Collaborative Environment for Ecosystem Science Analysis and Synthesis (CoESRA) is a cloud-based platform that aims to promote reproducible science. It provides a virtual desktop environment accessible through a web browser that contains tools like Kepler for building scientific workflows. CoESRA allows users to create reusable computational experiments and ensure their reproducibility over time on the same infrastructure. As a demonstration, a workflow is shown for assessing the risk level of Mountain Ash forests in Australia according to IUCN Red List of Ecosystem criteria.

1. Collaborative Environment for Ecosystem
System Science Analysis and Synthesis
(CoESRA)
Presentation by Siddeswara Guru

2. Outline
• Motivation
• Reproducible science
• Challenges
• CoESRA
• Use Case: IUCN Red List of Ecosystems
Assessment.
• Summary

3. Motivation
Reproducible Science
Duplicate the scientific experiments or
reproduce experiment results.
Source: nature.com

4. 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.1213847
2Freedman, 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

5. Reproducibility Spectrum
Peng, Roger D. (2011). Reproducible Research in Computational Science.
Science, 334(6060), 1226-1227. doi: 10.1126/science.1213847

6. 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]

7. 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.

8. Kepler Scientific workflow
Features
• 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

9. 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

10. CoESRA

11. CoESRA

12. CoESRA Home page
Registration
and login via
AAF

14. Virtual Desktop on Browser

15. IUCN Red List Ecosystem Assessment
of Mountain Ash Forest

16. 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

17. 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

18. Mountain Ash Forest risk assessment workflow

19. Sub- Workflow for Criteria A

20. Select Evaluation

21. Workflow

22. 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/login
Access to
virtual desktop
Access CoESRA
website

23. 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 you
s.guru@uq.edu.au
Register/login
Access the
desktop
Access CoESRA
website