Category: Training Session

Open Reviewers Workshop

Posted by on in Blog, Led by fellows, Training events, Training Session

In July, BIOS2 will host a 2-hour workshop on open peer review, hosted by our fellow Allegra Spensieri. Allegra has been selected as a PREreview Champion and is now bringing to our community the principles of a fair and open peer review, with the support of PREreview.

PREreview is an organization that develops infrastructure to support the pre-print peer review process from start to end. They develop and provide training on how to write helpful reviews for preprints, and have built a platform to submit preprint reviews on, as well as a community of researchers. The open reviewers workshop is a training program that PREreview has designed for researchers at all levels to learn how to write equitable peer reviews.

This 2-hour workshop will focus on the basics of open, preprint peer reviewing and becoming aware of biases in peer review. Registrations are free and open to everyone, but seats are limited.

When: July 10th, 2024 – 1pm EST
Where: Online
Registrations: https://us02web.zoom.us/meeting/register/tZIoce6tqz0vGtdpZPVtuBKMpLyxjR9WvqjN

Modeling and computational analysis of biological systems

Posted by on in Led by fellows, Training events, Training Session

This June 11 and 13, BIOS2 will host a new training on mathematical models in Ecology, hosted by our fellow Maxime Clenet!

This course is designed to deepen your understanding of theoretical models in ecology, such as population dynamics (Lotka-Volterra), spatial dynamics (metapopulation), or epidemiological models (SIR). The training is divided into two main parts.
First, we will look at the key steps in modelling and formalizing a biological problem in terms of equations and try to answer the questions: Why is it useful? And what are the main current theoretical approaches in population dynamics?
A rigorous mathematical analysis of the model will be carried out by presenting the main methodological tools useful for its analysis, such as equilibrium, Jacobian matrices and stability. This analysis will be integrated in the form of practical exercises and exchanges between the students.

The theoretical part will be followed by a numerical and data-oriented interpretation. You’ll learn how to develop a numerical method to find a solution to dynamical systems with some examples. At the end, the participants will have the opportunity to develop their own numerical simulations for their favourite dynamical model using an adapted and easily accessible programming tool (Python or R depending on programming preferences).

This training is an interdisciplinary project that aims to enhance technical skills, theoretical ecology understanding, and numerical and computational abilities. Trainees from diverse backgrounds are welcome, and the proposed formula will benefit everyone. The training will provide an opportunity for everyone to work on a simple model in three stages: understanding the basic mathematical ideas behind the model, the questions involved and the final numerical implementation of the model.

What: Short course on mathematical models in Ecology (8h)
When: June 11 and 13, 10am-4pm EST (includes lunch break)
Registration: https://us02web.zoom.us/meeting/register/tZMvcO2sqDMuHtOMCaTV2d_ro0bow8UfbZX9

Structural Equation Modelling – training

Posted by on in Led by fellows, Non classé, Training events, Training Session

We are pleased to announce our forthcoming workshop on Structural Equation Modeling (SEM), scheduled to take place from April 8th to 10th, 2024, from 10 am – 1 pm PT / 1 pm – 4 pm ET. This course offers a comprehensive exploration of SEM, delving into its theoretical underpinnings and practical applications. Participants will gain a profound understanding of causal modelling, latent variables, and the nuances of covariance-based and Partial Least Squares (PLS) SEM methodologies. Through in-depth instruction, attendees will learn to leverage prominent software tools to conduct sophisticated analyses of complex datasets. Covering conventions, terminology, model specification, and evaluation, this course equips professionals and researchers with the essential skills to navigate SEM effectively.

The training will be conducted by our fellow Varina Crisfield, an awarded PhD candidate in Key Biodiversity Areas at the Université de Sherbrooke. The workshop will be hosted virtually, and access information will be sent out to registered participants one day before the event.

To apply, please fill out this form by April 4th, 2024: https://forms.office.com/r/1dEg09Qhn0

Two workshops to get started with your data project

Posted by on in Led by fellows, Training events, Training Session

New Year, new project! In February, BIOS2 will offer two workshops to help you get started with your data projects: Project Set-Up and Data Wrangling. In a mix of best practices tips, tutorials and hand-holding activities, these very basic workshops are designed to make you think about your project and data organization before you start anything, but also to help you reshape your current ongoing projects to something more organized and reproducible. Registrations are open until two days before of the first day of each workshop, and seats are limited (max. 40 people each).

These workshops should be accessible to any graduate student, though prior experience in R is helpful. The workshop will be in English, with support in French, and it will be presented online. The link to access it will be communicated shortly before the workshop.

To register, fill out this form: https://forms.office.com/r/Y1Bs5VuTJh

Project Set-Up

Learn and practice project organization, reproducibility tips, project maintenance, and more!
Instructors: Andrew MacDonald and Gracielle Higino
When: February 5, 6 and 7 @ 11 am PT / 2 pm ET
Where: online

Data Wrangling

Learn the best practices on data tidying and follow along a tutorial on OpenRefine.
Instructors: Simran Bains, Lukas Van Riel and Timothée Poisot
When: February 13 and 15 @ 10 am PT / 1 pm ET
Where: online

If you have any questions, do not hesitate to contact us at pgm_bios2@usherbrooke.ca.

Handy tips for doing a statistical model

Posted by on in Training events, Training Session

When it comes to designing a statistical model, a lot of uncertainty comes to mind. In December, BIOS2 will offer a workshop which will give you some helpful strategies for fitting and understanding your regression models. Led by Dr Andrew MacDonald, the workshop will happen during 3h in two days on December 12 and 14, 2023, with lots of time for questions and discussions of your own work. This workshop should be accessible to any graduate student, though prior experience in R is helpful. The workshop will be in English, with support in French.

To register, fill out the form linked at the end of this page by December 9th, 2023.

Schedule

Day 1:

  • What’s zero? When and how to center a variable?
  • What are the units? Scaling a variable and why you should do it.
  • What does it mean? Making predictions.
  • Does it depend? Fitting and visualizing interactions.

Day 2:

  • What do you expect? Simulating datasets.
  • The secret weapon: fitting the same model multiple times.

When: 13h EST, Tuesday 12 Dec and Thursday 14 Dec, 2023.
Duration: 3h each day (total of 6 hours)
Where: Online - information to be sent one day before the workshop
Registration form: https://forms.office.com/r/BfUD8Gv61D
Registration deadline:  December 9th, 2023

Interpretable Machine Learning applied to SDMs

Posted by on in Training Session

Machine Learning is not a black box (unless we want to!). If you ever wondered what the results of a species distribution model actually mean, BIOS² is here to help you! On October 6, 2023, at 1pm – 3pm EDT, Professor Timothée Poisot will host a short and very participatory workshop on how to interpret machine learning models applied to SDMs.

In this workshop, participants will build a simple model to predict the distribution of the raccoon in the South of Québec based on observations. Rather than focus on “what is the prediction?”, we will ask questions about “why”. Specifically, by mixing the presentation of the results with mini group discussions, we will question how the model works, when it is acceptable to apply our best judgment and ignore some performance metrics, and how we can think about interpretable machine learning to improve model transparency. Attendees will get access to all the code and data at the end of the workshop.

The workshop will be hosted virtually, and information about access will be sent out to registered participants one day before the event.

To apply, please fill out this form by October 4th, 2023: https://forms.office.com/r/SLuu3gv9B1