Paper

Tools for reproducible neuroimaging: an example from diffusion MRI

In this talk, I will discuss tools for reproducible research in neuroimaging. I will present a set of open-source libraries developed in the python programming language for reading/writing MRI data, for analysis of MRI data and for constructing reproducible analysis pipe-lines. I will demonstrate the use of these tools with a project focused on modeling the micro-structure of brain anatomy from diffusion-weighted magnetic resonance imaging (DW-MRI) data.

Symposium: 

eResearch NZ 2013 session type: 

Submitted by Tim McNamara on

Humanities Networked Infrastructure (HuNI) Virtual Laboratory : Discover | Analyse | Share

The Humanities Networked Infrastructure virtual laboratory has been designed to meet the resource discovery needs of Australian humanities researchers and to support data processing and collaboration. This presentation is will explain to the audience what is “under the bonnet” in the HuNI virtual lab; the technology choices, design features, tools, and the capacity for extensibility and interoperability that has been built into the design.

Symposium: 

eResearch NZ 2013 session type: 

Submitted by Tim McNamara on

The Whiteroom: A partnership model for supporting eResearch

Massey University has completed phase one of a pilot study to develop and evaluate an integrated coordinated support service approach for eResearch. This approach also known as “the Whiteroom”, delivers an organic, evolving model of support engagement that expands eResearch (and teaching and stakeholder engagement) horizons.

This presentation will describe the approach and will report back findings and recommendations for the future implementation of a new ‘business as usual’ model for building and delivering technical expertise with and alongside researchers.

Symposium: 

eResearch NZ 2013 session type: 

Submitted by Tim McNamara on

Connecting Genetics Researchers to New Zealand eScience Infrastructure

The international explosion of genetic data means that genetics researchers are encountering increasingly large data sets, and are having to rely on computational methods when performing analyses. While there has been a corresponding increase in the availability of shared computing resources internationally, a major problem is that many genetics researchers are not computing experts, and are thus unable to easily access high-performance computing resources, despite the best efforts of those who administer such systems.

Symposium: 

eResearch NZ 2013 session type: 

Submitted by Tim McNamara on

New Zealand eScience Infrastructure's Experience as National Research Infrastructure

The New Zealand eScience Infrastructure (New Zealand eScience Infrastructure) provides High Performance Computing (HPC) and supporting services to New Zealand research communities. In the course of its first eighteen months, it has learned a great deal wishes to share some of its experiences. This presentation will provide an overview of e-infrastructure supporting the research system in New Zealand, New Zealand eScience Infrastructure’s role within that system and touch upon how that e-infrastructure system feeds into New Zealand’s innovation system as a whole.

Symposium: 

eResearch NZ 2013 session type: 

Submitted by Tim McNamara on

Myths vs Realities: the truth about open data

Open research data is gaining prominence as funders and governments increasingly require data as well as articles to be published and as new data journals launch to support this movement. Many researchers have reservations about publishing their own data, often concerned that doing so will be time-consuming, threaten their claim to their own IP, or not bring them any benefits. In reality preparing data with publication in mind can save time over the lifetime of a research project, IP issues can be managed, and publishing data brings increased citation and other advantages.

Symposium: 

eResearch NZ 2013 session type: 

Submitted by Tim McNamara on

Serving the long tail of eResearch

In this presentation we talk about our experience of seeing more and more cluster uptake from users who can't be considered traditional, 'pure' HPC users. Some of them use pre-installed and multi-core-optimized packages, some scale up their research by moving their compute from local laptops or small multi-core machines to the PAN cluster, often using less than 10,000 core hours a month but still doing research they would not be able to do without such compute infrastructure.

Symposium: 

eResearch NZ 2013 session type: 

Submitted by Tim McNamara on

Data transfer options in a research environment

This presentation discusses how to efficiently transfer data between sites. Unfortunately transferring data is not always trivial, it very much depends on the size of the files to be transferred, how many of them are there are, where it is located, and where it is supposed to go. Also: who is allowed to see it. We present an overview of several options that are available for researchers in New Zealand. Transfer protocols we will compare include: samba shares, ssh/scp/sftp, irods, and gridftp.

Symposium: 

eResearch NZ 2013 session type: 

Submitted by Tim McNamara on

Capturing the flux in Scientific Knowledge

Scientific knowledge is in constant flux and our own understanding continually evolves to accommodate and explain new observations, instances and facts. The continuous change or flux is an important and inescapable feature of scientific knowledge; however, it's still not captured and utilized in contemporary science practices.

Symposium: 

eResearch NZ 2013 session type: 

Submitted by Tim McNamara on

Science DMZ and New Zealand Genomics: A Demonstration in Network Agility

New genomics technology is transforming what biological and medical scientists can achieve – but it’s producing a serious amount of data that needs not only dedicated computing and data analysis resources, but also to move from place to place, across networks that are often “over configured” for requirements.

This demonstration will show how REANZ and NZ Genomics, implemented a Science DMZ, powered by Juniper Networks, to provide a network capable of far greater speeds for data transfer, through firewall bypass and reserved bandwidth speeds.

Symposium: 

eResearch NZ 2013 session type: 

Submitted by Tim McNamara on

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