December 2015 newsletter

News and events from NeSI, the New Zealand eScience Infrastructure.
Issue No. 25
December 2015
  • A message from the Director
  • Case Study: Software Carpentry in New Zealand
  • ResBaz hits NZ in 2016
  • eResearch NZ 2016
  • Join NeSI's team: Grow the computing and analytics capability of NZ researchers
  • Support over the holiday period
  • Access NeSI's HPC platforms
  • RDA 7th Plenary Meeting
  • Case Study: Ground-motion simulations of earthquakes in the North Island of New Zealand
  • Recent research outputs

A message from the Director

Our research system in New Zealand is evolving; as 2015 ends, NeSI completes a phase of significant change. Following on from a successful review and contract refresh with MBIE early last year, 2015 has seen NeSI reorganising as we adapt and enhance how we support research across New Zealand. NeSI now operates in a national team structure, and looks forward to introducing you to our new team and service innovations.

For the team, the year has culminated in last week’s annual team retreat. We spent two days reviewing progress and our plan of attack for 2016; new developments in High Performance Computing technology and the implications for research communities nationally; and welcoming our new team members. Admittedly we managed to squeeze orienteering into the mix, too.

The NeSI team post our forest orienteering adventure.

Reflecting on the year that has gone, it is reassuring to see increasing international evidence of the importance placed on research infrastructures by national governments. Earlier this month the Australian Government confirmed a decade of funding for science and innovation including $AUS 2.3 billion for research infrastructure. The intent of the plan is to drive greater risk taking and revitalise growth, through innovation and digital technologies. Mid year the Norwegian Government announced a package of investment totalling NOK 1.3 billion across research facilities, laboratories, scientific equipment and databases to lay a foundation for international cutting-edge research.

Locally, 2015 saw the release of the National Statement of Science Investment, with research infrastructures positioned as key Government ICT infrastructure investments, recognising ICT is transforming the way we work. Recognising the related digital skills deficit in research, NeSI piloted a new skills training initiative to lift researcher digital literacy. After this highly successful pilot, significant skills development activities are planned across New Zealand during 2016.

As NeSI moves to refresh essential high performance computation and analytics platforms early in 2017, the emerging convergence between HPC and Big Data sees NeSI moving to embrace research data, including support for related skills and methods. We look forward to working with institutions and research communities to prepare for these changes during 2016, and to ensure the research sector is well supported by essential digital infrastructure capabilities and skills.

Best wishes for your holidays, and for ringing in the new year.
Nick Jones, Director, New Zealand eScience Infrastructure

Case Study: Software Carpentry in New Zealand: The seed has been planted

Since 2014, after having identified a skills gap within the research community, NeSI has run a series of workshops to upskill researchers in digital research tools and methods. While modern research increasingly relies on computers, many researchers have inadequate training in computing and often resort to suboptimal solutions and tools.

As a national high-performance computing service provider, NeSI saw the need to support the growth of the computing capability of the New Zealand research community and, as such, became an official affiliate of the Software Carpentry Foundation. Read more

ResBaz hits NZ in 2016

The Research Bazaar (ResBaz) is a free-of-charge 3-day intensive conference where researchers from all disciplines and career stages can come together to up-skill with next generation digital research tools and skills. The purpose is to build a community that aims to equip researchers with the professional skills required to conduct cutting-edge research in the 21st century. Both Auckland and Dunedin will be hosting their own ResBaz’s on the 2-4th Feb 2016 and you should join in! 

At the core of ResBaz are Software Carpentry Workshops to teach basic skills for research computing. Software Carpentry workshops assume no prior programming experience, and build skills and confidence through hands-on training. ResBaz will also include various other sessions covering a broad range of other digital research skills topics*, along with many fun social and networking opportunities that encourage skills sharing, community building, and the creation of linkages that can last through participants careers.

ResBaz participants will also have the opportunity to shape the programme themselves in the form of an unconference - to have a say in highlighting, discussing, learning, or sharing skills or topics related to research or digital skills and tools that are increasingly important for research practice across the disciplines.

Places are limited so please head over to your respective city’s ResBaz site (Auckland and Dunedin) ASAP to register.


eResearch NZ 2016

It is eResearch NZ conference time again! eResearch NZ 2016 is being co-hosted by REANNZNeSI and NZGL. As a national forum for discussion, eResearch NZ aims to:
  • promote shared approaches to supporting eResearch needs
  • highlight current and emerging research priorities and trends
  • draw on experience from other regions
  • share work in progress and project outcomes.
eResearch NZ 2016 is being held in Queenstown from Tuesday 9 February to Thursday 11 February, 2016.  This year's conference theme is: eResearch Next Generation: Collaboration, Capabilities and Impact.  The deadline for submissions has been extended until January 13th with a variety of topics being covered including e-infrastructure, big data, data preservation and management and computational sciences.
For those of you who are interested in attending, we encourage you to register for the meeting and reserve your hotel rooms as quickly as possible. You can find information about accommodation on the conference website. 

We look forward to seeing you in Queenstown!

Join NeSI's team: Grow the computing and analytics capability of NZ researchers  

NeSI positions are currently available at the University of Otago and University of Auckland.

NeSI is offering unique opportunities to join a collaborative national team and work along side NeSI’s High Performance Computing (HPC) systems. We are currently recruiting for positions in Otago and Auckland. 

Join us as we continue to innovate and support the research community in New Zealand. In return we offer the chance to work for a group committed to HPC best practice and excellence.

New Zealand eScience Infrastructure is a collaboration of five research institutions, working in partnership with the Crown, providing HPC, analytics and consultancy services to the NZ Research sector, Government Initiatives/Agencies and Industrial Research.  NeSI’s primary aim is to grow the computing and analytics capability of researchers to ensure New Zealand’s future prosperity. Read more about available positions

Support over the holiday period

NeSI Support will be closed from 5:00 PM on Wednesday 23 December until 9:00 AM on Tuesday 5 January.

During the closedown period, we will continue to accept support requests. Requests received during the closedown period will be responded to by NeSI staff after normal operations resume on 5 January.

For emergency assistance during this period, please call 04 386 0900 to speak to our on-call technical staff, in addition to submitting a request to NeSI Support.

The NeSI team wish you a merry Christmas and an enjoyable and relaxing holiday.

Access NeSI's HPC platforms

All New Zealand researchers are invited to apply for access to New Zealand’s largest research computers. This call closes on Friday, 29 January 2016

NeSI's Access Policy outlines the terms and conditions for applying and how access is allocated. To better support NZ researchers, allocations of CPU core hours for Merit, Postgraduate and Proposal Development projects are provided at no cost.

RDA 7th Plenary Meeting

The 7th Plenary Meeting for the Research Data Alliance (RDA) is being held 1-3 March, 2016 in Tokyo, Japan.
The key theme for this meeting is “Making Data Sharing Work in the Era of Open Science”. Open science is fundamentally community driven and dependent on free knowledge sharing and access to tools and services. As an organisation of volunteers and self-formed collaboration, RDA is committed to promoting “openness” and delivering tangible outputs that improve data sharing across disciplines, technologies, and countries. Registration for the event is now open.  

Case Study: Ground-motion simulations of earthquakes in the North Island of New Zealand

Seismologist Yoshi Kaneko of GNS Science has used an advanced 3D wave propagation code on NeSI’s Power 6 supercomputer to simulate complex seismic wave propagation generated by earthquakes in the North Island of New Zealand.

With help from Dr Francois Bissey of NeSI’s Computational Science team, Yoshi and his research colleagues are trying to understand the influence of large-scale geological features, such as sedimentary basins, volcanic zones and stiffer subducted slab on the resulting surface ground motions.

Seismic waves generated by earthquake faulting in New Zealand travel through sedimentary basins, mountains, crust and deep subducted slab. By comparing simulated and observed waveforms recorded at seismometer stations, researchers can quantify their understanding of the crustal structure of New Zealand that was previously inferred from seismological and geophysical studies. Read more.

Recent research outputs

Below is a sample of research outputs that NeSI has been made aware of. To notify NeSI of upcoming publications, please email
  • The mechanism of industrial ammonia synthesis revisited: Calculations of the role of the associative mechanism. A. L. Garden and E. J. Skúlason. Phys. Chem. C 10.1021/acs.jpcc.5b08508
  • Inferring epidemiological dynamics with Bayesian coalescent inference: the merits of deterministic and stochastic models. A. Popinga, T. Vaughan, T Stadler and A. J. Drummond. Genetics 10.1534/genetics.114.172791
  • Signatures of the Very Early Universe: Inflation, Spatial Curvature and Large Scale Anomalies. G. Aslanyan and R. Easther. Phys Rev.
  • Target profiling of an antimetastatic RAPTA agent by chemical proteomics: relevance to the mode of action. M. V. Babak, S. M. Meier, K. V. M. Huber, J. Reynisson, A. A. Legin, M. A. Jakupec, A. Roller, A. Stukalov, M. Gridling, K. L. Bennett, J. Colinge, W. Berger, P. J. Dyson, G. Superti-Furga, B. K. Keppler and C. G. Hartinger. Chem. Sci10.1039/C4SC03905J 
If you would like to be kept up to date with research outputs as NeSI includes them, please join our Mendeley group.

Have a question?

If you would like to ask anything, please email us