inSileco

Environmental Management & Biodiversity Data Science

Solutions Support Training

Our Portfolio

Over the past four years, we have dedicated ourselves to training and assisting academics and government scientists. Drawing from our experience, we are equipped to assist you in managing your biodiversity data, improve your statistical analysis, optimize your R code, and assist you in creating interactive tools.

THE TIMING WINDOWS PROJECT - A RISK-BASED TOOL FOR PROTECTING FRESHWATER FISH DURING CRITICAL LIFE STAGES

March 27, 2025

Shiny App

Timing Windows Fish phenology Human interventions

The Timing Windows Project delivers a science-based, nationally scalable tool to inform the protection of freshwater fish species in Canada. Anchored by the National Timing Windows Database (NTWD) and an interactive Shiny web application—the Timing Windows Calculator—the project enables users to identify optimal timing windows to reduce ecological risks from water use activities (WUAs) such as dredging, dam operation, or shoreline construction. The tool integrates species-specific life stage data (spawning, migration, juvenile development) with environmental and phenological variables to assess risks across diverse regions and data availabilities. Through a structured five-step risk assessment framework, users can evaluate threats, explore timing windows, and generate recommendations. This flexible platform supports informed decision-making for environmental managers, regulators, and researchers seeking to align conservation measures with biological sensitivities.

University of Guelph & Fisheries and Oceans Canada

R PACKAGE FOR PREDICTING SUBMERGED AQUATIC VEGETATION IN THE GREAT LAKES

March 25, 2025

R package

Environmental science Modelling Spatial analysis

Fisheries and Oceans Canada (DFO) is developing decision-support tools to manage freshwater fish habitat. The Fish Ecology Science Lab created models to predict the presence and cover of submerged aquatic vegetation (SAV) in the Laurentian Great Lakes, using factors like fetch and depth. SAV is a key component of fish habitat and is often affected by in-water works or habitat restoration efforts. At inSileco, we developed an R package that implements DFO’s random forest model to make these predictions accessible, reproducible, and easy to integrate into existing workflows. The package was designed to support future development within DFO by standardizing inputs and outputs, facilitating integration with other tools, and ensuring that methods can be reused or extended as new needs arise.

Fisheries and Oceans Canada

SHINY APP FOR THE FISHERIES MANAGEMENT SUPPORT SYSTEM (FMSS)

March 20, 2025

Shiny App

Decision tools Modelling Fisheries Management strategies

The FMSS is a decision-support tool designed to explore the potential effects of management actions on fish populations, teach users key ecological principles, and help prescribe management solutions. In collaboration with the Ministry of Natural Resources and Forestry of Ontario, we at inSileco integrated the core model—an age- and size-structured population under fishing pressure—into a Shiny App. The app allows users to select biological parameters and fishing scenarios, and compare performance metrics across different management strategies.

Ministry of Natural Resources (Ontario)

WATERSHED PRIORIZATION

March 1, 2025

Reproducibility R package

Ecological analysis Spatial analysis Watershed prioritization Interactive mapping tool

This watershed prioritization project, led by a researcher at Fisheries and Oceans Canada (DFO), aims to identify priority watersheds across Canada for four freshwater fish conservation goals: area-based protection, habitat restoration, species at risk management, and invasive species management. Using national spatial data on fish diversity, stressors, and community change, priority areas were mapped based on expert-defined criteria. inSileco contributed by updating the analysis, developing an R package to ensure full reproducibility, and enhancing the existing Shiny app to allow users to generate custom maps that guide conservation efforts.

Fisheries and Oceans Canada (DFO)

MAPPING COMMERCIAL FISHING PRESSURE IN EASTERN CANADA FROM LOGBOOK DATA (2000–2020)

February 15, 2025

Cumulative effects assessment

Commercial fisheries

This project characterizes the intensity and distribution of commercial fishing in eastern Canada using 20 years of logbook data from Fisheries and Oceans Canada. Over 3 million fishing events were analyzed, encompassing 100 species and 57 gear types. Data were standardized, cleaned, and integrated into a suite of monthly, gear-specific raster layers representing fishing effort and landings across the region. By classifying gear types and linking species traits, we developed spatially explicit indicators of fishing pressure—including effort by gear, landings by target and bycatch species, and depth-specific activity. This high-resolution dataset reveals spatial and temporal trends in fishing pressure and supports cumulative impact assessments, fisheries management, and marine conservation planning.

Canadian Wildlife Service, Environment and Climate Change Canada

MAPPING ANTHROPOGENIC OIL SPILLS AND OFFSHORE INDUSTRIAL ACTIVITIES IN THE NORTHWEST ATLANTIC TO INFORM MARINE CONSERVATION AND MANAGEMENT

January 31, 2025

Cumulative effects assessment

Environmemntal stressors Marine birds

Human activities such as oil pollution, vessel traffic, and artificial light pose increasing threats to marine ecosystems. This project provides an integrated view of anthropogenic stressors in Atlantic Canadian waters through a high-resolution spatiotemporal dataset covering the Exclusive Economic Zone (EEZ) and adjacent areas. By combining open-access and proprietary data sources — including ISTOP, NASP, NEEC, AIS, and VIIRS satellite observations — we modeled risk layers representing petroleum pollution, offshore infrastructure, maritime traffic, and light exposure. These layers were developed using reproducible workflows and are distributed as cloud-optimized GeoTIFFs with detailed metadata. Our approach supports ecosystem-based ocean management by filling critical gaps in cumulative effects assessment and conservation planning, including for vulnerable species such as the Leach’s Storm-Petrel.

Canadian Wildlife Service, Environment and Climate Change Canada

CUMULATIVE EFFECTS OF GLOBAL CHANGES ON THE FOOD WEBS OF THE ST. LAWRENCE SYSTEM

January 24, 2025

Cumulative effects assessment

Cumulative effects Environmental drivers Food webs

Biodiversity extends beyond species, encompassing diverse interactions crucial for ecological dynamics and ecosystem functioning. Still, these interactions remain overwhelmingly overlooked in environmental management. Here, we assess the cumulative effects of 18 stressors on 193 species between 2010 and 2015 in the St. Lawrence marine ecosystem in eastern Canada. We use a novel approach that explicitly considers the less obvious yet no less significant effects arising from species interactions in a multiple stressors framework. We uncover overlooked threats, particularly for exploited or endangered fishes and marine mammals. This highlights potentially significant gaps in management and recovery strategies that generally overlook interactions. Our novel ecosystem-based approach fills this void by incorporating the less obvious yet no less significant effects arising from species interactions in a multiple stressors framework.

NUNATSIAVUT BIRD TRACKERS SHINY APP

January 16, 2025

Shiny App

Geocomputation Bird movement visualisation Data pipeline

As part of a multi-year initiative, the Nunatsiavut Government, in partnership with Environment and Climate Change Canada and SeaDuck Joint Venture, has been tracking marine birds to better understand their origin, key habitats, and the threats these birds face on their way to and from Labrador Inuit lands and waters. These projects have been developed in response to community concerns and priorities around wild food and bird populations. We developed an Shiny app to provide an intuitive user interface to visualize these data. Additionally, we created a data pipeline to ensure the app’s data remains up-to-date, enabling seamless tracking and management of bird observations.

Michelle Saunders, Nunatsiavut Government

SHINY APP FOR THE GOTEDNA PROJECT

September 30, 2024

Shiny App

Geocomputation Data visualization eDNA

We helped conceive and develop a Shiny app for the GOTeDNA project, which provides guidance on optimal eDNA sampling periods for effective monitoring programs. Our team worked closely with the GOTeDNA team to create an intuitive, user-friendly tool that enabled researchers to input environmental data, analyze sampling conditions, and receive recommendations for the best sampling times. By combining our technical expertise in Shiny app development with the scientific principles from GOTeDNA, we supported the optimization and interpretation of eDNA sampling strategies for biodiversity monitoring.

Anaïs Lacoursière, Fisheries and Oceans Canada

SUPPORT FOR THE DATA MANAGEMENT PLANS OF THE ARCTICNET RESEARCH PROGRAM

June 6, 2024

Research Data Management

Data management Data infrastructure

The ArcticNet research programm is a Canadian network of over 230 researchers studying the Arctic’s human health, natural sciences, and social sciences. We supported principal investigators with adopting best practices in terms of data management by reviewing their data management plan in light of the FAIR Principles.

ArcticNet, Université Laval

ASSESSING THE CUMULATIVE EFFECTS OF GLOBAL CHANGES ON HABITATS AND SPECIES OF THE SCOTIAN SHELF

March 31, 2024

Cumulative effects assessment

Cumulative effects Environmental drivers Food webs Habitats

Recently, two independent analyses performed for the Scotian Shelf sought to assess cumulative effects to species (Beauchesne et al. 2023) and habitats (Murphy and Kelly 2023). The goal of this project was to combine both assessment into an ecosystem-scale cumulative effects assessment that considers direct effects to habitats and species as well as indirect effects to species arising from species interactions and habitat use. It results in the assessment of the cumulative effects of 17 environmental stressors on 21 habitats and 205 species of the Scotian Shelf Bioregion.

Fisheries and Oceans Canada

DEVELOPING A CUMULATIVE EFFECTS TOOL FOR CETACEAN AT RISK ON THE SCOTIAN SHELF

March 31, 2024

Cumulative effects assessment

Cumulative effects Environmental drivers Food webs Marine mammals

The objective of this project was to update the assessment of cumulative effects on the food webs of the Scotian Shelf Bioregion with new data from the Department of Fisheries and Oceans on the distribution of beaked whale habitat and trophic relationships, and create a proof of concept interactive application to explore the assessment at the species scale. The expected outcomes of this project were to enhance our understanding of endangered beaked whale species and their ecosystem dynamics, ultimately leading to more effective management strategies and better-informed decision-making processes.

Fisheries and Oceans Canada

SUPPORT FOR THE MANAGEMENT OF ECOSYSTEM MONITORING DATA FROM BYLOT ISLAND

February 29, 2024

Research Data Management

Data management Data infrastructure

After 30 years of data collection on Bylot Island, researchers have generated more than 20 databases used for long-term ecosystem monitoring. Throughout this project, we analyzed the specific challenges linked to these databases and we proposed concrete solutions to improve data management practices.

Pierre Legagneux, Université Laval

ECOLOGICAL CLASSIFICATION SYSTEM FOR SOUTHERN QUEBEC

January 26, 2024

Repoductibilité

Géocomputation Classification supervisée Écologie forestière

The Ministry of Natural Resources and Forests (MRNF) conducted a comprehensive ecological survey of southern Quebec, involving more than 25,000 observation points, which was used to develop a hierarchical system for ecological classification. This system is based on vegetation classification using inventory data and allows for the definition of indicator species groups, forest types, and potential vegetation. The classification plays a major role in land management and is subject to ongoing evaluation, particularly due to climate change. We contributed to supporting part of the research on these classifications by making recent analyses fully reproducible through the creation of an R package.

Pierre Grondin, Ministère des Ressources naturelles et des Forêts

CUMULATIVE EFFECTS OF GLOBAL CHANGES ON THE FOOD WEBS OF THE SCOTIAN SHELF

March 31, 2023

Cumulative effects assessment

Cumulative effects Environmental drivers Food webs

Assessment of the cumulative effects of 17 environmental drivers (climate: 4; coastal: 6, fisheries: 5; marine traffic: 2) on 205 species (marine species: 172 marine; marine mammals: 8; sea birds: 25) of the Scotian Shelf Bioregion in eastern Canada.

Fisheries and Oceans Canada

CUMULATIVE EFFECTS OF MARINE ACTIVITIES IN THE ST. LAWRENCE AND SAGUENAY RIVERS

March 15, 2023

Cumulative effects assessment

Cumulative effects Environmental drivers Valued components

Assessment of the cumulative effects of 7 environmental stressors originating from marine vessel activities on the bank integrity, habitats, marine mammals and areas of cultural, heritage and archeological interest in the St. Lawrence and Saguenay rivers.

Transport Canada

BUILD SHINY APPLICATION

November 24, 2022

Workshop

R Shiny App

During this workshop we showed how to build Shiny web applications.

Canadian Wildlife Service, Environment and Climate Change Canada

SUPPORT FOR THE IMPLEMENTATION OF THE SCI 1031 COURSE FROM TÉLUQ

June 27, 2022

Teaching material

Geocomputation Git GitHub Deployment

We helped structure the GitHub repository and automate the deployment of the course SCI 1031 de la TÉLUQ. We also contributed to writing portions of two chapters of the course.

Élise Filotas, TÉLUQ

SHINY APP FOR SPATIAL REPRODUCIBLE REPORTING

March 1, 2022

Shiny Application

Geocomputation Reporting GitHub

We developped a Shiny Application to generate reproducible reports for species at risk. After the release of the second version of the application, we enhanced the capabilities of DFO staff by providing training to maintain and further develop the application. The application is now actively maintained and developed by DFO (see DFO repository).

Fisheries and Oceans Canada

TEAMWORK WITH GIT & GITHUB

February 18, 2022

Workshop

R Git GitHub Code management

During this workshop, we showed how to collaborate concretely and efficiently on projects with git and GitHub.

Bedford Institute of Oceanography, Fisheries and Oceans Canada

RASTERS WITH R

March 23, 2021

Workshop

R Geocomputation Visualisation

During this workshop, we showed, using concrete examples, how to manipulate and visualize spatial data with R.

Canadian Wildlife Service, Environment and Climate Change Canada

REPRODUCIBLE WORKFLOWS

March 1, 2021

Workshop

R R Markdown Reproducibility

During this workshop, we discussed issues related to reproducibility and we showed how to organize your work process with R.

Bedford Institute of Oceanography, Fisheries and Oceans Canada

INTERACTIVE RASTER VISUALIZATION WITH R

January 12, 2021

Workshop

R Geocomputation Visualization

During this workshop, we showed the power of R tools to efficiently manipulate and visualize raster files.

Bedford Institute of Oceanography, Fisheries and Oceans Canada

EDRIVERS

June 24, 2020

Shiny application

R Geocomputation Visualisation Environmental drivers St. Lawrence

eDrivers is an open knowledge platform focused on sharing knowledge on the distribution and intensity of environmental drivers such as shipping and commercial fisheries. This application provides a user interface to visualize the distribution and intensity of individual and combined drivers in the estuary and gulf of St. Lawrence.