coesra: platform for collaborative research

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 yous.guru@uq.edu.au

Register/loginAccess the

desktopAccess CoESRA

website