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

notebook	notebook file	open in Google colab / ARDC Jupyter Notebook Service	complementary materials	DOI
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

notebook	notebook file	open in Google colab / ARDC Jupyter Notebook Service	complementary materials	DOI
Marxan Connect		N/A
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

EcoCommons used for modelling

Chintala, Sudhakar Reddy & Malik, Kritika & Shaik, Vazeed & Sundaram, Reeja. (2026). Identifying Potential Invasion Hotspots of Chromolaena odorata using Species Distribution Models. https://www.researchgate.net/publication/402883088_Identifying_Potential_Invasion_Hotspots_of_Chromolaena_odorata_using_Species_Distribution_Models

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. https://doi.org/10.1007/s41324-026-00669-w

Sukmawati, J. G., Helmanto, H., Kurniawan, H., Prasetyo, E., & Humaida, N. (2025, December). Species Distribution Modeling Reveals Autecological Determinants of Vachellia nilotica in Java and the Lesser Sunda Islands. In International Conference on Sustainable Energy: Toward Energy Transition and Net-Zero Emission (ICOSE 2025) (pp. 165-180). Atlantis Press. https://www.atlantis-press.com/proceedings/icose-25/126019687

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. https://doi.org/10.20938/afo42093106

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. https://doi.org/10.1016/j.envsoft.2024.106255

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. https://doi.org/10.7226/jtfm.31.1.1

Norman, Patrick, and Brendan Mackey. “A decision support tool for habitat connectivity in Australia.” Pacific Conservation Biology 30, no. 5 (2024). https://doi.org/10.1071/pc24008

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). https://doi.org/10.15517/rev.biol.trop..v72i1.42716

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). https://doi.org/10.21203/rs.3.rs-4249551/v1

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. https://doi.org/10.1088/1755-1315/1133/1/012026

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. https://doi.org/10.1088/1755-1315/1182/1/012007

EcoCommons used for data

Brunton, E. A., Brunton, A. J., & Conroy, G. (2025). From safe to stranded: Land use and climate change threaten habitat of iconic Australian macropods. Ecology and Evolution, 15(10), e72236. https://pmc.ncbi.nlm.nih.gov/articles/PMC12508624/

EcoCommons mentioned

Rodas Toral, Ricardo Adolfo. Análisis de susceptibilidad a deslizamientos aplicado a grupos socioeconómicos vulnerables, mediante Máxima entropía (MaxEnt), en las parroquias: Cuenca, Nulti, Paccha, El Valle y Turi, del cantón Cuenca. Quito, 2025, 98 p. Tesis (Maestría en Gestión del Riesgo de Desastres). Universidad Andina Simón Bolívar, Sede Ecuador. Área de Gestión. http://hdl.handle.net/10644/10573

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. https://doi.org/10.1007/978-981-97-7671-9_10

Levett, Kerry, Jonathan Smillie, and Andrew Treloar. “Putting the R into PlatfoRms.” International Journal of Digital Curation 17, no. 1 (2023): 12-12. https://doi.org/10.2218/ijdc.v17i1.843

Blair, G. S., Bassett, R., Bastin, L., Beevers, L., Borrajo, M. I., Brown, M., … & Watkins, J. (2021). The role of digital technologies in responding to the grand challenges of the natural environment: the Windermere Accord. Patterns, 2(1). https://doi.org/10.1016/j.patter.2020.100156

Publications used BCCVL

BCCVL used for modelling

Iryadi, R., Saputra, M. H., SukmawatI, J. G., Hani, A., Swari, K. K. I., Sari, D. A. I., … & van Etten, E. (2024). Assessing Habitat Suitability for the Invasive Species Lantana camara on Bali Island: A Model Using the Biodiversity and Climate Change Virtual Laboratory (BCCVL). Journal of Tropical Forest Management/Jurnal Manajemen Hutan Tropika, 30(3).
https://doi.org/10.7226/jtfm.30.3.305

W. Hallgren, F. Santana, S. Low-Choy, Y. Zhao, B. Mackey (2019). Species distribution models can be highly sensitive to algorithm configuration, Ecological Modelling,408. doi.org/10.1016/j.ecolmodel.2019.108719.

Taylor, C. M., Keppel, G., Peters, S., Hopkins, G. R., & Kerr, G. D. (2018). Establishment and potential spread of the introduced spotted-thighed frog, Litoria cyclorhyncha (Ranoidea cyclorhynchus), in South Australia. Transactions of the Royal Society of South Australia, 142(1), 86-101. doi:10.1080/03721426.2018.1444911

Sumoto. S. & van Etten, E. (2017). Species distribution model of invasive alien species Acacia nilotica for Central-Eastern Indonesia using Biodiversity Climate Change Virtual Laboratory (BCCVL). https://smujo.id/td/article/view/1644

Mackey, B., Cadman, S., Rogers, N., & Hugh, S. (2017). Assessing the risk to the conservation status of temperate rainforest from exposure to mining, commercial logging, and climate change: a Tasmanian case study. Biological Conservation, 215, 19-29. https://www.sciencedirect.com/science/article/pii/S0006320717305773?via%3Dihub

Low-Choy, S., & Huijbers, C. (2017). Experimenting with Modelling via a Virtual Laboratory: Evaluating pseudo-absence strategies to refine a species distribution model. Paper presented at the 22nd International Congress on Modelling and Simulation, Hobart, Tasmania. https://www.mssanz.org.au/modsim2017/G8/lowchoy.pdf

Hallgren, W., Santana, F., Low-Choy, S., Rehn, J., & Mackey, B. (2017). Sensitivity Analysis to Configuration Option Settings in a Selection of Species Distribution Modelling Algorithms. Paper presented at the 22nd International Congress on Modelling and Simulation, Hobart, Tasmania. https://www.mssanz.org.au/modsim2017/A1/hallgren.pdf

Santana, F., Hallgren, W., Rehn, J., Chiu, L., & Holewa, H. (2017). Implementing best practices and a workflow for modelling the geospatial distribution of migratory species. Paper presented at the 22nd International Congress on Modelling and Simulation, Hobart, Tasmania. https://www.mssanz.org.au/modsim2017/C3/santana.pdf

Hallgren, W., Beaumont, L., Bowness, A., Chambers, L., Graham, E., Holewa, H., . . . Price, J. (2016). The biodiversity and climate change virtual laboratory: where ecology meets big data. Environmental Modelling & Software, 76, 182-186. https://www.sciencedirect.com/science/article/pii/S1364815215300839?via%3Dihub

BCCVL mentioned

Booth, T. H. (2018a). Species distribution modelling tools and databases to assist managing forests under climate change. Forest Ecology and Management, 430, 196-203. https://www.sciencedirect.com/science/article/pii/S0378112718310879#

Booth, T. H. (2018b). Why understanding the pioneering and continuing contributions of BIOCLIM to species distribution modelling is important. Austral Ecology. https://onlinelibrary.wiley.com/doi/abs/10.1111/aec.12628

Langenheim, N., White, M., Barton, J., & Eagleson, S. (2017). Designing with Data for Urban Resilience. In S. Geertman, A. Allan, C. Pettit, & J. Stillwell (Eds.), Planning Support Science for Smarter Urban Futures (pp. 113-133). Cham: Springer International Publishing. https://link.springer.com/chapter/10.1007%2F978-3-319-57819-4_7

Palmer, R., Dharmawardena, K., & Holewa, H. (2017). Adapting Enterprise Architecture for eScience. Paper presented at the e-Science (e-Science), 2017 IEEE 13th International Conference. https://ieeexplore.ieee.org/abstract/document/8109160/

Ramalho, C. E., Byrne, M., & Yates, C. J. (2017). A Climate-Oriented Approach to Support Decision-Making for Seed Provenance in Ecological Restoration. Frontiers in Ecology and Evolution, 5(95). doi:10.3389/fevo.2017.00095 https://www.frontiersin.org/articles/10.3389/fevo.2017.00095/full

Santana, F., Pariente, C. A. B., & Saraiva, A. M. (2017). Species Distribution Modeling with Scalability: The Case Study of P-GARP, a Parallel Genetic Algorithm for Rule-Set Production. Paper presented at the Information Reuse and Integration (IRI), 2017 IEEE International Conference. https://ieeexplore.ieee.org/abstract/document/8102933/

Wolski, M., Howard, L., & Richardson, J. (2017). The importance of tools in the data lifecycle. Digital Library Perspectives, 33(3), 235-252. doi:doi:10.1108/DLP-11-2016-0042 https://www.emeraldinsight.com/doi/full/10.1108/DLP-11-2016-0042

Booth, T. H. (2017). Assessing species climatic requirements beyond the realized niche: some lessons mainly from tree species distribution modelling. Climatic Change, 145(3), 259-271. doi:10.1007/s10584-017-2107-9 https://link.springer.com/article/10.1007/s10584-017-2107-9

Belbin, L., & Williams, K. J. (2016). Towards a national bio-environmental data facility: experiences from the Atlas of Living Australia. International Journal of Geographical Information Science, 30(1), 108-125. doi:10.1080/13658816.2015.1077962 https://www.tandfonline.com/doi/full/10.1080/13658816.2015.1077962?scroll=top&needAccess=true

La Salle, J., Williams, K. J., & Moritz, C. (2016). Biodiversity analysis in the digital era. Philosophical Transactions of the Royal Society B: Biological Sciences, 371(1702). doi:10.1098/rstb.2015.0337 http://rstb.royalsocietypublishing.org/content/371/1702/20150337