E-science, Auckland GEON Workshop, 2007
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Geoscience Collaboration and the Geosciences Network (GEON) . Sponsored by: GEON: The Geosciences Network The National Science Foundation (USA) BeSTGrid, New Zealand School of Geography, Geology and Environmental Science, U. Auckland. Day 1: e-Science Collaboration.

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Geoscience collaboration and the geosciences network geon l.jpg

Geoscience Collaboration and the Geosciences Network (GEON)

Sponsored by:

GEON: The Geosciences Network

The National Science Foundation (USA)

BeSTGrid, New Zealand

School of Geography, Geology and Environmental Science, U. Auckland


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Day 1: e-Science Collaboration

09:40 : General Introduction to the workshop and e-science : Mark Gahegan

10:15 : Cyberinfrastructure and e-science at the San Diego Supercomputer Center : Chaitan Baru

11:00 : Coffee break

11:30 : AuScope - An overview & future plans : Rob Woodcock

12:00 : The NZ Geospatial scene - Government Geospatial Office perspective : Brendon Whiteman

12:30 : Lunch

13:30 : An overview of BeSTGRID : Tim Chaffe

13:45 : An overview of SCENZ-GRID : Robert Gibb

14:00 : Challenges for collaboration : panel discussion with Chaitan Baru, Mark Gahegan, Rob Woodcock, Robert Gibb

14:45 : Discussion forum on collaboration & breakout groups

15:30 : Coffee

16:00 : Summaries presented

16:30 : Adjourn for welcome drinks from School of Geography, Geology and Environmental Science

e-science, Auckland GEON Workshop, 2007


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Day 2: GEON

09:00 : Coffee & mingling

09:30 : Introduction to GEON and i-GEON : Chaitan Baru

10:00 : Geoscience needs and challenges : Dogan Seber

10:30 : Knowledge-based data integration (+web portal demo?) : GEON Team

11:00 : Coffee

11:30 : Geon Architecture, Systems & Development : Sandeep Chandra

12:30 : Lunch

13:30 : Presentations by local researchers

  • Peter Leary Institute of Earth Science Engineering, University of Auckland

  • David Park Geospatial Research Centre

  • Robert Gibb and Paul Grimwood Landcare Research and GNS

    15:30 : Coffee & mingling, adjourn when finished

e-science, Auckland GEON Workshop, 2007


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Day 3: More GEON

09:00 : Coffee & mingling

09:30 : Science applications of GEON : Dogan Seber

  • Synthetic Seismogram

  • Lidar Workflows

  • PaleoIntegration

    10:15 : Capturing, representing and sharing meaning : Mark Gahegan

    11:00 : Coffee Break

    11:30 : Exploration, discussion and confirmation of specific strategies for follow-up and collaboration.

    Themes may include

  • Emerging e-science and e-education

  • Geoscience standards

  • Workflow, analysis and visualization tools

    Formal close of workshop just before lunch

    12:30 : Lunch

    13:30 : Informal discussions and meetings (with each other, with the GEON team)

e-science, Auckland GEON Workshop, 2007


E science collaborative science enabled by computational systems l.jpg

e-Science: Collaborative science, enabled by computational systems

Mark Gahegan

Professor of Geography,

Affiliate Professor of Information Science and Technology

GeoVISTA Center, Department of Geography

The Pennsylvania State University, USA


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e-Science (from Wikipedia)

The term e-Science (or eScience) is used to describe computationally intensive science that is carried out in highly distributed network environments, or science that uses immense data sets that require specialized (grid) computing;

…the term sometimes includes technologies that enable distributed collaboration, such as the Access Grid

Examples of e-Science include:

  • social simulations,

  • particle physics,

  • earth sciences and

  • bio-informatics.

e-science, Auckland GEON Workshop, 2007


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Goals of e-Science

  • Helping communities of researchers and educators to do better science by sharing their resources:

    • data, tools, models, protocols, results

  • Making specialized and expensive equipment and computers available to distributed users

  • Providing fast networks and distributed data stores for data intensive computing

  • Litmus tests:

    • Contributing to e-Science becomes an integral part of the way scientists/educators work

    • The ‘three pillars of science’: communication, repeatability, refutability

    • Can we ourselves remember what we did? Will future generations of scientists be able to follow our work?

e-science, Auckland GEON Workshop, 2007


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Four sample e-science projects

The Fungal Plant Pathogen Database http://fppd.cbio.psu.edu/index.html

Human Environment Regional Observatories (HERO): www.hero.psu.edu

Learning Activities in Digital Libraries: www.dialogplus.org

ArchaeoInformatics: http://archaeoinformatics.org/index.html

e-science, Auckland GEON Workshop, 2007


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Fungal Plant Pathogen Database

Genetic sequencing, comparing and tracking different pathogen strains



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A cyber-infrastructure for plant pathogen research: Motivations

  • Plant pathogen culture collections are essential resources in our fight against plant disease

  • Yet available infrastructure in support of culture collections is in serious need of improvement, and we continually face the risk of losing many of these collections due to the lack of support.

  • Genetic sequencing and alignment is computationally intensive

  • Need for timely identification and monitoring of novel and reemerging plant pathogens that threaten agriculture

  • Archiving is essential for rapid assessment of potential risk and can help track the change and movement of pathogens.

e-science, Auckland GEON Workshop, 2007


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Plant pathogen application examples Motivations

e-science, Auckland GEON Workshop, 2007


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part of a phylogenetic tree representing sequences from the MotivationsActin marker of the fungal species Lettuce Drop (Sclerotinia sclerotiorum)

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n = 1

W. Canada

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n = 1

Norway

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n = 1

Norway

n = 7

SE, USA

N. Zealand

n = 2

E. Canada

n = 5

SE, USA

N. Zealand

n = 69

SE, USA

NE, USA

W. Canada

Norway

N.Zealand

n = 2

Norway

e-science, Auckland GEON Workshop, 2007


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GeoGenetics Motivations: Geographical mapping of isolates

A linked map and taxonomic tool (called Taxa, from Napier U. Scotland). Users can study how far apart in the genetic tree different isolates are and how far apart they are geographically.

e-science, Auckland GEON Workshop, 2007


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0.084 Motivations

0.113

0.027

0.085

0.143

0.118

0.117

0.004

0.120

0.015

0.001

0.002

0.012

4

3

6

5

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n = 1

W. Canada

8

n = 1

Norway

2

1

n = 1

Norway

n = 7

SE, USA

N. Zealand

n = 2

E. Canada

n = 5

SE, USA

N. Zealand

n = 69

SE, USA

NE, USA

W. Canada

Norway

N.Zealand

n = 2

Norway

Isolates related to regional climate of their geographical location

  • Climate graph: Isolates are grouped according to region:

  • New Zealand (pink squares),

  • SE United States (green triangles),

  • NE United States (red circle),

  • Norway (purple asterisks),

  • W Canada (blue diamonds).

e-science, Auckland GEON Workshop, 2007


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Human-Environment Regional Observatories Motivations

Likely impacts of global climate change on local places



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Facilitating the development of a Motivationsclimate change vulnerability index

e-science, Auckland GEON Workshop, 2007


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HERO Concept emergence (day 1…) Motivations

e-science, Auckland GEON Workshop, 2007


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(…day 7…) Motivations

e-science, Auckland GEON Workshop, 2007


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(…day 28) Motivations

e-science, Auckland GEON Workshop, 2007


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Researcher convergence??? Motivations

Day 1

Day 28

e-science, Auckland GEON Workshop, 2007


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Semantic distance between participants Motivations

e-science, Auckland GEON Workshop, 2007


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DialogPLUS: e-Science meets e-Education Motivations

Sharing learning activities between institutions






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…Semantic metadata describes content and pedagogy Motivations

Chris Bailey (Soton, UK): DialogPLUS

e-science, Auckland GEON Workshop, 2007


Designing a learning activity connecting pedagogy domain concepts and resources l.jpg

Learning Activity Motivations

Designing a learning activity: connecting pedagogy, domain concepts and resources

Learning Approach

Subject (GPS)

Outcomes

Interactions

Tasks

e-science, Auckland GEON Workshop, 2007




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ArchaeoInformatics Motivations

Working with the archaeological community



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New project—funded by the Mellon Foundation Motivations

e-science, Auckland GEON Workshop, 2007


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Need for data integration Motivations

Need for search / query tools

Mapping, GIS, visualization

Large-scale simulations & shared computing?

Data must be remain at local sites

Obfuscating sensitive data

Custodianship is contested

No data standards and controlled vocabularies

Is archaeology different?

e-science, Auckland GEON Workshop, 2007


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SUMMARY: Added value for e-science researchers Motivations

  • Access to remote equipment, computing power and in-silico experiments

  • Collaborative tools & workspaces

  • Access to large collections of data & results (international?)

  • Integration & translation of data between formats

  • Curation of data into the long term

    • How is the effort sustained?

  • More efficient science?

e-science, Auckland GEON Workshop, 2007


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Many challenges Motivations

  • Technical…

  • Conceptual…

  • Sociological…What needs to change?

    • Ongoing funding for e-Science?

    • Participation and adoption by science communities (risk, resistance)?

    • Recognition that contributing to e-Science is a valid and worthwhile outcome (just like publishing papers)?

e-science, Auckland GEON Workshop, 2007


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End Motivations

Questions?


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