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Complexity in Biological Systems E5: Unravelling Complexity in Coupled Earth, Environmental, Economic, Ecological and Evolutionary Systems

Advancing Biodiversity Informatics and Ecological Modelling

Environmental scientists urgently need a unified strategy for biodiversity data management as concerns over climate change, land use change, pollution, and natural resource exploitation rise and the global crisis for biodiversity conservation continues.The Mathematical Sciences Hub (BioMath) in the Mathematical Sciences Department at Stellenbosch University is exploring innovative new ways to synthesise and analyse vast amounts of ecological data to develop a more holistic understanding of our environment. This type of understanding is essential for park managers and scientists to design ways to halt, or ideally even reverse, biodiversity loss.Together with the NITheCS and South African National Parks (SANParks), BioMath is working towards a future where biodiversity data is more easily accessible by designing user-friendly tools, reproducible workflows and models to consolidate biodiversity data sources and predict future dynamics of biodiversity change.

Principal Investigator: Cang Hui (Stellenbosch University)

Research Programme Team Members and Collaborating Researchers

  • Emmanuel Dufourq (African Institute for Mathematical Sciences)
  • Cang Hui (Stellenbosch University)
  • Lorène Jeantet (African Institute for Mathematical Sciences)
  • Pietro Landi (Stellenbosch University)
  • Sandra MacFadyen (Stellenbosch University)
  • Vernon Visser (University of Cape Town)

Administrative Team Members

  • Hanlie Swart
  • Mathilda van der Vyver

Projects

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News

Ecology Hackathon

We will host a hackathon in late-October to develop workflows (and/or Wiki pages) relevant to important unanswered questions in ecology. Prizes, totalling R50 000.00 up for grabs. Watch this space!

Carbon sequestration in Savanna Ecosystems

Assess the role of Savanna ecosystems in global carbon accounting measures. Review the current state of knowledge in this field, and assess the practical implementation using study sites in Kenya and the Kruger National Park. The carbon credit market has grown exponentially in the past few years. Savannas represent the third largest global store of carbon after tropical and temperate forests. Due to the relative difficulty in estimating carbon stores in savanna systems, which are subject to much higher environmental variability, limited research has focussed here. Despite these challenges, we will explore the use of remote sensing of savanna carbon stores, an active field of research, using different machine learning, mechanistic and traditional parametric approaches.

An ecologist’s data pipeline toolkit

Develop a biodiversity data pipeline that is locally relevant and globally integrative. The pipeline aims to improve the management, presentation, discovery, exploration, integration, and analysis of biodiversity data. We aim to develop reproducible workflows that ecologists (non-data or computer scientists) can to use as a toolkit for local biodiversity data pipeline design and implementation. The programme will also focus on identifying challenges facing biodiversity informatics in South Africa, with an emphasis on developing solutions for national biodiversity monitoring bodies and protected area managers, like those in SANParks.

Behavioural analysis of the endangered African penguin

Discover novel insights into the behaviours of the Endangered African penguin (Spheniscus demersus). Not enough behavioural insights are known about this species with respect to different contexts. We will develop automated machine learning algorithms that can learn about penguin behaviours – from video and acoustic recordings – within a colony setting and within an individual or smaller group setting. Different contexts will be analysed such as penguins in captivity as opposed to in the wild, seasonality and how the presence of humans or other species impact their individual and social behaviours. Video and acoustic data will be collected at key sites such as Stony Point, Simon’s Town, Algoa Bay, St Croix (Port Elizabeth) and the Two Oceans Aquarium.

Biodiversity Informatics Symposium

The symposium brought together researchers, managers and practitioners from across South Africa and abroad, with expertise in a wide range of fields including conservation, ecology, information science, information technology, mathematics and statistics.

Publications

Ecology Hackathon

We will host a hackathon in late-October to develop workflows (and/or Wiki pages) relevant to important unanswered questions in ecology. Prizes, totalling R50 000.00 up for grabs. Watch this space!

Carbon sequestration in Savanna Ecosystems

Assess the role of Savanna ecosystems in global carbon accounting measures. Review the current state of knowledge in this field, and assess the practical implementation using study sites in Kenya and the Kruger National Park. The carbon credit market has grown exponentially in the past few years. Savannas represent the third largest global store of carbon after tropical and temperate forests. Due to the relative difficulty in estimating carbon stores in savanna systems, which are subject to much higher environmental variability, limited research has focussed here. Despite these challenges, we will explore the use of remote sensing of savanna carbon stores, an active field of research, using different machine learning, mechanistic and traditional parametric approaches.

An ecologist’s data pipeline toolkit

Develop a biodiversity data pipeline that is locally relevant and globally integrative. The pipeline aims to improve the management, presentation, discovery, exploration, integration, and analysis of biodiversity data. We aim to develop reproducible workflows that ecologists (non-data or computer scientists) can to use as a toolkit for local biodiversity data pipeline design and implementation. The programme will also focus on identifying challenges facing biodiversity informatics in South Africa, with an emphasis on developing solutions for national biodiversity monitoring bodies and protected area managers, like those in SANParks.

Behavioural analysis of the endangered African penguin

Discover novel insights into the behaviours of the Endangered African penguin (Spheniscus demersus). Not enough behavioural insights are known about this species with respect to different contexts. We will develop automated machine learning algorithms that can learn about penguin behaviours – from video and acoustic recordings – within a colony setting and within an individual or smaller group setting. Different contexts will be analysed such as penguins in captivity as opposed to in the wild, seasonality and how the presence of humans or other species impact their individual and social behaviours. Video and acoustic data will be collected at key sites such as Stony Point, Simon’s Town, Algoa Bay, St Croix (Port Elizabeth) and the Two Oceans Aquarium.

Biodiversity Informatics Symposium

The symposium brought together researchers, managers and practitioners from across South Africa and abroad, with expertise in a wide range of fields including conservation, ecology, information science, information technology, mathematics and statistics.

Focus Area