Web Accessible Virtual Research Environment for Ecosystem Science Community Presentation by Siddeswara Guru.

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Presentation transcript:

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 data Test the outcome Make inferencePublish results

Computational Options Option 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 2 Use 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)

CoESRA The public and personal workspace for users

Publish and share your workflow

Publish your workflow

Kepler workflow System

Kepler Workflow System Director 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 river The acoustic tagged data of spear tooth shark Marxan: 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/login Access the desktop Access CoESRA website

The system will be available from 15 th of June 2015 Please check near to the release date. Your feedback is very valuable

TERN is supported by the Australian Government through the National Collaborative Research Infrastructure Strategy and the Super Science Initiative Project Sponsors collaborators

More information TERN website: Thank you