eResearch Symposium 2011 Presentations and Recordings

The Kiwi Advanced Research and Education Network (KAREN) is New Zealand’s high-speed broadband network that connects research and educational organizations both nationally and internationally. KAREN is a key component of the infrastructure that supports the use of ICT for research, education and innovation here in New Zealand. Provision of KAREN has opened the window on exciting opportunities and ensures New Zealand Inc. may keep pace with R, E and I advances worldwide. 

Science and network technology continues to advance and this opens new avenues, and with it opportunities for research and education. It is important that KAREN is not a stagnant network but flexible and able to adapt to the ever-advancing needs of the KAREN community. 

For example, the National eScience Infrastructure (NeSI) project will provide scientists’ access to world class high performance-computing facilities enabling computational models to be developed that would otherwise be unobtainable in New Zealand. The main users are KAREN members, the CRIs and Universities, and these are distributed throughout the country. KAREN will enable access to NeSI by this distributed community.

We present an overview of KAREN and its supporting role in the New Zealand R, E and I communities. Identifying projects that have been, or are currently enabled or supported by KAREN will serve to demonstrate how broad the eResearch spectrum is in New Zealand.

To ensure KAREN evolves to meet community needs REANNZ provides tools that allow members to be actively involved in developing the community, these will be briefly outlined.

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The KAREN Video Conferencing Service (KVCS) was launched mid last year to enable staff and students across Universities, CRIs and other institutions on KAREN to join medium to large scale video conferencing meetings using desktop tools and other common communication platforms. Since then KVCS now averages over 1,000 meetings per month with over 3,500 connections. AVCC will be looking to enhance the services this year by including shibboleth authentication sign on for users and creating a custom interface booking system through its API from within the AVCC website. By adopting these methods, we hope to provide a productive and easy to use remote collaborative service tool for researchers within New Zealand.

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Tuakiri, New Zealand Access Federation project which started in May 2010, has delivered the following to date:
  1. Interim Governance Committee
  2. Development and Test Environment
  3. Pilot Federation Service
  4. Website, technical tools and documentation for Identity Provider and Service Provider deployments. (SAML implementation with Shibboleth Software)
  5. Federation Rules for the participating institutions
  6. Tuakiri Test Federation Terms of Use, and
  7. Tuakiri Test and Pilot Federation Usage Policy
Tuakiri Pilot Federation Service is now available for institutions in the higher education and research sector to join in as early adopters.
Tuakiri will make sharing protected online resources easier
  • Tuakiri will eliminate the need for researchers, students, and academics to maintain multiple passwords and usernames.
  • Reduced complexity for the service providers on maintenance of the user accounts. Identity providers manage the levels of their users' privacy and information exchange.
  • Tuakiri Federation Service has deployed SAML-based authentication and authorization systems (Shibboleth®) to enable scalable, trusted collaborations among its community of participants.
Tuakiri will connect virtual communities and enable collaboration.
The workshop on Friday 1 July will cover:
1)      An introduction to Tuakiri
2)      Technical information and implementation on the relevant software components
                                i)            IdP deployment
                               ii)            SP deployment
                             iii)            VHO – IdP Service
3)      How Tuakiri can support your organisation with the implementation.
Come and talk to the Tuakiri Team, Sat Mandri, Daniela Dunn and Aaron Hicks at the eResearch Symposium. And you can find more information at www.tuakiri.ac.nz

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Digital relationships between individuals are becoming as important as their real world counterparts. For many people Social networks provide a primary means of communication between friends, family and co-workers. As relationships within online social networks are largely based on real world relationships, we can therefore use them to infer a level of trust that underpins the online community in which they exist. Existing Cloud environments typically provide a range of abstractions of computation, storage and other services. Computation and storage act as building blocks from which higher level services and service mash-ups can be created. There are a large number of commercial Cloud providers such as Amazon EC2/S3, Google App Engine and also many smaller scale open Clouds like Nimbus and Eucalyptus. These Clouds provide elastic access to commoditized scalable virtualized resources (computation, storage, applications).

A Social Cloud however, is a scalable computing environment in which virtualized resources contributed by users are dynamically provisioned amongst a group of friends or colleagues. The social cloud will enable scientists to collaborate by sharing data and computing power through leveraging their existing social networks. We believe that this will encourage highly cooperative structures between research groups and other small organizations to forge entangled mutually constructive scientific communities. The early work on this project has generated significant interest in the cloud computing community. The purpose of this presentation is to introduce the ideal of a Social Cloud to the NZ scientific community, and to report on our progress in the development of the Social Cloud.

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This talk introduces a new visualisation system (called Alfred) that is designed to be the portal by which an eResearch community can retrieve and understand its resources, such as papers, methods, people, ontologies and datasets.  Once digital resources are gathered into collections, users need to be able to locate and interpret the (usually small) subset of resources that is useful to them in a very specific context.  But the starting point and path taken during this search is unpredictable; it depends on the user’s experience and knowledge.

Alfred
is named for Alfred North Whitehead, a famous philosopher of science of the early 20th century, who described meaning in science as being situated within a Nexus of connections, rather like a spider’s web: the meaning attached to some resource is acquired entirely via its relationships to other things (such as users, methods, datasets).  This meaning is brittle, and becomes lost or distorted if the connections to its history and ontological commitments are not maintained. 

The challenge, then, is to be able to show the many connections that exist between resources in ways that support multiple search strategies, that emphasise how resources relate to domain semantics and that also reflect the evolving pragmatics of use-case and provenance.  Alfred supports multiple dynamic views, that are highly coordinated, and that can reorganise themselves as the user searches for useful connections to explore.  Alfred is built on top of Eclipse, using Java, and openGL for fast graph-based visualisation.  It is designed to be highly flexible in terms of query and visualisation power, and these aspects will be explained during the talk, along with a use-case that describes the National eScience Infrastructure (NeSI) community.

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The Print Culture eResearch Hub at Victoria University of Wellington was established in 2010 to support three projects: the Marsden-funded "The Printers' Web. Typographical Journals and Global Communication Networks in the Nineteenth Century"; the NZ-Reading Experience Database, an international collaboration devoted initially to reading in the Great War; and the Digital Colenso, a prosopographical collaboratorium to support a new collective biography of the nineteenth-century polymath William Colenso. This presentation situates these e-nitiatives in the context of new humanities scholarship overseas and poses several challenges for how we conceptualise and promote digital humanities as part of the world of e-Science.

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The Humanities Computing Unit at the University of Canterbury was established in 2010 to develop complementary streams of digital humanities scholarship: heritage digitization projects, scholarly research, and associated teaching and assessment methods. Key achievements have been the creation of a digital library framework; an honours course on Electronic Scholarly Editing which focuses on XML publishing using the TEI (Text Encoding Initiative) Guidelines; the launch of an inaugural corpus, the Roy Bruce Letters; and the establishment of an open Journal Systems server offering hosting for academic journals.

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Whilst BeSTGRID technologies and processes have matured significantly, we recognise that newcomers to the technology still need some help in getting up and running on occasions and that as existing users become more familiar with what is achievable they attempt more and more ambitious uses of the technology.

To provide support to both types of user we propose to hold a “drop-in” series of clinics where researchers can get in-depth one to one or small group assistance with a range of technical issues or discuss their research requirements to get advice on appropriate solutions.

Examples of potential clinics include:

  • Grid Development: This clinic would provide support for those developing or who wish to develop applications that interface with the grid.
  • Batch Job Submission: This clinic would provide support for those who wish to programmatically submit multiple jobs into the BeSTGRID environment from one program or script
  • Authentication & Getting Access: This clinic would provide support and assistance to those who wish to get started with BeSTGRID systems and provide a service to those who wished to get a grid certificate approved.

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Some projects require the submission of many computation jobs to HPC resources, in some cases 'many' may mean tens, hundreds, or even thousands of jobs. This workshop will guide researchers and developers through the process of automating the submission of jobs to the BeSTGRID/NeSI computation resources using Python scripts and the Grisu Jython library. Although Python will be the language demonstrated at the workshop, the methods shown should also work with Java, and should be suitable for integrating into job submission applications.

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This hands-on tutorial session will provide new users to BeSTGRID services with the handson confidence to effectively use BeSTGRID tools. The particular focus of this tutorial session will be on the Data and Collaboration Components of the BeSTGRID tool suite.

Users will be walked through and encourage to try out

  • Signing into services with ARCS/Tuakiri or Institutional Credentials or signing up forTuakiri/ARCS VHO credentials if they don’t have institutional credentials.
  • Using Grix to create a MyProxy Certificate
  • Sakai
  • Creating a new Sakai Collaboration Site
    • Basic configuration of the site
    • Adding members to the site
  • DataFabric
    • Accessing via Shibboleth and a web browser.
    • Accessing via WebDAV using MyProxy credentials
  • GlobusOnline?
    • Transfer data from DataFabric to another institution
  • Overview of other services
    • EVO
    • Computation Grid
    • GenePattern/Galaxy
    • What is coming in NeSI?

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