Research Projects using the BeSTGRID Data GRID

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[edit] Auditory Scene Analysis

Project Lead
Dr Michael Hautus, Psychology, Senior Lecturer, tel: 85924
Usage
40 GB of DataGrid, FTP server account
Project Description

Dr Hautus (University of Auckland) and Dr Johnson (Macquarie University) are collaborating on a project to elucidate some of the brain mechanisms underlying the separation and assignment of auditory stimuli to auditory objects; sometime referred to as auditory scene analysis. This requires the collection of electrophysiological data (EEG, fMRI, and MEG) which needs to be accessed by the teams working at Auckland and Macquarie.


[edit] Grid Enabled Internet instruments

Project Lead
Peter Komisarczuk
Usage
40 GB of DataGrid, FTP server account
Project Description

This project located at Victoria University of Wellington is investigating the use of grid computing for instrumenting the Internet and analysing the data from the deployed sensors. Currently we have been investigating the use of the Grid for Internet Background Radiation (IBR) analysis, client honeypot deployment enhancement using Grid workflows.


[edit] Network Design and Simulation Group

Project Lead
Nick Jones
Contacts
Dr Michael O'Sullivan and Dr Cameron Walker
Usage
1 TB of Datagrid, VM
Project Description

Drs Walker and O'Sullivan have been actively collaborating on automatic SAN Design since 2001. They have developed new mathematical programming formulations for SAN design and pioneered new techniques for solving these formulations. They have published their research in international journals and presented at international conferences. As consultants for HP Labs they developed software for the automatic reprovisioning of SANs in 2002. They have also generated Core-Edge SAN designs for the Content Management System (CECIL) at the University of Auckland.
Currently they are extending this research to include simulation of SANs for evaluation purposes.


[edit] Austronesian Basic Vocabulary and Bantu Language Databases

Project Lead
Prof Russell Gray, Psychology, tel: 88525
Assistant
Simon Greenhill, Psychology, Assistant Research Fellow, tel: 85506
Usage
.5 TB, VM
Project Description
  • Austronesian Basic Vocabulary Database: This database contains 125,000 lexical items from 580 languages spoken throughout the Pacific region. These languages all belong to the Austronesian language family, which is the largest family in the world. It contains between 1,000 and 1,200 languages.
  • Bantu Language Database: This database contains 2,388 lexical items from 6 Bantu languages
www 
http://language.psy.auckland.ac.nz/

[edit] Ecology and Animal Behaviour

Project Lead
Dr Stuart Parsons, Biological Sciences, Senior Lecturer, tel: 85322
Usage
1 TB
Project Description
  • Acoustic identification of bats - a collaboration with Humboldt State University, funded by the US department of Defense. The project requires the exchange of large sound files between Auckland and Humboldt as well as storage of large (high sample rate) sound files
  • Acoustic identification of birds - a collaboration with Humboldt State University, funded by the California Department of Transport. The project requires the exchange of large sound files between Auckland and Humboldt as well as storage of large (high sample rate) sound files.
  • Underwater noise levels in Milford and Doubtful Sounds - a collaboration between SBS, Physics and NIWA, funded by the Department of Conservation. The project requires space to store and exchange large sounds files containing underwater noise recordings.

[edit] Human Immunology

Project Lead
A/Prof Rod Dunbar, Biological Sciences, tel: 85765
Tech Contact
Oliver Horlacher
Usage
1 TB
Project Description

[edit] NZ NEES @ Auckland

Project Lead
Assoc. Prof. Jason Ingham, Civil & Environmental Engineer, tel: 87803
Usage
2 TB
Project Description
  • New Zealand Network for Earthquake Engineering Simulations, a network for collaborative Earthquake Engineering research to mitigate the impacts of earthquake related effects.
  • A project with research partners from United States, United Kingdom, Taiwan and China.
  • The remote controlling and participation of experiments requires a large volume of numeric and video data to be exchanged in real time.
  • Focus areas of research include: Integrated structure-foundation design of bridges, Self-centering structural systems and Distributed hybrid testing.

[edit] New Zealand Biomirror

Contact
Peter Tsai, Biological Sciences, tel: 83777
Usage
5 TB
Project Description

Bio-Mirror is a public bioinformatics service in New Zealand for high-speed access to up-to-date DNA & protein biological sequence databanks. In genome research, these databanks have been being growing tremendously, so much that distribution of them is hampered by existing Internet speeds. The Bio-Mirror project is devoted to facilitate timely access to important large data sets for this research. High speed access is provided by Internet2 infrastructure of the Very High Speed Backbone Service (vBNS), Abilene, TransPAC, the Australian Academic Research Network (AARNet) and the Asia-Pacific Advanced Network (APAN).

Using Standalone BeSTGRID BLAST Server for high-speed search of GenBank (a database of protein sequences).

www
http://www.biomirror.org.nz/
ftp
ftp://biomirror.auckland.ac.nz/

[edit] SBSBS project of Laboratory of Structural Biology

Project Lead
Prof Ted Baker, Biological Sciences, tel: 84415
Contact
Dr Neil Paterson, Biological Sciences
Usage
2 TB
Project Description

Research at the Laboratory of Structural Biology focuses on the central importance of three-dimensional structure in biology. Our multidisciplinary approach to biological questions includes research in structural genomics, structure-based drug design, protein engineering, and structure determination by X-ray crystallography and NMR.

The laboratory forms a central part of the Maurice Wilkins Centre of Molecular Biodiscovery, one of seven New Zealand national Centres of Research Excellence


[edit] Passive DNS

Project Lead
Bojan Zdrnja, ICT Security, ITS
Usage
1 TB, VM
Research

Our sensors are deployed at various networks around the world. The sensors passively parse network traffic and collect all authoritative DNS responses. All responses are sent to a central collector which stores them into a database. The information collected include the query, response, resource record type, TTL, timestamp and the sensor that collected this information. The database also stores first seen and last seen time stamps.

This allows us to do various analysis on the collected data. As the database stores all historical information about the seen DNS records, we are working on a reputation based system for certain domains and/or IP addresses, based on their history. Besides this, it is possible to correlate information received from various sensors so we can see geographical spread of DNS responses. Collected information can easily identify fast-flux hosts; this can help with analysis of security incidents.

Technical Description

DNS data is captured passively by sensors at the network edge, using an architecture designed to make implementation of sensors as simple as possible. A sensor is connected to a router SPAN port in order to get complete access to all network traffic. Sensors run tcpdump, configured to write captured packets to a pcap file. Since we are only interested in DNS messages, we used the following tcpdump filter:

udp port 53 and ( udp[10] & 0x04 != 0 )

Note that our filter only captures UDP DNS replies from authoritative sources, since we filter on their "Authoritative Answer" bit. We ignore TCP (for now) to simplify our parsing code, and because we observe relatively little TCP DNS traffic at the router. Since DNS replies always include the query data (in the Question section), there is little need to also collect DNS queries. Alas, our filter can cause some problems on certain large responses. If the DNS reply is larger than the path MTU, the UDP message will be fragmented. If that occurs, the first fragment usually contains enough information for anomaly detection.

Since our sensor is placed at the network perimeter, we see two types of DNS responses: those destined for the University's local caching resolvers, and responses leaving the University's own authoritative nameservers. The former are most interesting for our purposes here, but we did not attempt to filter out the latter from our database.

The sensors have a cron job that runs every hour. First, a new tcpdump process is launched. Then, the existing tcpdump process is killed. The pcap file containing data from the previous hour is compressed and sent to the collector.

Our database resides on the collector. The database holds only collected DNS data relevant for our research. The relevant data includes:

  • Query name (name of the original query)
  • Resource Record (RR) type (query type, ie A for address records)
  • Resource Record data (answer returned by the authoritative DNS server)
  • TTL (Time To Live) - value in seconds, set by the authoritative server, that allows the client DNS server or resolver to cache the answer
  • First Seen Timestamp - timestamp showing when the sensor first saw this record
  • Last Seen Timestamp - timestamp showing when the sensor last saw this record
  • Sensor ID - ID of the sensor showing its geographical location

Rows in the database correspond to resource records in the Answer section of the DNS reply. We do not store records from the Authority or Additional sections. Incoming pcap files are preprocessed by a program that unpacks the DNS messages and removes any duplicate entries. Duplicates typically occur for popular names with short TTLs. Since the only timestamp in our database is the First Seen column, a duplicate answer does not update the database and can be safely discarded. After all the new pcap files have been properly parsed, the program imports the data to the database.


[edit] Quantum Optics

Project Lead
Prof Howard Carmichael, Physics, tel: 88899
Assistant
Dr Levente Horvath
Usage
100 GB
Project Description
  • Quantum stochastic processes for composite systems: It is an area of quantum optics that studies correlations and entanglement of quantum states where stochastic processes are important. Apart from the basic understanding of light and matter interactions, this area is important for quantum information.

[edit] Whole Genome Association Studies

Project Lead
Dr. Sharon Browning, Statistics, Senior Lecturer, tel: 88745
And
Dr. Brian Browning, Statistics, Research Fellow , tel: 88745
Usage
2000 GB
Project Description
  • Whole genome association scans involve genotypes on genetic markers spanning the human genome in large numbers of individuals with and without a disease, with the aim of identifying genetic variants responsible for increasing disease risk. The Wellcome Trust Case Consortium data consist of 500,000 genotypes per individual on 19,000 individuals, with associated quality scores and other relevant information.

[edit] Ocean Biogeographic Information System (OBIS)

Project Lead
A/Prof Mark J. Costello, Leigh Marine Research Centre, Associate Professor, tel: 83608
Usage
OBIS virtual machine on Pleyads, 20GB of disk space.
Project Description
  • OBIS publishes data on behalf of scientists from government agencies, museums, universities, commercial companies, and non-governmental organisations. OBIS is always seeking new contributors.
  • OBIS is a marine biogeographic information system, meaning that we concentrate on datasets that record particular species (or higher taxonomic group) from particular marine locations, at particular times. At present, we can only publish data where the locations are recorded as latitude and longitude, not as place names. Our focus is on high taxonomic quality, so datasets where organisms have been identified by professional or trained biologists are our priority. In the near future, we will be expanding to take in environmental datasets (i.e. coverage of physical, chemical, and geological parameters) that are relevant to understanding the distribution of species. So we are interested in hearing from potential contributors of these datasets, and welcome your contact, but are still in the process building this facility.
www
http://www.iobis.org

[edit] The Polyhedrin Project, School of Biological Sciences

Project Lead
Assoc Prof Peter Metcalf, Biological Sciences, tel: 84810
Usage
500GB
Project Description
  • The polyhedrin project is an international research collaboration based in Auckland involving research groups in Japan and Switzerland. The project was established in November 2002 with the initial aim of determining the atomic structure of cypovirus polyhedra, tiny micron-sized protein crystals produced inside cells of silk worms infected with this virus. The micro-crystals are formed from the viral protein polyhedrin and contain virus particles embedded within a crystalline lattice of polyhedrin molecules. The virus containing micro-crystals are remarkably stable and can remain infectious in the environment for years after the death of the infected silk worms. The initial aim of the project was accomplished in mid-2006 and the results published in the prestigious journal Nature in March 2007. The cypovirus atomic structure is important because it enables protein engineering methods to be used to develop the micro-crystals into a range of stable protein based devices, including stabilized enzyme chips, biosensors and stable micro-containers for vaccine delivery.
  • The specific aims of the research currently being carried out by the collaborators include the atomic level analysis of engineered cypovirus micro-crystals and the determination of the atomic structure of related micro-crystals produced by other insect viruses. In this work, the engineered cypovirus micro-crystals are provided by the laboratory of Professor Hajime Mori at the Kyoto Institute of Technology and preliminary analysis of these and other samples is carried out in Auckland. Protein crystallography experiments are carried out using the specialize micro-X ray beam at the Swiss Light Source synchrotron near Zurich, where we work in collaboration with the group of Clemens Schulze-Briese. These experiments produce large amounts of data (currently ~50 GB per trip, two or three times per year) and arranging convenient international access and secure storage has become a significant problem. BeSTGRID is expected to provide an ideal solution for our data storage/access requirements.

[edit] DING Proteins

Project Lead
Dr. Ken Scott, Biological Sciences, Senior Lecturer, tel: 88240
Contact
Andrew Suh, Biological Sciences, Teaching Assistant
Usage
500GB
Project Description

DING proteins are a family of proteins with the characteristic DINGGG- N-terminus. They have been isolated from species of all kingdoms and the proposed biological functions of the various members differ greatly. DING proteins may have roles in some of the most prevalent human diseases including rheumatoid arthritis, kidney stone disease, atherosclerosis, cancer and HIV.

Our lab is currently working on the structure-function relationship of DING proteins from various Pseudomonas species. Work on eukaryotic DING isolates may provide potential therapies for a number of human diseases such as breast cancer. Genetic identification of eukaryotic DING genes is also a priority as this may allow early diagnosis of the noted diseases.


[edit] Molecular mechanisms of learning and memory

Project Lead
A/Prof Nigel Birch, Biological Sciences, tel: 81978
Contact
Victor Borges, Biological Sciences, Technician
Usage
2000GB
Project Description

One of the many intriguing questions in the neural sciences is: How are memories stored within the brain? Eric Kandel (Nobel Laureate, Kandel, 2001) stated “One of the most remarkable aspects of an animal’s behaviour is the ability to modify that behaviour by learning, an ability that reaches its highest form in human beings”. Many neurobiologists now strive to understand these important cognitive phenomena at the molecular level. We are interested in molecules that are expressed in the developing and adult nervous system which modulate nerve cell morphology and connectivity. Our approach is to manipulate levels of gene expression in cultured neurons, capture the changes by high resolution imaging of fixed and live cells, and then quantify the changes using image analysis software tools.


[edit] The Microarray facility

Contact
Liam Williams, Biological Sciences, Technician, tel: 87653
Usage
400 GB
Project Description

The Microarray facility is part of the Centre for Genomics and Proteomics in The School of Biological Sciences. It provides gene expression and genotyping services to public and private researchers.


[edit] Antarctica Research Projects

Contact
Dr Craig Millar, Biological Sciences, Senior Lecturer , tel: 85186
Usage
200 GB
Project Description

Dr Millar collaborates extensively with Prof David Lambert with his CoRE research focussed in two areas:

The determination of evolutionary and mutation rates in Adelie penguins from the Antarctic. They have used ancient DNA from well preserved Adelie penguin remains in Antarctica to directly measure the rate of DNA evolution. This novel approach has allowed accurate and precise estimates of the rate of evolution. Their present objective is directed at estimating a mutation rate in Adelie penguins. These data in combination, with their earlier estimates of evolutionary rates will provide the first empirical test of neutral theory.

The molecular ecology of the endangered Chatham Island Taiko. The Chatham Island Taiko is one of the world's rarest seabirds and we are using a range of DNA basd techniques to investigate its breeding ecology. Specifically they are investigating the relationship between genetic variation and extinction.


[edit] Cortical and sub-cortical processing of visual information

Contact
Dr Ben Thompson, Optometry & Vision Science, Lecturer, tel: 86020
Usage
500 GB
Project Description

Dr Thompson (University of Auckland) is working in collaboration with research teams in Canada (Prof Robert Hess, McGill University, Prof Christian Casanova, University of Montreal) and the USA (Prof Zili Liu, UCLA, Drs Allan Wu and Yoon-Hee Cha, UCLA) on projects exploring the function of visually responsive areas of the human brain. These projects employ functional magnetic resonance imaging (fMRI) to measure neural function, a technique that generates large data sets which need to be accessible to all members of the research team.


[edit] Microbial Ecology and Genomics

Contact
Duane Knight, Biomedical Science Division, Operations Manager, tel: 81944
Usage
200 GB
Project Description

The project is aligned with the Microbiology and Virology Research Group, based in the School of Biological Sciences at the University of Auckland.

An aim is to combine the disciplines of microbial ecology, genomics and bioinformatics to address fundamental questions about microbial community structure and function in natural and industrial settings.


[edit] Proteomics and Biomedicine

Contact
Dr Shaoping Zhang, Engineering Science, Senior Research Fellow, tel: 86265
Contact
Cynthia Tse, Biological Sciences, Research Manager, tel: 87394
Usage
100 GB, Samba
Project Description

The research interests of the Proteomics & Biomedicine Research group, led by Professor Garth Cooper, include diabetes, cardiovascular and other metabolic diseases, human immunology, and neurodegenerative disorders.

Garth Cooper’s group has made major advances in the understanding of disease mechanisms in diabetes and related syndromes such as obesity and cardiovascular disease, and based on these mechanisms, to the development of effective new strategies for disease detection and therapy, with an emphasis on prevention of progression. Our group has developed an orally-active molecule which we recently identified and demonstrated to reverse cardiovascular disease in diabetes through regeneration of the diseased heart and arteries.

Kerry Loomes’ group is interested in myo-inositol oxygenase (MIOX), which is involved in the breakdown of inositol compounds, and whose activity is increased in diabetes. The research has collaborative outreach into structural biology and synthetic chemistry areas and offers a platform for new therapeutic strategies for diabetes.

Rod Dunbar's team focuses on human immunology. A core project is the design and testing of peptide-based vaccines to stimulate T cells. These vaccines have applications as both therapeutic vaccines for cancer and preventative vaccines for infectious diseases.

Studies by Shiva Reddy's group focus on the identification of the cellular and molecular processes which underlie destruction of the insulin-producing beta cells during autoimmune type 1 diabetes, and to development of potential therapies which may protect beta cells during the early stages as well as promoting beta cell regeneration after disease onset.

Russell Snell’s group aims to unravel the molecular mechanisms of simple and complex neurodegenerative disorders such as Huntington’s disease, Alzheimer’s disease, Parkinson’s disease and Spinocerebellar ataxia. Utilizing knowledge of causal genes and their pathways, we are developing model systems with which to investigate the molecular pathogenesis of these disorders and ultimately to screen for and test potential therapeutic agents.


[edit] Plant Molecular Science

Contact
Dr Karine David, School of Biological Sciences , tel: 83793
Usage
100 GB, Samba
Project Description

The Plant Molecular Science Research Group comprises members of the School with primary research interests in molecular aspects of plant science. Current interests of members of the group focus on the following topics: the molecular function of genes involved in flowering control; the structure, function, biosynthesis and evolution of plant cell walls; wine yeast genetics; magnesium transporters and aluminium tolerance; hormone signalling, regulation of cytokinesis and molecular plant taxonomy and biogeography.

Karine's group is investigating the early events of auxin signalling. Auxin is one of the major plant hormone implicated in virtually every aspect of plant growth and development. Despite its established biological and agronomic importance, the molecular mechanisms underlying the auxin early response remain unclear.

Karine is particularly interested in the auxin extracellular receptor ABP1 (Auxin-binding protein 1), an essential membrane-bound protein that control early events in auxin signalling.


[edit] Fish Sensory Biology

Contact
Prof John Montgomery, Leigh Laboratory, Marine Sciences , tel: 83611
Usage
100 GB, Samba
Project Description

Fish have a range of interesting sensory systems in addition to vision. These include the mechanosensory hearing and lateral line systems, and in some fishes, a system to detect weak electric fields. Our research has covered a wide range of fishes, from nocturnal sharks and rays, and Antarctic fish which feed in winter darkness, to New Zealand native freshwater fish and coastal reef fishes. We use field and laboratory studies to understanding the natural history and behavior of these fish and neurophysiology to investigate the underlying neural and sensory basis of these behaviors - an approach known as neuroethology (web address). In a collaborative study with David Bodznick at the Woods Hole Marine Biological Laboratory we have been examining the hindbrain processing of electrosensory information, which allows rays to distinguish between their own electric fields and the fields of their prey. We have demonstrated a sophisticated adaptive filter which learns to cancel any input associated with the animal's own movement.

Many interesting and important fish behaviors, such as migration, habitat selection, and feeding, involve sensory biology. We are putting our knowledge of sensory biology to use by contributing to a range of applied problems in freshwater and marine fish biology and fisheries. Of recent note is our work on the use of acoustic clues for pre-settlement reef fish to find their way back to the reef.


[edit] Cetacean societies in the South Pacific

Contact
Dr Rochelle Constantine, School of Biological Sciences, tel: +64 (0)9 373-7599 ex 85093, Fax: +64 (0)9 373-7417
Usage
500 GB, FTP, Samba
Project Description

In late 1993 the group began to study the population size, ranging behavior, social associations, genetic relatedness and demographics of whale and dolphin populations. In NZ there are two long-term research projects, 1) the bottle-nose dolphins in north-eastern New Zealand waters and effects of tourism on this population, and 2) Bryde’s whales in the Hauraki Gulf. Both of these projects use photo-ID to track individuals and also molecular markers to understand their population genetics and relatedness.

Since 1995 the team has worked in collaboration with Prof. Scott Baker and the South Pacific Whale Research Consortium. This research focuses on the endangered humpback whales throughout the South Pacific and has concentrated on using capture-recapture methods to determine population size and ranging behavior, molecular markers to understand the genetic relatedness of these recovering populations of whales and acoustics in collaboration with Dr Mike Noad at the University of Queensland. Most of this research relies on collaborations with a number of scientists both in New Zealand and overseas, government agencies, tour operators and non-government organizations.

Underpinning all whale studies is a large database of individual whales and whale groups defined by photographic and genetic identification methods correlated with distribution maps. Such identification methods form part of a global whale database requiring the large file storage capacity of BeSTGRID.


[edit] Information processing in the human brain

Image:rccn.jpg

Contact
Assoc Prof Ian Kirk, Department of Psychology, Phone: +64 9 3737599 x88524(office) x88421(Lab)
Usage
1000 GB, FTP, Samba
Project Description

The Research Centre for Cognitive Neuroscience (RCCN) is based within the Department of Psychology at the University of Auckland, New Zealand. The Centre comprises members of staff and graduate students with a common interest in determining the biological bases of mental events in humans. The research conducted by members of the RCCN is diverse, ranging from basic research on cognition and perception, to understanding the neural bases of cognition in healthy adults, to clinical research investigating neural and neuropsychological function in various patient populations. Our research programmes utilize a variety of neuroimaging, cognitive and neuropsychological approaches.

The purpose of the Centre is to encourage collaborative research, and so increase the likelihood of receiving substantial research funding. The Centre also holds regular research meetings. It is hoped that graduate students working with members of the Centre will benefit from the range of expertise provided, and will themselves contribute to its communal activities.