AIMS Biodiversity Summer School: 10 – 21 May, 2021
BIODIVERSITY INFORMATICS: Creating, Accessing and Analyzing biodiversity data
Course aim
To build the next generation of interdisciplinary professionals in biodiversity informatics, with the ability to make an informed decision to pursue a career path in biodiversity or bio-mathematics research.
Course Outcomes
- Awareness of key mathematical concepts applied to analysis of biodiversity data.
- Understanding of key ecological concepts such as competition, mutualism, stability.
- Awareness and understanding of different kinds of biodiversity data (as classified in the Essential Biodiversity Variables concept).
- Knowledge of availability of data on Essential Biodiversity Variables (EBVs) from freely available and restricted databases
- Ability to synthesize data to create a biodiversity database.
- Ability to apply R programming skills to process and analyse biodiversity data, in particular ecological network analyses and species distribution modelling.
Scope
The United Nation’s Sustainable Development Goal #15 calls for the ‘Protection, restoration and promotion of a sustainable terrestrial ecosystem, sustainable management of forests, to combat desertification, a halt and reversal of land degradation and a halt of biodiversity loss by the year 2030 (https://sdgs.un.org/). Over 31 000 species are currently at risk of extinction, and this is occurring at an even faster rate that before.
Anthropogenic activities and climate change are major threats to our ecosystem. Climate for instance is promoting biome shifts for many plants and animal species. At the same time, the climate is exacerbating antagonistic plant interactions which are caused by pathogens and pests. Along with anthropogenic activites, climate is also influencing mutalistic plant interactions such as plant-insect pollination which is important to over 70% of known plant species. Most of these plants produce the food which we consume.
The successful attainment of the SDG #15 would trigger the success of several other SDGs such as zero hunger (goal #2), clean water and sanitation (goal #6), climate action (goal # 13) among others. This is so because our ecosystem (agro, forest, grassland or aquatic) provides essential services which mankind benefits from. These services include (i) supporting services, e.g. nutrient recycling, primary production and soil formation; (ii) provisioning services e.g. food, crops, raw materials, organic matter, fodder, fertilizer, genetic resources, water, biogenic minerals, medicinal resources, energy; (iii) regulating services e.g. pollination, carbon sequestration, climate regulation, waste decomposition, detoxification, water purification, air purification, pest and disease control; and (iv) cultural services e.g. therapeutic, spiritual, recreational, educational, science (MA, 2005).
The importance to fully understand, monitor and regulate ecosystems can therefore not be overstated. This requires a constant and comprehensive documentation of components in the system, how sub-units interact internally and with the whole, the changes occurring over time and space, drivers that alter their structure, how their distribution is affected and how this evidence could be used for decision making. The advent of computing is now playing a critical role to provide deep insights in the field of biodiversity in a cost- and time-effective manner. This creates a transdisciplinary space where biologists, mathematicians, computer scientists, policy makers, industy and the community can collaborate to generate research-driven solutions to conserve and sustain our ecosystems. Building a critical mass of such interdisciplinary professionals is paramount.




Application deadline:
5th May 2021
Final Selection:
7th May 2021
Pre-school activities:
8th – 9th May, 2021
Delivery dates:
10th to 21st May, 2021
Participants can expect to spend up to 4-6 hours per day for the two week duration of the school
Delivery format:
Virtual
Programming environment:
R
Google Earth Engine (GEE)




This summer school will be beneficial to postgraduate students, researchers and professionals from around the world who are interested in the interface between biodiversity and modelling (biodiversity informatics) for decision making.
Applicants should have a background in one or more of the following disciplines: biodiversity and conservation, mathematics, bio-mathematics, ecology, ecological modelling, or their related disciplines.
Kindly use this link to submit your application on or before the 5th May, 2021
Only selected applicants will be contacted.




Main topics to be covered:
- Quantifying biodiversity
- Bio-demography
- Geographical Information Systems (GIS) for biodiversity
- Ecological networks
Lectures will be paired with practical exercises in data handling, analysis, and visualisation to cover the majority of Essential Biodiversity Variables (EVB) classes https://geobon.org/ebvs/what-are-ebvs/).
Several seminar-style presentations will be included in which researchers will highlight their research in the field of biodiversity and mathematical ecology.
Students will also be able to work on practicals in their own time if they desire; four practicals are allocated as ‘catch-up sessions’ to provide additional assistance to students.
Practicals will progressively develop skills in R-programming over the two-week period and provide hands-on training in ecological networks and species distribution modelling.
Theory lectures will be approximately 45 minutes long and practicals will be 1-2 hours long.
Participants can expect to spend up to 4-6 hours per day. Recordings of lectures will be made available only to participants.
We anticipate:
- 14 conceptual lectures (± 45 minutes)
- 6 research seminars (±30 minutes talk and 15 minutes questions)
- 16 hands on practical sessions (1-2 hours) that will progressively develop skills in R programming and Google Earth Engine Skills for biodiversity informatics.
Schedule: Download the schedule here
All times are in Central European Time (CET) = GMT+2
Day | Activity | Title | Details | R packages | Datasets and Databases | EBV classes | EBVs | Lecturers |
---|---|---|---|---|---|---|---|---|
Day 0: 08 – 09 May, 2021 | ||||||||
14:00 – 16:00 | Installing software | Getting started in R with Rstudio and the Google Earth Engine interface. |
Students to be given instructions, help to be made available during specific hours. Troubleshooting to make sure everyone has managed to download R, Rstudio, and install packages. Importantly students must set up a GEE account a few days before the course starts, as there is often a lag in the account approval system |
R base, dplyr ggplot2 | Barro Colorado 50ha veg plotPanama Veg plots | Community Composition | Species Richness (Taxonomic/Phylogenetic diversity) | Volunteers |
Day 1: Mon. 10 May | ||||||||
9:00 – 09:15 | Opening | Introduction | Dr Rosita Yocgo and Dr James Rodger | |||||
09:15 – 10:15 | Lecture 1. | Ecology and EBVs | Concept of Essential Variables in general and EBVs in particular. EBV classes and (proposed) EBVs. Link to global change. | NA | NA | All classes | Dr Venuste Nsengiman | |
10:30 – 12:30 | Lecture 2. | Quantifying biodiversity. | Species diversity (alpha, beta, gamma diversity) how it is measured, how to how to quantify diversity at different scales. | NA | NA | Community Composition | Species Richness (Taxonomic/Phylogenetic diversity) | Dr James Rodger |
Break |
Break |
Break |
Break |
Break |
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13:30 – 14:30 | Prac. 1. | Processing data with dplyr (and using it to calculate diversity) | Grouping data and using the five main functions of dplyr | R base, dplyr ggplot2R base, dplyr ggplot2 |
Barro Colorado 50ha veg plot Panama Veg plots |
Community Composition | Species Richness (Taxonomic/Phylogenetic diversity) | Dr James Rodger |
14:45 – 16:45 | Prac. 2 | Data visualisation in R with ggplot2 | Create scatterplots in R with ggplot2 package and base graphics. | R base, dplyr ggplot2 | Barro Colorado 50ha veg plotPanama Veg plots. | Community Composition | Trait diversity | Dr James Rodger |
Day 2: Tue. 11 May | ||||||||
09:15 – 10:15 | Lecture 3 | Zeta-diversity: quantifying biodiversity across scales. | Introduction to use of zeta diversity to quantify diversity across multiple scales. | NA | NA | Community Composition |
Species Richness (Taxonomic/ Phylogenetic diversity) |
Dr James Rodger |
10:30 – 12:30 | Prac. 3 | Calculating diversity with vegan and zetadiv |
Tidying data and using the vegan package to calculate Alpha, Beta, Gamma, diversity. Use Zeta package to investigate Zeta diversity. |
tidyr, vegan, zetadiv |
Barro Colorado 50ha veg plot, Panama Veg plots. |
Community Composition | Dr James Rodger | |
Break | Break | Break | Break | Break | ||||
13:30 – 14:30 | Lecture 4.. | Seminar: modelling the creation of diversity through adaptive dynamics | How adaptation can lead to diversity. The mathematical framework for describing this. | NA | NA | Community Composition | Species Richness and Trait Diversity | Mr. A. Suleiman |
14:45 – 16:45 | Prac. 4. | Merging datasets, importing data and exporting data and graphs. | Synthesise data with the merge function in R. Apply meta-analysis to a synthesised dataset. | R base, dplyr, tidyr,ggplot2 |
Barro Colorado 50ha veg plot Panama Veg plots. Traits dataset from Clark et al J. Ecology. |
Multiple | Multiple | Dr James Rodger |
Day 3: Wed. 12 May | ||||||||
09:15 – 10:15 | Lecture 5. | Seminar: Simulating long-term population dynamics with the logistic model | Stochastic and deterministic population growth. | NA | NA | Species Population | Species Abundance | Ms Asmaa Tbaeen |
10:30 – 12:30 | Prac. 5. | Catch-up days 1-2. | Lecturers and tutors available to assist with any problems in analysis for the first two days |
Community Composition |
Dr James Rodger | |||
Break | Break | Break | Break | Break | ||||
13:30 – 16:30 | Session 6: Open Session | Contents of this session will depend on participant requests. Dr James Rodger and the volunteers will be available to assist anyone who has queries regarding analysis of their own data. We can also discuss topics raised by participants. | NA | NA | Dr James Rodger | |||
Day 4: Thu. 13 May | ||||||||
09:15 – 10:15 | Lecture 7. | Seminar: nestedness and interaction switching in mutualistic networks | Seminar on Phd project. | NA | NA | Community Composition | Interaction Diversity | Dr Assumpta Nnakenyi |
10:30 – 12:30 | Prac. 7. | Population monitoring and time series. | Analyse temporal trends in populations. Identify declining versus increasing species and responses to environmental events (e.g. hurricane, drought). | TBC | Barro Colorado 50ha veg plot Panama Veg plots. | Species Populations | Species Abundance | Dr James Rodger |
Break | Break | Break | Break | Break | ||||
13:30 – 14:30 | Lecture 8. | Population Structure and Matrix Projection Models-Asymptotic Dynamics | Introduction to matrix Projection models. | NA | NA | Species Populations | SSpecies Abundance | Dr James Rodge |
14:45 – 16:45 | Prac 8. | Population Structure and Matrix Projection Models-Asymptotic Dynamics | Calculate deterministic and stochastic long-term population growth rate, perform population viability analysis. | Popbio, popdemo | Compadre, Comadre | Species Populations | Species Abundance | Dr James Rodge |
Day 5: Fri. 14 May | ||||||||
09:15 – 10:15 | Prac. 9. | Key Biodiversity datasets, Ethics and etiquette of data use | An An introduction to some key biodiversity databases including occurrences, abundance, taxonomy and traits. | NA | NA | Community Composition | Trait diversity | Dr James Rodger |
10:30 – 12:30 | Lecture 9. | Contributing to biodiversity databases | Learn how to contribute to the inaturalist database | NA | NA | Community Composition | Species Richness | Dr James Rodger |
Break | Break | Break | Break | Break | ||||
13:30 – 14:30 | Lecture 10. | Species Distributions and Niches | Understand how abiotic factors, biotic interactions, and dispersal limit species distributions. | NA | NA | Species Populations | Species Distribution | Ms Ashleigh Basel |
14:45 – 16:45 | Prac. 10. | Species Distributions and Niches | Map distributions using GBIF data. | dismo maptools rgdal raster sp | gbif | Species Populations | Species Distribution | Ms Ashleigh Basel |
Day 6: Mon. 17 May | ||||||||
09:15 – 10:15 | Lecture 11. | Seminar: Stability and complexity in ecosystems | Mathematical predictions for stability and complexity. | NA | NA | Community Composition | Species Richness (Taxonomic/ Phylogenetic diversity) | Mr Mmmatlou Kubyana |
10:30 – 12:30 | Prac. 11. | Joining data in dplyr | Combining datasets | dplyr | Community Composition | Dr James Rodger | ||
Break | Break | Break | Break | Break | ||||
13:30 – 14:30 | Lecture 12. | Species Distribution | Theory of SDMs and ENMs. Distinguish between different modelling approaches (e.g. machinelearning, statistical (glm, gam), maxent) Utility and limitations of using predicted climate data for predicting future and past distributions, potential distributions of invasive species. | NA | NA | Species Populations | Species Distribution | Dr Sandra MacFadyen |
14:45 – 16:45 | Prac. 12. | Modelling species distribution with QGIS, GEE and R | Use SDMS for finding new populations (E.G. Miombo). Compare the performance of different models Use SDMs and ENMS for mapping future and past distributions, potential distributions of invasive species. | dismo maptools rgdal raster sp | gbif | Species Populations | Species Distribution | Dr Sandra MacFadyen |
Day 7: Tue. 18 May | ||||||||
09:15 – 10:15 | Lecture 13. | Climate and ecosystems | Biome Concept. Understand how climate affects vegetation structure, how vegetation structure affects animal communities, including the impact of land use on vegetation. | NA | NA | Ecosystem Structure | Live Cover Fraction, Vertical structure, Ecosystem (Biome) Distribution | Dr Sandra MacFadyen |
10:30 – 12:30 | Prac. 13. | Exploring landscape patterns from space | Use remote sensing data to identify vegetation types, land use/land cover types. | TBC | TBC | Ecosystem Structure | Live Cover Fraction, Vertical structure, Ecosystem (Biome) Distribution | Dr Sandra MacFadyen |
Break | Break | Break | Break | Break | ||||
13:30 – 14:30 | Lecture 14. | Ecosystem-Climate Feedbacks | Vegetation climate feedbacks through water cycling, carbon cycling, albedo. | NA | NA | Ecosystem Function | Primary Productivity, Ecosystem Phenology, Ecosystem Disturbances | Dr Sandra MacFadyen |
14:45 – 16:45 | Prac. 14 | Identifying ecologically relevant variables | Quantify ecologically relevant variables from remote sensing data, e.g., albedo, photosynthesis, Live Cover Fraction. | TBC | TBC | Ecosystem Function | Primary Productivity, Ecosystem Phenology, Ecosystem Disturbances | Dr Sandra MacFadyen |
Day 8: Wed. 19 May | ||||||||
09:15 – 10:15 | Lecture 15. | Biodiversity gradients | Global patterns in species richness and rarity and threats (latitudinal gradient, biodiversity hotspots). | NA | NA | Community Composition | Species Richness (Taxonomic/ Phylogenetic diversity) | Dr Sandra MacFadyen |
10:30 – 12:30 | Prac. 15. | Catchup days 6-7 | Help available for any pracs days 6-7. | Ecosystem Function | Dr Sandra MacFadyen | |||
Break | Break | Break | Break | Break | ||||
13:30 – 14:30 | Lecture 16. | iNaturalist demonstration | Demonstration of citizen science biodiversity website inaturalist | NA | NA | Community Composition | Species Richness (Taxonomic/ Phylogenetic diversity) |
Dr James Rodger |
14:45 – 16:45 | Prac. 16 | Tidyverse recap | Recap on the most important concepts from dplyr and tidyr | Dr James Rodger | ||||
Day 9: Thu. 20 May | ||||||||
09:15 – 10:15 | Lecture 17. | Bipartite networks | Bipartite networks as tool for understanding ecological communities | NA | NA | Community Composition | Interaction Diversity | Dr Jurene Kemp. |
10:30 – 12:30 | Prac. 17. | Bipartite networks | Calculating metrics in bipartite networks (session 1). | bipartite | TBC | Community Composition | Interaction Diversity | Dr Jurene Kemp |
Break | Break | Break | Break | Break | ||||
13:30 – 14:30 | Lecture 18. | Seminar: Bipartite Networks | Complexity and stability in ecological networks. | NA | NA | Community Composition | Interaction Diversity | Dr Ony Minoarivelo |
14:45 – 16:45 | Prac. 18. | Bipartite networks | Calculating metrics in bipartite networks (session 2). | bipartite | TBC | Community Composition | Interaction Diversity | Dr Jurene Kemp |
Day 10: Fri. 21 May | ||||||||
09:15 – 10:15 | Lecture 19. | Seminar: Pollinator Contribution to plant reproduction: assembly of a global dataset | The experience of gathering and assembling a large dataset with an international group of collaborators | NA | NA | Community Composition | Trait diversity | Dr James Rodger |
10:30 – 12:30 | Prac. 19. | Resilience in ecological networks. | Simulating extinction cascades in mutualistic networks. | bipartite | TBC | Community Composition | Interaction Diversity | Dr Jurene Kemp |
Break | Break | Break | Break | Break | ||||
13:30 – 14:30 | Lecture 20. | Career paths in biomathematics. | Building a career in biomathematics. | NA | NA | NA | NA | Prof. Cang Hui |
14:45 – 16:45 | Prac. 20. | Catch up days 8-10 | Help available for problems with Pracs days 8-10. | Community Composition | Interaction Diversity | Dr Jurene Kemp |




Lecturers/Facilitators
- Prof Cang Hui
- Dr James Rodger
- Dr Venuste Nsengimana
- Prof Bamba Sylla
- Dr Sandra McFadyen
- Dr Jurene Kemp
- Dr Oni Minoarivelo
- Dr Assumpta Nnakenyi
- Mr A. Suleiman
- Mr Mmatlou Kubyana
- Ms Asmaa Tbaeen
- Ms Ashleigh Basel




Programming environment:
- R
- Google Earth Engine (GEE)
Before the start date of the school, you should have:
- downloaded all the necessary software and data sets,
- set up accounts on different platforms
- visited youtube and study the basics of R using any of the many beginner’s R videos
Account set-up:
R studio download:
- Link to download R (coming up)
Data sets:
- Links to data sets (coming up)
Beginner’s video to R and R studio:
- YouTube link (coming up)
Trouble shooting sessions:
- On the 8th May 2021 from 10 am to 2 pm CAT, online tutors will be available to assist you with technical issues
- Tutors will also be available
- On the 9th May from 10 am to 2 pm to give you insight into R and R studio: the basics.
- Tutors will also be available through out the 2 week period to further support you for two hours , at the end of each day.
Software downloads and data set information




Organizing Institutions
- African Institute for Mathematical Sciences (AIMS) Rwanda
- Mathematical Biosciences Hub, Stellenbosch University
- Centre of Excellence for Biodiversity and Natural Resource Management, University of Rwanda
Organizers
- Dr Rosita Yocgo: Research group leader, Plant Interactions and the Environment (AIMS Rwanda)
- Dr James Roger (University of Stellenbosch)
- Prof Cang Hui: South African Research Chair in Mathematical and Theoretical Physical Biosciences, AIMS South Africa, University of Stellenbosch
- Dr Venuste Nsengimana: Lecturer (UR-CE) & Deputy Director (CoEB-CST), University of Rwanda
- Prof Bamba Sylla: AIMS-Canada Research Chair in Climate Change Science (AIMS Rwanda)




We acknowledge the gererous financial support from the AIMS-Canada Research Chair in Climate Change Science at AIMS-Rwanda, within the framework of the project Mathematical Sciences for Climate Resilience at AIMS Next Einstein Initiative: https://nexteinstein.org/




Applications and feedback:
Mrs. Carine Umulisa
summerschool@nexteinstein.org
Program information:
Dr. James Rodger
rodgerjg@gmail.com
General information:
Dr. Rosita Yocgo
rosita.yocgo@aims.ac.rw









