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Web Accessible Virtual Research Environment for Ecosystem Science Community
Presentation by Siddeswara Guru
Typical Analysis and Synthesis
Formulate a problem
Define hypothesis
Gather data to conduct
experiment
Analyse dataTest the outcome
Make inference
Publish results
Computational OptionsOption 1:
• Tools: Matlab, R, python, statistical packages etc,.• Individual programs run separately to conclude the meta-analysis.
Advantages• Develop in any desktop environment• Lower barrier for running analysis
Disadvantages• Reproducibility and transferability is not that easy
Computational options
Option 2Use of 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.
Computational Options
Popular Workflow systems• Kepler, Taverna, Galaxy, VisTrails, Triana
Advantages:• GUI interface to compose workflow• Ability to create components in different programming
languages• Easy to run workflows as distributed tasks• Ability to track and collect provenance information• Platform independent re-usable experiments• Possibility of repeatability and reproducibility
Computational Options
Disadvantages:• New tool to learn• Strong informatics focus
Challenges
• access to compute resource• access to large storage if required• Setup new Environment
If organization IT services doesn’t support• Apply for compute allocation from NeCTAR research cloud• Apply for storage allocation from RDSI• Setup the platform• Use the system for analysis and synthesis activities.
How about all the above is available and accessible from the web browser
CoESRA
• Access the cloud-based linux desktop via a browser
• The 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.
Registration and login using Australian Access Federation (AAF)
CoESRAThe public and personal workspace for users
Publish and share your workflow
Publish your workflow
Publish your workflow
Kepler workflow System
Kepler Workflow SystemDirector
Actor
Data flow
Workflow parameters
Kepler Workflow System• Open source scientific
workflow system
• More than 300 re-usable components (Actors)
• Widely used in different domains• Ecology, Geoscience,
Biology etc.
Sample Workflows
Gross Primary Production
The ecosystem Production in Space and Time (ePiSaT) project was supported by the Australian National Data Service (ANDS). ANDS is supported by the Australian Government through the National Collaborative Research Infrastructure Strategy Program and the Education Investment Fund (EIF) Super Science Initiative.
Spear tooth shark conservation plan
Main objective: minimize the impact of Spear tooth shark by-catch while optimising the crab fishing in Wenlock riverThe acoustic tagged data of spear tooth sharkMarxan: conservation planning tool
Conceptual workflow
Conclusion
• Enable web-based access to a platform to conduct analysis and synthesis
• Scientific workflow approach is used• Promote repeatability, reproducibility• Ability to make the workflow discoverable
from RDA.
Register/loginAccess the
desktopAccess CoESRA
website
The system will be available from 15th of June 2015
Please check www.coesra.org.au near to the release date.
Your feedback is very valuable
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TERN is supported by the Australian Government through the National Collaborative Research Infrastructure Strategy and the Super Science Initiative
Project Sponsors
collaborators
