EcoCommons Notebooks

EcoCommons Notebooks represent an exciting expansion of the platform’s capabilities, offering a new layer of flexibility for advanced users. By incorporating notebooks, EcoCommons enhances its ability to serve the environmental data science community, enabling users to engage with cutting-edge methods, customize workflows, and increase reproducibility in their research. These notebooks, hosted on trusted cloud providers, provide a transparent, open-access approach to environmental data analysis while adhering to the FAIR principles. With planned monthly releases, EcoCommons Notebooks will empower users to explore complex topics such as species migration, community modeling, and data cleaning for biodiversity research.

🐢 Hello

EcoCommons is a national digital platform hosted by QCIF Ltd and supported by the Australian Research Data Commons, an NCRIS facility. The platform provides a range of services to support the Australian ecological research community, including access to data and ecological modelling tools.

This repository contains examples and tutorials with the objective of mirroring the functionalities offered in the EcoCommons platform.

🐨 Ecological Modelling (5 notebooks)

notebook	notebook file	open in Google colab / ARDC Jupyter Notebook Service	complementary materials	repository / paper
GLM
Extent and Area of Occurrence / Occupancy
Random Forest
Single-Species Single-Season Occupancy Model - Conceptual
Single-Species Single-Season Occupancy Model - Practical

🌍 Geo/ecological skills (13 notebooks)

notebook	notebook file	open in Google colab / ARDC Jupyter Notebook Service	complementary materials	repository / paper
Marxan Connect
Environmental Data Preparation (Raster)
Imbalanced dataset (Part 1)
Imbalanced dataset (Part 2)
Richness and Diversity
Get Species Data from Multiple Sources
Converting Rasters from ASCII (.asc) to GeoTIFF (.tif) Format
Converting Rasters from GeoTIFF (.tif) to ASCII (.asc) Format
Converting GeoTIFF (.tif) to Shapefile (.shp) Format
Converting Shapefile (.shp) to GeoTIFF (.tif) Format
Converting GeoTIFF (.tif) to NetCDF (.nc) Format
Converting NetCDF (.nc) to GeoTIFF (.tif) Format
Reclassify a Continuous Raster

🐛 Bugs and 🫡 Contribution

Welcome to the EcoCommons Notebooks! As ecological and environmental research advances, we strive to keep our resources up-to-date with the latest developments. If you encounter any issues with the notebooks, please submit a bug report so we can address them. We’re also open to new ideas—if there’s a tutorial or feature you’d like to see, create a feature request, or check out our contribution guide if you’d like to contribute directly. We’re here to support your research journey, so don’t hesitate to reach out.

Publications used EcoCommons Platform

Reddy, C. S., & Pranathi, G. (2026). In search of survival grounds—Habitat preference analysis and species distribution modelling of critically endangered Jerdon’s Courser, Rhinoptilus bitorquatus. Spatial Information Research, 34(2), 18.

Young, David A., Steve Harwin, and Jamie B. Kirkpatrick. “Regional-scale predictive model identifies restricted nesting habitat of the Grey Goshawk’Tachyspiza novaehollandiae’in Tasmania.” Australian Field Ornithology 42 (2025): 93-106.

Bayraktarov, E., Low-Choy, S., Singh, A. R., Beaumont, L. J., Williams, K. J., Baumgartner, J. B., … & Mackey, B. (2025). EcoCommons Australia virtual laboratories with cloud computing: Meeting diverse user needs for ecological modeling and decision-making. Environmental Modelling & Software, 183, 106255.

Humaida, N., Wahab, L., Saputra, M. H., Kurniawati, F., Atmaja, M. B., Pujiono, E., … & Wahyuningtyas, R. S. (2025). Species Distribution Model and Conservation of Mentaok (Wrightia javanica) in Indonesia. Jurnal Manajemen Hutan Tropika, 31(1), 1-11.

Newton, Peter, et al. “Digital Innovations for City Sustainability Analysis and Decision-Making.” Future Cities Making: Mission-oriented Research for Urban Sustainability Transitions in Australia. Singapore: Springer Nature Singapore, 2024. 215-240.

Norman, Patrick, and Brendan Mackey. “A decision support tool for habitat connectivity in Australia.” Pacific Conservation Biology 30, no. 5 (2024).

Isaza-Toro, Estefania, John Josephraj-Selvaraj, and Alan Giraldo. “Geographical distribution model of the fish Coryphaena hippurus (Perciformes: Coryphaenidae) according to climate change in the Pacific Oriental Tropical.” Revista de Biología Tropical 72, no. 1 (2024).

Torkkola, Janne, Harry Hines, Alienor Chauvenet, and Paul Oliver. “Are species richness and endemism hotspots correlated within a biome? A test case in the fire-impacted subtropical rainforests of Australia.” (2024).

Saputra, M. H., Humaida, N., & Hadiyan, Y. (2023). Smart farming: modeling distribution of Xanthomonas campestris pv. oryzae as a leaf blight-causing bacteria in rice plants. In IOP Conference Series: Earth and Environmental Science (Vol. 1133, No. 1, p. 012026). IOP Publishing.

Saputra, M. H., & Humaida, N. (2023, June). Potential future distribution of Scirpophaga incertulas (Walker) in Indonesia. In IOP Conference Series: Earth and Environmental Science (Vol. 1182, No. 1, p. 012007). IOP Publishing.

Levett, Kerry, Jonathan Smillie, and Andrew Treloar. “Putting the R into PlatfoRms.” International Journal of Digital Curation 17, no. 1 (2023): 12-12.