Workshop: Advances in data management practices and technologies for ecosystem 

science

Where Ecology Meets Big Data

By Dr Willow Hallgren, Professor Brendan Mackey and Mr Andrew Bowness

Presented by Willow Hallgren

Aim of Presentation

Learn what a Virtual Laboratory is, and what it can do

Introduce you to, and give you a quick tour, of the Biodiversity and Climate Change Virtual Laboratory (BCCVL)

Hopefully get you to start thinking how Big Data is influencing research, and how you might apply the BCCVL in your own research, to utilise your own datasets and expand the scope of the research questions you ask in the future.

Current capabilities in terms of the concept of Virtual Laboratories

BCCVL specific details and video

How to use the BCCVL

Example experiment

Future Directions for the BCCVL.

Outline of Presentation

Current capabilities of Virtual Laboratories

Virtual Laboratories: Are formed around engaged research communities

Build on existing research capabilities

Support research workflows

They are designed to:

Allow much easier access to data archives and modelling tools, thereby reducing the technical barriers to using state of the art tools,

Facilitate the sharing of data, experiments and results

Reduce the time to conduct scientific research studies

Provide a platform for collaboration and contributions by the Australian research community.

Currently Existing Virtual Labs Biodiversity and Climate Change – Griffith University

Understanding Biodiversity response to climate change through integrated observation and modelling

Genomics Virtual Laboratory – University of Queensland Collaborative genomics workflows in the cloud

Virtual Geophysics Laboratory – CSIRO Workflows and access to geophysical tools, data and resources

Marine Virtual Laboratory (MARVL) – University of Tasmania Virtual environments to unify marine modelling and observation

Climate and Weather Science Laboratory – BoM Integrated environment for climate and weather science modelling and data

Industrial Ecology Virtual Laboratory – Sydney University Supporting comprehensive environmental footprinting and sustainability assessments

Currently Existing Virtual Labs All Sky Virtual Observatory – ANU

Federating astronomy data: SkyMapper and the Theoretical Astronomical Observatory

Humanities Networked Infrastructure – Deakin University Unlocking and uniting Australia’s cultural data

Human Communications Science – University of Western Sydney Above and beyond Speech, Language and Music: A national collaborative

environment for HCS research.

Endocrine Genomics VL – University of Melbourne Integrating –omics capabilities to realise personalised e-Health in a translational

researcher-oriented environment

Characterisation Virtual Laboratory – Monash University Research environments for exploring inner space

www.bccvl.org.au

BCCVL specific details and show The Biodiversity & Climate Change Virtual Laboratory (BCCVL)

provides an easy-to-use, web-based platform for modelling the potential responses of Australia’s biodiversity to climate change.

The BCCVL gives researchers access to a suite of modelling tools, data collections, access portals and visualisation capabilities to facilitate and accelerate research on the impact of climate change on biodiversity

Modelling can be at multiple scales down to 250 m resolution

The BCCVL allows you to upload your own data, share it with other BCCVL users and conduct modelling experiments on it.

BCCVL specific details and show

The BCCVL helps researchers transform biodiversity and climate change research by: Enabling existing research questions to be investigated far more efficiently

and effectively; Providing the means for Australian researchers to address new important

questions.

Quantitative modelling is one of our most transparent and science-based tools for the prediction of how (e.g.) species ranges will shift as a result of climate change

The Information generated is needed to inform adaptation management strategies for species and ecosystems.

How to use the BCCVL

STEP 1: Go to www.bccvl.org.au (Beta release)

STEP 2: Log in with your Australian Federated Password (your Institutional user name and password)

(1)

(2)

(3)

Datasets

• Species location and trait data,

• Current and future climate data, and

• Other environmental data, (e.g., soil, geological and vegetation type)

Experiments

• Access a suite of statistical modelling tools.

Knowledge Base

• Documentation and relevant literature.

The BCCVL is organised under three main headings:

STEP 3: Find the datasets you want to use:

BCCVL Datasets

• Many datasets already uploaded into BCCVL• Species data (distribution, traits), climate data, environmental data• 3 icons: view map, download, metadata

Search among the datasets listed

• Facility to search the web for desired data• Currently restricted to Atlas of Living Australia• Search, download into BCCVL, and view

Discover a dataset on the web

• Can upload species occurrence, abundance or trait data, or other environmental datasets

• View, download, metadata, share with other BCCVL users

Upload your own dataset

BCCVL Experiments

• Find current potential distribution of a speciesSpecies Distribution Modelling Experiment

• Project a species distribution into the future based on a climate projection, for one or more emission scenarios Climate Change Experiment

• Calculate biodiversity statistics (species richness and endemism) based on SDM resultsBiodiverse Experiment

• Find current or future distribution of a particular species trait e.g. Leaf Area Index ***

Species Trait Modelling Experiment

• Use multiple models- either SDMs or climate models- or emission scenarios, to mitigate the uncertainty in the single-model/scenario approachEnsemble Modelling

STEP 4: What do you want to do with the data? You can run 5 types of experiments:

BCCVL Knowledge BaseSTEP 5: Learn more, before you start, or as you go.

Knowledge base• Species Distribution Modelling Experiment

• Find current potential distribution of a species

• Reference datasets available for use in the BCCV• Environmental (geoscientific, elevation, vegetation)• Climate (current and future climate, water availability, PET, etc.) • Biological (Atlas of Living Australia, eBird, GBIF)

• Functional response (i.e. species trait) modelling

• Glossary…

• etc. (still very much a work in progress!)

Example experiment

(1) Species Distribution Modelling Experiment: Predicting the current and future distribution of the Snow Gum

(Eucalyptus Pauciflora).

Example Experiment

• (plan to add more slides or videos to show how to conduct an experiment in the BCCVL)

Future Directions

Utilisation of more, and different types of datasets (e.g., palaeodata)

Possibility of incorporating more algorithms and different types of modelling tools

Expand the BCCVL internationally

Contact Details

Dr Willow Hallgren, Research Fellow

Griffith Climate Change and Adaptation Program

Griffith University, Southport Campus, Gold Coast

Email: w.hallgren@griffith.edu.au

Relevant Links and References

Links:• www.bccvl.org.au

References• Peters, D. P. C., K. M. Havstad, J. Cushing, C. Tweedie, O.

Fuentes, and N. Villanueva-Rosales. 2014. Harnessing the power of big data: infusing the scientific method with machine learning to transform ecology. Ecosphere 5(6):67. http://dx.doi.org/10.1890/ES13-00359.1