with the Québec Centre for Biodiversity Sciences can contact the coordinator to have their registration fee covered or reimbursed.