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Collaborative Environment for Ecosystem System Science Analysis and Synthesis (CoESRA)
Presentation by Siddeswara Guru
Outline• Motivation
• Reproducible science
• Challenges• CoESRA• Use Case: IUCN Red List of Ecosystems
Assessment.• Summary
Motivation
Reproducible Science
Duplicate the scientific experiments or reproduce experiment results.
Source: nature.com
Challenges• Lack of culture to make scientific claims
reproducible• Lack of detailed information about data
and code even after they are published• “lack of an integrated infrastructure for
distributing reproducible research to others”1
• Despite the journal Biostatistics’ policy since 2009, as of 2011 only 4% of articles had “R” kite-mark.
• In US, $28 billion per year spent on clinical research that are not reproducible2.
1Peng, Roger D. (2011). Reproducible Research in Computational Science. Science, 334(6060), 1226-1227. doi: 10.1126/science.12138472Freedman, L. P., Cockburn, I. M., & Simcoe, T. S. (2015). The Economics of Reproducibility in Preclinical Research. PLoS Biol, 13(6), e1002165. doi:10.1371/journal.pbio.1002165
Source: experimentalmath.info
Reproducibility Spectrum
Peng, Roger D. (2011). Reproducible Research in Computational Science. Science, 334(6060), 1226-1227. doi: 10.1126/science.1213847
Integrated Infrastructure
• Cloud-based platform• Scientific workflows executable
on a easily accessible platform
"one of the most effective ways to promote high-quality science is to create free open-source tools that give scientists easier and cheaper ways to incorporate transparency into their daily workflow:"3
3 Stuart Buck, Solving reproducibility, Science 26 June 2015: 348 (6242), 1403. [DOI:10.1126/science.aac8041]
Scientific workflow• Series of structured
interconnected computational activities
• Visual front-end to build experiments using components.
• Components can be implemented in high-level and/or scripting languages.
Kepler Scientific workflowFeatures
• Ability to create components in different programming languages
• Reusable components: actors and Directors
• Easy to run workflows as distributed tasks
• Platform independent re-usable experiments
• Possibility of repeatability and reproducibility
We want to develop an infrastructure where computational experiment e that has been developed at time t on a hardware and software infrastructure h using data d is reproducible at time t1 on same hardware and software infrastructure h using the same data d.
Cloud-based virtual desktop accessible to applications and data over a web browser.
GOAL
CoESRA
CoESRA
CoESRA Home page
Registration and login via
AAF
Virtual Desktop on Browser
IUCN Red List Ecosystem Assessment of Mountain Ash Forest
Mountain Ash Forest Ecosystem Risk Assessment
• Unique biodiversity, • World tallest flowering plants (over 100 m),• Contribute to water and timber production,• subject to wildfire. • Apply IUCN Red List of Ecosystem criteria for risk assessment2
Source: abc.net.au
2Burns, Emma L., Lindenmayer, David B., Stein, John, Blanchard, Wade, McBurney, Lachlan, Blair, David, & Banks, Sam C. (2015). Ecosystem assessment of mountain ash forest in the Central Highlands of Victoria, south-eastern Australia. Austral Ecology, 40(4), 386-399. doi: 10.1111/aec.12200
Application of IUCN Red List of Ecosystems Categories and Criteria
No. of Hollow bearing trees
Temp and precipitation
Spatial distribution
Abundance of hallow bearing trees
Degradation through lost bioclimatic suitability
Mountain ash forest
Mountain Ash Forest risk assessment workflow
Sub- Workflow for Criteria A
Select Evaluation
Workflow
CoESRA
Access to cloud-based linux desktop via a browser
Virtual desktop comes with Kepler scientific workflow and other tools
Both personal and public storage space Ability to distribute the execution Free to use, build and/or execute workflows.
Register/loginAccess to
virtual desktopAccess CoESRA
website
TERN is supported by the Australian Government through the National Collaborative Research Infrastructure Strategy and the Super Science Initiative
Project Sponsors collaborators
The Workflow shown is accessible from https://www.coesra.org.au
Thank [email protected]
Register/loginAccess the
desktopAccess CoESRA
website