BCCVLcncdiversitas.org/sites/default/files/download/8... · 6. Industrial Ecology Virtual Lab 7....

BCCVL Chinese Academy of Sciences Workshop

Hamish Holewa, Program Manager, Biodiversity and Climate Change Virtual Laboratory, Griffith University

P - +61 400027653

hholewa@quadrant.edu.au

WeChat ID: hholewa

Australian Virtual Laboratories and eReseach Initiatives

Australian Collaborative

eResearch Infrastructure

38,000+ cores Multi-petabyte storage Education network Data management programs

Virtual Laboratories

• Formed around engaged research communities

• Built on existing research capabilities

• Support research workflows

• Easier access to data and analysis tools

• Facilitate sharing of data and results

• Provide platform for collaboration and contributions

Australian Virtual Labs

National eResearch Collaboration Tools And Resources

1. All Sky Virtual Lab (Astronomy)

2. Virtual Geophysics Laboratory

3. Humanities Network Infrastructure

4. Marine Virtual Laboratory

5. Genomics Virtual Lab

6. Industrial Ecology Virtual Lab

7. Climate & Weather Science Virtual Lab

8. Virtual Hazards, Impact and Risk VL

9. Microbial Genomics Virtual Lab

10. Characterization Virtual Lab

11. ALVEO (Human Communication)

12. Endocrine Genomics Virtual Lab

13. Biodiversity and Climate Change VL

Virtual Laboratories uptake

• NeCTAR Virtual Laboratories are:

– Demonstrably successful in:

• Supporting research communities across the breadth of

Australian research

• Harnessing sector co-investment to sustain the infrastructure

– Increasingly supporting key NCRIS domain capabilities

• Eg. Genomics, characterisation,, climate and weather science,

astronomy, biodiversity and climate change

• In future, Virtual Lab program should:

– Improve strategic alignment with NCRIS domain

investments

• While continuing to address broad needs across the Australian

research sector

7

Continuing growth in uptake: • Over 10,000 registered research users

Aggregating and processing research data: • Over 120,000 datasets uploaded

Over 250 TeraBytes Uploaded

The Biodiversity and Climate Change

Virtual Laboratory

A big collaborative effort…

08

Prof Brendan Mackey

Climate Change

Griffith University

Prof Emeritus Henry Nix AO

Climate Change

A/Prof Shawn Laffan

Geospatial analysis/ Biodiversity

University of New South Wales

A/Prof Jeremy VanderWal

Ecology

James Cook University

Dr Linda Beaumont

Climate Ecology

Macquarie University

Our Experts

A/Prof Sama Low Choy

Statistics

Griffith University

A/Prof Fabiana Santana

Computer Science

University of Canberra

Mr Lee Belbin

Ecology

Atlas of Living Australia

A/Prof Mark Kennard

Freshwater ecology

Griffith University

How?

Access to data

Photo: © Shane Ruming

Species occurrence data

Annual precipitation 30 arcsec (~1 km resolution)

Max temperature warmest month 30 arcsec (~1 km resolution)

Major vegetation groups 3 arcsec (~90 m resolution)

Gross Primary Productivity 9 arcsec (~250 m resolution)

> 4000 Climate data layers

– Current and future climate

– Range of climate change scenarios and global climate models

> 300 Environmental data layers

(soil, vegetation, run off, GPP, fPAR etc)

Access to data

Advanced modelling capability

Potential distribution of species under current climatic

and/or environmental conditions

Species Distribution Experiment

Multi-Species Distribution Experiment

Effect of environment on

species traits

Species Trait Experiment

Advanced modelling capability

Effect of climate change on predicted species

distributions

Thorny devil, 2045 RCP 8.5 ‘business as usual’

Thorny devil, 2085 RCP 8.5 ‘business as usual’

Climate Change Projection

Analysis of biodiversity, species richness, rarity,

endemism

Biodiverse Experiment

Combine model outputs to reduce uncertainty

Mean

Min

Max

Ensemble Analysis

Results

Bioclim 01 (annual mean temperature)

Bioclim 12 (annual precipitation)

Advanced modelling capability

Education topics Our users do cool things!

Supporting forest managers in finding pre-

adapted tree populations to

mitigate climate impacts in Hungary

Education topics Our users do cool things!

Local government mapping raptor nests to inform management decisions

Current 2085

Education topics Our users do cool things!

Modelling species of interest in Tanzania

Matilda’s Horn Viper

Kipunji Monkey

Education topics Our users do cool things!

Education topics Our users do cool things!

Modelling hotspots of richness for

>500 acacia species

3 months – 1 hour

Education topics Our users do cool things!

Refining models at the click of a button

Noxious weed

Education topics Our users do cool things!

Undergraduate curriculum

assessment item

• Data types

• Providers

• Licensing

• Data cleaning

• Data generation

• Spatial interpolation

• Scale

• Resolution

Data

BCCVL

Education topics Education topics

• Purpose

• Problem definition

• Experimental design

• Underlying principles

• Model assumptions/

limitations

• Algorithms

• Taxonomy

• Statistics

• Model evaluation

Science

Knowledge Base

Education tools

This content downloaded from 132.234.251.230 on Tue, 22 Sep 2015 02:05:02 UTCAll use subject to JSTOR Terms and Conditions

Education tools

1 – Intro to Species Distribution Modelling

2 – Ecological theory of SDMs

3 – Data

4 – Designing a SDM

5 – Presence only models

6 – Statistical regression models

7 – Machine learning models

8 – Model evaluation

9 – SDMs and climate change projections

10 – Case studies in the BCCVL

Online Open Course

Education tools Education tools

Workshops

• BCCVL & ALA workshop

• Different audiences – Undergraduate

– Academic

– Industry

• 24 workshops run = 723 participants

Education tools Education tools

Champions Program

Outcomes Outcomes - reach

Tota

l nu

mb

er o

f u

sers

Star

t w

ork

sho

ps

Rel

eas

e O

OC

Firs

t u

nd

erg

rad

co

urs

e

international

.gmail etc.

.org

.gov.au (Government)

.edu (University)

Tota

l nu

mb

er o

f in

stit

uti

on

s Outcomes

Star

t w

ork

sho

ps

Rel

eas

e O

OC

Firs

t u

nd

erg

rad

co

urs

e

Supporting Infrastructure

• National Research Cloud • 38,000 Cores • Multi-petabyte storage • Openstack Cloud Platform

Computation and Data Infrastructure

• National User Support Network • National Help Desk

• Phone Number • Chat • Email

• Training Programs

• Software Carpentry • Champions Program

Support and Education Infrastructure

• Computation • 400 workers • Scalable

• Storage • Object Storage • API Access to external data

• Software

• R-Server • Rabbit MQ • Plone

• Management

• Containers/ Kubernetes • Github

BCCVL Infrastructure

Scalable - Servers can be in Australia, New Zealand, China - Capacity can be increased quickly and easily

Benefits

Data - Data can be stored in locally - Restrict access to users or groups - Access external data easily

Customise and expand - Experiments and analysis added

Latest technology - Quick setup and operation - Run on any Cloud - Repeatable

• Computation • 400 Cloud Computers • Expandable

• Storage

• Limitless (Cloud based) • Access to external data

• Software

• R-Server • GIS • Python

• Management

• Containers/ Kubernetes • Github

BCCVL Infrastructure

Scalable - Servers can be in Australia, New Zealand, China - Capacity can be increased quickly and easily - Doesn’t use own laptop

Benefits

Data - Data can be stored in locally - Restrict access to users or groups - Access external data easily

Customise and expand - Experiments and analysis added easily - Tailor for use - Publishable workflows

Latest technology - Quick setup and operation - Run on any Cloud - Repeatable

Enabling – General Modelling Platform

New Zealand Specific Environmental and

Climate

NZ - BCCVL M- BCCVL

?? BCCVL

Marine SDM and Traits

Marine Data

Country

Domain

Methods

Future Programs and Opportunities

Data Challenges

• Access to Dynamic Data

• Weather data

• High resolution, country specific data

• Environmental, climate, biological

• Combine traits, genomics, phenology data

• Vector based data (e.g. Biosecurity threats)

• Shipping lanes, people, movement

Potential Research Programs

• Invasive Species

• China/ Australia have similar land area

• Similar amount of identified invasive species

• Migratory Modelling

• Australia/ China Migratory Bird Agreement

• Integrating current and future land cover and land use change into SDM/ Climate Change Models

• Trait expression as a function of time and space

Potential Research Programs

• Invasive Species

• China/ Australia have similar land area

• Similar amount of identified invasive species

• Migratory Modelling

• Australia/ China Migratory Bird Agreement

• Integrating current and future land cover and land use change into SDM/ Climate Change Models

• Trait expression as a of environmental correlates

Localisation

• Chinese specific datasets

• Environmental

• Biodiversity (Occurrence)

• Language

• Internet Explorer

• Authentication

Future Data Challenges

• Access to Dynamic Data

• Weather data

• High resolution, country specific data

• Environmental, climate, biological

• Combine traits, genomics, phenology data

• Vector based data (e.g. Biosecurity threats)

• Shipping lanes, people, movement

Opportunities

Data • Dynamic Data – Daily

Interpolated weather data • Trait Data – Environmental/

Genetic • Anthropogenic and urban

layers • International datasets

Models • Species Trait - Function of

Time and Space • Mechanist/ Functional • Self-calibrating models • Data preparation (NicheA?)

Training • Industry targeted • Micro accreditation

Prediction Services • Constantly updated models

(when new data available) • Self calibrating models • Environmental prediction

services

Proposal #1 China-Australia

collaboration on developing

Biodiversity & Climate Change

Modeling Platforms (Virtual Labs) and

Data Hubs

Collaboration & Resource Sharing

• Exchange of existing platforms and knowhow

• Co-development of these platforms functionality

• Sharing and linking for collaborative research purposes of existing and new biological, climate and environmental data

• Co-development of new tools, techniques and experiments

• Collaborate on training and teaching materials and activities.

Proposal #2 International network of

modeling platforms (Virtual Labs) and

Data Hubs?

Broader international collaboration, e.g. Asia-Pacific network

Sharing access to modeling and data platforms

Access (with permission) international high resolution country specific data;

Share and iteratively develop best practice models;

Develop new tools, techniques and experiments;

Share and collaborate on training and teaching materials.