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How to use Quarto

BIOS² is delighted to invite you to a training session on Quarto, organised by our partner program, QCBS!

Quarto is a quick and easy way to turn your R scripts into beautiful documents, presentations and even websites. It’s a new and improved version of Rmarkdown. This workshop will showcase the benefits of Quarto, including quotes, figures, maps and more. Participants may be familiar with Rmarkdown or new to it. We’ll finish by working on a project: choose between a presentation, an article or a website!

When: 18 Feb 2025 Tuesday – 2pm to 4pm ET
Where: Online and at Concordia Library LB-322 (third floor of the library)
Registration: https://us02web.zoom.us/meeting/register/R4cL3vLzRiiNBDk-vYMSyQ

Workshop R and Git: from code to collaboration

BIOS2 is holding a one-day workshop on programming and version control for data science and research. Our newly Certified Carpentries Instructors Francis Banville and Gabriel Dansereau will be giving an introduction to the Tidyverse, a collection of R packages for data manipulation and visualisation. They will also introduce Git, a collaboration and version control tool useful for research work. The lessons covered will be inspired by those developed by The Carpentries (Data Analysis and Visualization in R for Ecologists and Version Control with Git).

The workshop is free and will take place in person at the Campus MIL of University of Montreal (with snacks!) and the language of instruction will be French. We have a very limited number of places, so register early!

You must have R and RStudio and Git Bash installed before the workshop. If you need help with installation, please email Francis or Gabriel, or arrive 60-30 minutes before the workshop starts.

What: Workshop on R (Tidyverse) and Git
When: Saturday 18 January from 9:00 to 17:00 ET
Where: Campus MIL (Université de Montréal), room B-2061
Contacts: Francis Banville (francis.banville [at] umontreal.ca) and Gabriel Dansereau (gabriel.dansereau [at] umontreal.ca)

Registration form:

Student-Led research group call 2024/25

The concept and idea of a “working group” varies immensely in academia, but in the industry, it has a very clear definition: it is a group of people working on a very specific problem within a timeframe. Although the time to digest and rethink deeply complex ecological problems is instrumental for scientific progress, very often scientists are called to act, to propose a specific solution for a specific problem (even more in the rapidly changing world we’re living in).

The Student-Led Working group aims to promote leadership opportunities for BIOS2 fellows while fostering diversity, inclusion and accessibility in research environments. This call simulates a project development pipeline, with four phases: initiation, planning, execution and closing. Proponents of a working group would submit a project where the organization and leadership are well-defined in the project, as well as expectations, budget and timelines. BIOS2 fellows are invited to submit a project proposal with a schedule for up to seven months, including at least the execution and closing phases of a research project.

A budget of up to CAD$ 5000 is available for travel, accommodation, material and publication fees. In-person event coordination and/or mentoring for organizers can be provided by the BIOS2 coordination team.

Project submission

Each project would clearly define a roadmap including the four phases of project development cited above.

The project should not last more than one academic year and can be very short to include only the final phase of the working group. For example, if a student have already gone through the ideation phase, but needs help planning and executing their projects, they should include the ideation phase in the project and describe the outcomes that would be the input of the planning phase.

Additionally, the group members should be defined by the proponent. A very important aspect of a working group is the choice of the people who will work together. It requires planning and leadership skills to identify the people with the technical baggage, interests and availability to work on a project. It’s up to the proponent how they will find the right people. If needed, the applicant group can open a call for applications to invite more participants, and BIOS2 can help publicizing this call, but the final selection should be made entirely by the proposal’s leadership group. BIOS2 will consider the diversity of the group and justifications for the group composition when deciding if the project will be funded.

The project may or may not include in-person meetings, but should include at least one sprint period. Sprints are short, time-boxed periods when a team works to complete a very well-defined set amount of work. The amount of work defined by the leaders must be compatible with the length of the sprint: the shorter the period, the smaller the number of tasks to be completed. An imbalance in this ratio will certainly lead to burnout and frustration. The sustainability and inclusivity of in-person meetings must be considered during the selection process.

The application package will consist of a written project (that can be supported by other media, such as videos, audio, images, websites, etc.), a lean canvas proposal, a budget spreadsheet and a timeline of ideation (when applicable), planning, execution and closing phases. This timeline must comprise any period between December 1st, 2024 and August 31st, 2025, including the closing phase.

The written project and supporting media should expand on the bullet points added to the lean canvas, and there, proponents must define:

  • One clear problem to be solved and why it’s important to solve it. Applicants should include their problem in a good theoretical context that can be understood by specialists and non-specialists.
  • Description of the human resources of the group, i.e., names and contributions of each participant. Applicants must not attach any CVs – instead, they should explain why they decided to invite these people to help them solve the problem defined before.
  • Expected outcomes: explicit what and how many products they expect to deliver by the end of the timeline, why they are important, and how they can be used as a measure of success.
  • The budget document must be filled in in detail. Applicants should include itemized expenses instead of broad categories (i.e., instead of “support for participants”, they should try to describe which kind of support they are talking about – child care? transportation? translation? masks?).
  • Applicants must also include a description of regular activities, depending on the number of phases they include in the project (frequency of virtual and in-person meetings, visits, training, etc.).

The templates for the lean canvas and budget are available below:

Eligibility

Applicants must be currently registered in a study program in ecology, environmental science, evolution or a related discipline in a Canadian university and be a BIOS2 fellow. The other members of the group don’t need to fulfill these requirements, but only students can receive funds from BIOS2. Non-students in the group should be funded by other sources.

Selection process and deadlines

Applications must be submitted by November 8th, 2024. The selection committee will be composed of BIOS2 and QCBS staff members and alumni. Results are to be expected in the last two weeks of November, 2024.

Application packages should be submitted as one single zip file through this form: https://tally.so/r/31vypW

Dealing with spatial data in R – workshop

The first workshop of the 2024-2025 calendar will be about spatial data analysis, and registrations are now open! Perfect for researchers and data analysts with a foundational understanding of R, this workshop will cover Google Colab, reproducible workflows, biodiversity and spatial data sets available online, shapefile and raster operations, and Google Earth Engine (GEE) integration. You should have access to Google Suite applications like Google Drive and Google Colab via an email account to participate. The workshop instructors are Lionel Leston (University of Alberta) and Mobina Gholamhosseini (Université de Montréal).

Registration Details

Date: September 17th, 19th, 24th and 26th, 2024
Time: 10 am PT / 1 pm PT
Venue: Online (Zoom and Google Colab)
Registrations: https://us02web.zoom.us/meeting/register/tZUkdOmsqT4vGNTLsbPoZIezkRH2x6Vhc8zJ

Registrations are free and open to everyone, but seats are limited. If you have any questions, don’t hesitate to get in touch with us at pgm_bios2 [at] usherbrooke.ca.

Open Reviewers Workshop

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

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