0 comments on “Calcul Québec Spring School in High Performance Computing – French”

Calcul Québec Spring School in High Performance Computing – French

Registrations are now open for the Calcul Québec Spring School in High Performance Computing!

May 11-15, 2020 at Orford Musique
All levels
Please note that classes are mostly given in French.

The Calcul Québec Spring School in high-performance computing (HPC) allows graduate students, post-docs, researchers and professionals to learn how to make effective use of high-performance computing resources while at the same time benefiting from privileged access to Calcul Québec analysts for an entire week.

Two distinct streams for the workshops, designed to meet the needs of the greatest number of individuals, are proposed:

  • Data analysis and visualization with Python (beginner)
  • Parallel programming (advanced)

For more information, visit Calcul Quebec website

Early Bird rates end March 31. Register now!

0 comments on “Working Group in Biodiversity Synthesis: Graduate Student Call”

Working Group in Biodiversity Synthesis: Graduate Student Call

CIEE and BIOS² are co-sponsoring a data-driven working group in biodiversity synthesis. We invite graduate students from CIEE Member Universities and BIOS² Universities to submit an application for a one week working group at UBC May 4-8, 2020.

The objective of this activity is to provide graduate students the opportunity to get experience in team projects oriented toward biodiversity synthesis and data analysis. Providing students a stimulating training environment is central to the activity. Working groups consist of a small group of researchers who meet in person in a single location, and work intensively and collaboratively on a research question, using best practices in team science and digital collaboration.

Synthesizing fifty years of ecological change in the southern Gulf of St. Lawrence

 The abundance and composition of marine animals in the southern Gulf of St. Lawrence changed dramatically in the last 50 years, with the near extinction of large ground fish species like Atlantic Cod, and a rapid increase of invertebrates such as Lobster and Snow Crab. This working group will analyse change in population size and distribution of marine taxa, drawing on a unique long-term database based on yearly bottom-trawl surveys conducted by Fisheries and Oceans Canada since 1971. The working group will be composed of ten graduate students selected from across Canada, and led by Dr. Nicolas Rolland (Fisheries and Oceans Canada) and Dr. Guillaume Blanchet (Université de Sherbrooke). On the first day, Rolland and Blanchet will present the structure of the dataset, explain how to manipulate spatiotemporal data and provide the training you will need on cutting-edge methods in statistical modelling. Following, the CIEE will provide training on the working group method. During the other days, the group will work collaboratively on analysing change in different taxa (fish, invertebrates) in relation to time and potential drivers (e.g. climate, fishing, natural mortality), and co-write a paper summarizing these results for publication in a peer-reviewed journal. By interacting with a Fisheries and Ocean Canada scientist and understanding the data that is gathered by this federal institution, participants will gain insight into the type of research being carried out in this government department. By developing an understanding of past drivers and trajectories of change, this project will help Fisheries and Oceans Canada predict the future of this important marine ecosystem and guide management measures that support sustainable development in a changing environment. 

Application process :  

For information about the application and selection process, visit the CIEE Funding Page:
Or refer to the PDF here.

Participation in the working group, including transportation, is fully funded by CIEE and BIOS².

Applications due: March 6, 2020

0 comments on “The time I talked about data bias at the BES annual meeting – Gracielle Higino”

The time I talked about data bias at the BES annual meeting – Gracielle Higino

For someone who started the year of 2019 not quite believing in my own research, being in an international conference in December showcasing my latest results and making people intrigued by what I’ve found was a huge leap.

Minutes before I accidentally glued my hand inside my pocket. Because if a dress has pockets, you gotta use them.

From December 10th-13th I was in the BES Annual Meeting in Belfast, Northern Ireland, and the first morning was a landmark in my career. It was the first time I was in an international conference, and the first time I had the chance to make an oral presentation about my research. Giving that the days before the meeting I was extremely stressed about not having the results I wanted, the first thing I learned was that, in science, every bit of result counts.

In my presentation, I talked about how the digital knowledge on the biodiversity of terrestrial vertebrates in the Atlantic Rainforest is hugely biased and incomplete, even with the recent (Herculean) efforts to gather information in data papers. I investigated three kinds of biases, and I’ll try to summarize them here.

Taxonomic bias

Do you think we know more about birds than mammals? Or do we know more about reptiles? Or maybe our knowledge about these groups are correlated?

Well, I found that we know way more about birds and mammals than we do about reptiles and amphibians. More than that, the places where we know more about birds, we also know more about mammals, and the same happens to reptiles and amphibians. This may be an outcome of how science is organized: herpetologists are scientists that study these last two groups, so probably the way they do research is highly correlated. On the other hand, mammals and birds are majorly endothermic groups with similar biographical stories, so maybe mastozoologists and ornithologists tend to revisit regions with similar environmental characteristics.

Geographic bias

It is intuitive to think that we know more about the biodiversity of easily accessible places or of those near research centres. This is true for plants in Brazil, where we know a lot more about them near the roads, and it’s also true for our vertebrates. The majority of unique data comes from the southeast of Brazil, where most traditional research centres, museums and funding are.

Environmental bias

Although social variables can explain the geographic bias of our data, I wondered if environmental factors (such as temperature, biomass availability and topography) could also guide the research agenda of our scientists.

The answer is: it depends. For example, in the northeast and central regions of Brazil, the temperature is a good predictor to how much we know about reptiles. On the other hand, vegetation availability is more important for our knowledge about mammals in the north and southwestern regions of the Atlantic Rainforest.

After the talk

After the storm of excitement that preceded my talk, I could appreciate a good amount of amazing talks from other scientists. Ironically, the one right after mine was about how biases don’t matter that much, but sampling efforts do, when it comes to species distribution model performance (at least for birds in Ireland). This was amazing, because Willson and I got to talk about our ideas, how we plan to test them, and why our views are somewhat different about the same topic. This is the magic of conferences!

I also got to watch Mathilde’s talk about how species with less and negative interactions are more persistent in an evolutionary timescale, William’s poster about the effects of climate and interactions in predicting species range limits, and Oliver’s talk about how pollen can help us understand the past, present and future of Araucaria in Brazil. We also had the chance to brainstorm about inclusiveness in science, outreach and education initiatives, and to challenge our creativity to represent Macroecology with plastic clay.

Winning the challenge of representing Macroecology with plastic clay. Don’t ask.

After MozFest (read about it here and here), it was really difficult for me to be interested in conventional academic conferences, but BES Annual Meeting was a great surprise. Their concern about inclusion, diversity, minimal environmental impact, the design to promote connection and the friendly crowd of attendees exceeded my expectations. I am truly grateful to the PoisotLabBIOS² and QCBS for making that experience possible: thank you!

Read the original blog here.

Atlantic Rainforest Photo Credit: VJ pixel

0 comments on “Training session: Mathematical Modeling in Ecology and Evolution”

Training session: Mathematical Modeling in Ecology and Evolution

BIOS2 presents a training session about:

Mathematical Modeling in Ecology and Evolution with Mathematica and Maxima.

This online training will be led by Dr. Sarah P. Otto (UBC) and held in two parts : January 14 and January 16, 2020, from 10 to 12:30 PST / 1 to 3:30 EST.

This workshop will introduce participants to the logic behind modeling in biology, focusing on developing equations, finding equilibria, analyzing stability , and running simulations.  Techniques will be illustrated with the software tools, Mathematica and Maxima.

The workshop will be led by BIOS² co-PI Sally Otto, a professor in the department of Zoology at University of British Columbia with strong expertise on quantitative analysis and mathematical modeling for biologists.

To register to this training, please fill this form by January 7, 2020:

0 comments on “Call for proposals : BIOS² – CIEE synthesis group”

Call for proposals : BIOS² – CIEE synthesis group

Applications due: January 8, 2020.

We invite experienced biodiversity researchers from both academic (universities) and non-academic organizations (e.g. government departments, non-profit organizations, Indigenous organizations, community groups, industry) to submit proposals for a one week working group focused on a question in biodiversity science.

Working groups would consist of a small group of researchers who meet in person in a single location, and work intensively and collaboratively on a research question, using best practices in team science and digital collaboration. We will provide funding for a working group consisting of 10 graduate students and one or two experienced biodiversity researchers to be held May 4-8, 2020 at the University of British Columbia.

The 10 graduate students will be chosen through a separate national competition co-led by the BIOS² – CREATE program and the Canadian Institute for Ecology and Evolution (CIEE), and will have skills in data synthesis and analyses relevant to biodiversity science.

The one or two experienced biodiversity researcher(s) submitting the proposal are expected to coordinate the scientific aspects of the working group. In addition, a member of the CIEE will mentor all participants in working group organization and dynamics before and during the meeting.  Travel, accommodation and meal costs will be covered for all participants.

For more information, please refer to the instruction file.

See the call in the CIEE – ICEE Website.

0 comments on “Training session : Intellectual property and open science”

Training session : Intellectual property and open science

BIOS2 presents a training session about:

Intellectual property issues in the context of open and collaborative science

To be held on December 13, 2019, from 1 to 4 PM (local time) at UQAM, Montreal, Room SH-2540 (Sherbrooke Hall).

The training session will be led by Eve-Lyne Comtois-Dinel, a research scientist and PhD candidate in sociology at UQAM, affiliated with TÉLUQ. Eve-Lyne is also research professional at CIRANO.

She is interested in the societal impacts of contemporary technological advances and the role of open science and open data in the knowledge-based society. She is currently working on a thesis on numerical Governance, within the more general framework of the sociology of quantification.

Eve-Lyne completed an internship at the OECD in summer 2018 at the Global Science Forum, Science, Technology and Innovation Division, on public engagement in open science. She holds an LL. M. Master in law from the Université de Montréal. 

It will be possible to attend the training session in person or online. 

Free of charge, registration required :

For more information :