Position Details
Job Title:
CSIRO Undergraduate Vacation Scholarships – Health & Biosecurity
Reference No:
2103
Classification:
CSOF1.1
Stipend:
$1462.77 per fortnight
Location:
Please refer to the List of Projects at the end of this document
Tenure:
8 to 12 weeks from November 2015 to February 2016
Role Purpose:
The 2015/16 Vacation Scholarship Program is designed to provide students
with the opportunity to work on real-world problems in a leading R&D
organisation.
Participation in the Vacation Scholarship Program has influenced previous
scholarship holders in their choice of further study and future career options.
Many have gone on to pursue a PhD in CSIRO or to build a successful
research career within CSIRO, a university or industry.
Project
Description:
How to Apply:
Please refer to the list of Projects on the following pages of this document.
If you require further information please contact the person listed as the
contact for the project.
Please apply for this position online at www.csiro.au/careers
You will be required to:
1. select your top 2 research projects in order of preference;
2. submit a CV which includes:

the reasons why the research project/s you have selected are of
interest to you; and how your previous skills/knowledge and
experience meets the project requirements; and

an outline of your longer-term career aspirations and detail
how this program will help you achieve them.
3. upload your academic results.
Referees: Please ensure that your resume includes the name and contact
details of your academic supervisor and at least one other referee (work or
university).
If you experience difficulties applying online call 1300 984 220 and someone
will be able to assist you. Outside business hours please email: csirocareers@csiro.au.
Please do not email your application. Applications received via this method
may not be considered.
About CSIRO:
The Commonwealth Scientific and Industrial Research Organisation (CSIRO)
is Australia’s national science agency. At CSIRO we shape the future. We do
this by using science to solve real issues. Our research makes a difference to
industry, people and the planet.
Project
Number
H&B01
Health and Biosecurity Flagship - Vacation Scholarships Project Details
Project Title
Are feral honeybees healthier?
Project Description
This project will involve collecting honeybees from feral nests and testing for several
honeybee pathogen using genetic markers. Pathogen levels will be compared with those
of local managed honeybees.
Project Duties/Tasks


Identify and collect samples from feral honeybee colonies
Use genetic markers to test for honeybee pathogens
Relevant Fields of Study

Molecular biology
Location: Black Mountain, ACT
Contact: Dr John Roberts on (02) 6246 4019 or email john.roberts@csiro.au
H&B02
Project Title
Disease tolerance in honeybees
Project Description
This project will involve exposing different genetic lines of honeybees to viruses in lab
assays to investigate variation in disease tolerance.
Project Duties/Tasks

Isolate and genetically analyse honeybee viruses

Conduct lab infection assays with honeybees
Relevant Fields of Study
 Molecular biology
Location: Black Mountain, ACT
Contact: Dr John Roberts on (02) 6246 4019 or email john.roberts@csiro.au
H&B03
Project Title
Mobile Application for Biosecurity Data Collection
Project Description
Effective biosecurity management relies on digitalised biosecurity data collection and
management. The student is expected to develop a mobile-based application for
biosecurity data collection.
Project Duties/Tasks



Investigate existing approaches on mobile application development
Design mobile interface for biosecurity data collection
Implement the mobile application
Relevant Fields of Study
Strong JAVA and JaveScript programming, with experience in user interface design and/or
some mobile application development a plus
Location: Sandy Bay, Tasmania
Contact: Dr Qing Liu and via phone on (03) 6237 5698 or email Q.Liu@csiro.au
H&B04
Project Title
Evaluation of plant pests and pathogens impact using internet and social media metrics
Project Description
This project will attempt to assess whether different measures of electronic interactions
can be related to actual impacts where there is data, with the aim of using them as
predictors where there is no data. For example, is the nuber of web pages found on a
search under the scientific name of an organism sufficient or is the common name better?
Are the terms “pest” or “damage” necessary as well? Is a crop name required? Is the
number of twitter threads better?
Project Duties/Tasks







Critically research background of using electronic statistics to assess social
phenomena (Daniel Watts) and produce summary of methods and supporting
evidence
Research availability and reliability of data on economics of pests and pathogens
on official lists (supplied), consult experts for ground truthing
Continue research and produce summary
Decide electronic media search sources and search strategies (what to search,
what terms and what metrics (eg pages, hits, traffic, threads etc) and commence
data collection
Data collection; produce summary
Analyse relationships between different measures of impact
Write report; presentation of report and feedback
Relevant Fields of Study
Biology/ecology, however other disciplines considered.
Location: Black Mountain, Canberra
Contact: Dean Paini on (02) 6246 4178 or email Dean.Paini@csiro.au
H&B05
Project Title
The Digital Doctor: predict adverse drug reactions from a patient’s genome
Project Description
Drugs that are usually safe can cause severe adverse reactions in patients with a particular
genotype. This project aims to validate genomic markers for drug toxicity in whole
genome sequencing data from the 1000 genomes project. The analysis will contribute to
a journal publication detailing the application of pharmacogenomics markers in Australian
clinical practice.
Project Duties/Tasks



Compare genotype information of pharmacogenomics markers with the LDderived exonic surrogate markers as well as imputed genotypes
Summarize and visualize comparison results
Contribute towards manuscript
Relevant Fields of Study




Bioinformatics
Information Technology
Biostatistics
Computational Biology
Location: North Ryde, Sydney NSW
Contact: Denis Bauer on (02) 9325 3174 or denis.bauer@csiro.au
H&B06
Project Title
Tele-Medicine based clinical decision support system for sight threatening eye disease
Project Description
In this project, we will be developing image analysis and machine learning algorithms for
early detection of eye disease such as diabetic related eye disease. The algorithms
developed and properly validated will be integrated into an electronic health record
system or a telemedicine system for use in the field in hospitals to screen for sight
threatening eye diseases.
Project Duties/Tasks



Develop image processing algorithms and machine learning techniques for
detection of retinal pathologies (e.g. bright lesions) related to diabetic retinopathy
and other retinal diseases
Validation of algorithms based on a large retinal image data set
Build an end-user program which could be integrated into our Remote-l
telemedicine system
Relevant Fields of Study




Signal processing
Image processing
Biomedical engineering
Software engineering
Location: Perth, WA
Contact: Dr Di Xiao on (08) 9333 6147 or Di.Xiao@csiro.au
H&B07
Project Title
Mobile Health for diabetes
Project Description
In this project we intend to review and summarise users’ feedback on mobile apps for
diabetes. The aim of this research is to identify the most important features and
functions of mobile health apps from consumer’.
Project Duties/Tasks



To search for diabetes related mobile apps (for iOS, android, or both) and select
the best ones
To extract and summarise user’s feedback on the selected apps
To qualitatively research the findings using content analysis and thematic mapping
techniques
Relevant Fields of Study





Marketing
Management
Public Health
Psychology
Medicine (prior experience with qualitative research is an advantage)
Location: Herston, Brisbane, Qld
Contact: Farhad Fatehi on (07) 3253 3617 or farhad.fatehi@csiro.au
H&B08
Project Title
Identification of biomarkers associated with early identification of Alzheimer’s Disease
Project Description
In an effort to identify biomarkers for the early detection of Alzheimer’s Disease, the
current project aims to investigate over 1000 protein markers from both Australia and
overseas. Once the most informative biomarkers have been identified, graphical network
analyses will be compared with Gene Ontology (G.O.) pathway information to assess their
functional significance.
Project Duties/Tasks

Conduct feature selection analyses of biological data related to Alzheimer’s
Disease
 Conduct graphical network analyses and compare results with G.O. pathways
available online
 Contribute towards manuscript with results identified
Relevant Fields of Study
 Biostatistics
 Mathematics
 Computational Biology
 Statistical Genetics
Location: Herston, Brisbane, Qld
Contact: James Doecke on (07) 3253 3697 or james.doecke@csiro.au
H&B09
Project Title
Enhance and optimize the performance of automatic diabetic retinopathy grading
algorithm in our tele-medicine software
Project Description
This project will involve improving our image processing routines that analyse retinal
images. The student will work on optimizing the algorthyms within our tele-medicine
system to reduce the time it takes in processing the images and providing initial grading to
our clinical users.
Project Duties/Tasks
 Investigate the use of various computer science techniques in the existing
software, including parallel processing and multi-threading (e.g. using
boost/openMP)
 Utilising GPU for faster image processing (e.g. using CUDA libraries)
 Work with our tele-medicine platform (Remote-l) to integrate the new grading
algorithm
 Re-write existing C++ code in Python
 Time permitting we will also investigate the use of cloud computing platforms such
as Google’s or Amazon to investigate potential to move the grading to a cloud
based system
Relevant Fields of Study
 Signal processing
 Image processing
 Biomedical engineering
 Software engineering
Location: Floreat, WA
Contact: Janardhan Vignarajan on (08) 9333 6132 or janardhan.vignarajan@csiro.au
H&B10
Project Title
Early identification of need for surgery for Crohn’s Disease
Project Description
Investigate the magnetic resonance enterology (MRE) biomarkers from participants with
Crohn’s disease to identify markers of inflammation that associated with surgery. Using a
combination of clinical phenotype information with the MRE data, the project aims to
identify those individuals that are at risk of needing surgery so that early intervention
maybe provides as an alternative.
Project Duties/Tasks



Identify those MRE biomarkers that are associated with inflammation leading to
surgery
In addition to the MRE markers, find associated clinical phenotype markers that are
also predictive of surgery
Write a report from work conducted that will be used to contribute to a journal
publication
Relevant Fields of Study




Biostatistics
Mathematics
Medical science
Medical imaging
Location: Herston, Brisbane, Qld
Contact: Jason Dowling on (07) 3253 3634 or jason.dowling@csiro.au
H&B11
Project Title
CSIRO Health Diet Score
Project Description
The CSIRO Healthy Diet Score allows Australians to measure the quality of their eating
habits using a simple online assessment tool. This project will see the development of the
next generation tool for the CSIRO healthy diet score. The project will produce a mobile
app that will use of smart phone features to gather information and will provide users
with recommendations for products that will help them to improve their health.
Project Duties/Tasks



Work with domain experts to develop requirements including novel food recall
techniques
Develop mobile prototype (iOS/Android/HTML5)
Conduct user testing
Relevant Fields of Study


Computer science
Computer engineering
Location: Marsfield, NSW
Contact: Jill Freyne on 02 9372 4453 or email jill.freyne@csiro.au
H&B12
Project Title
Health indicator for grocery shopping
Project Description
This project will develop a persuasive tool to help shoppers understand their grocery
shopping. The tool will combine purchase data with nutrition information to raise
awareness of the food choices. The candidate would work with technical, behavioural
science and nutrition experts to design and develop the tool.
Project Duties/Tasks



Work with domain experts to develop requirements
Develop mobile or web prototype
Conduct user testing
Relevant Fields of Study


Computer science
Computer engineering
Location: Marsfield, NSW
Contact: Shlomo Berkovsky on 02 9372 4235 or email shlomo.berkovsky@csiro.au
H&B13
Project Title
Foetal Brain Development – 3D MRI reconstruction and analysis
Project Description
Fast Magnetic Resonance Imaging (MRI) sequences enables acquiring stacks of 2D images
of the foetus in-utero. However, because of the constant foetal motion, random
displacement occurs in-between images, and reconstructing an accurate 3D volume for
quantitative evaluation is challenging. Novel super-resolution techniques combine N
stacks of low resolution MRIs and remove the effect of random displacements to produce
a motion free high-resolution 3D reconstruction. This project will involve building a
reliable 3D foetal imaging workflow that is useful for our clinical partners.
Project Duties/Tasks

Building a reliable 3D foetal imaging reconstruction workflow using recent open
source and in-house software tools (C++ or Bash or Python)

Adapting, optimizing or writing new software modules to adapt the reconstruction
method to the images provided by our clinical partners (C++ and/or CUDA)

Analyse the accuracy of the proposed solution
Relevant Fields of Study




Medical physics
Computer science
Software engineering
Biomedical engineering
Location: Herston, Brisbane, Qld
Contact: Jurgen Fripp on (07) 3253 3660 or email jurgen.fripp@csiro.au
H&B14
Project Title
Neuroimaging Analysis and Executive Functions
Project Description
This project will examine the relationship between behavioural presentations of three
syndromes characterized by executive dysfunction (disinhibited, apathetic and
dysexecutive) and functional neuroimaging measures using the resting state FDG-PET
amongst older adults. The vacation scholar will learn about the analysis of the
neuroimaging data, and the administration, scoring and interpretation of
neuropsychological tests.
Project Duties/Tasks

Data collection and involvement in the neuropsychological tests

Developing the current statistical analysis platform in R/python/C++

Analysing the correlation between neuroimaging and psychometric data

Documentation, preparation of scientific/technical report, or an conference
abstract
Relevant Fields of Study




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Computer science
Electrical engineering
Mathematics
Statistics
Psychology
Neuroscience
Location: Hollywood Private Hospital (Offsite, WA)
Contact: Kaikai Shen (08) 6298 6313 or email Kaikai.Shen@csiro.au
H&B15
Project Title
Neuroimaging Analysis at Ultra High Fields
Project Description
This project will involve developing software and analysis techniques to segment the brain
and calculate the thickness of the cortex from very high resolution MR data acquired at
the University of Queensland on their new 7T MRI scanner. In addition, the project will
extract myelin and T2* surface maps of the brain.
Project Duties/Tasks

Customize and extend MilxView’s C++ neuroimaging software to accurately
segment and calculate cortical thickness from very high resolution MR data.

Support anatomist in performing manual analysis and validation of software.

Write technical report on results.
Relevant Fields of Study



Computer science
Electrical engineering
Mathematics
Location: Herston, Brisbane, Qld
Contact: Kaikai Shen (08) 6298 6313 or email Kaikai.Shen@csiro.au
H&B16
Project Title
SunLite: promoting the awareness of UV exposure using wearable technologies
Project Description
Understanding the impact of ultraviolet (UV) exposure on the healthy body can help
people to decrease the risks of sunburn and skin cancer. This project focuses on the use of
wearable technologies for the design of persuasive interventions to make people aware of
their UV exposure and provide them with tailored protection guidelines.
Project Duties/Tasks

Study and evaluate commercial wearable UV ray monitoring devices (API, logging,
communication, battery life, etc)

Develop an application for recording UV exposure using the selected wearable
technology and collecting essential user data

Design and implement several graphical visualisation (charts, diagrams, etc) of the
UV exposure user data

Implement tailored persuasive interventions (alerts, text messages, etc) for
increasing user awareness of their UV exposure levels.
Relevant Fields of Study



Computer science
Information technology
Human computer interaction
Location: Marsfield, NSW
Contact: Shlomo Berkovsky: (02) 9372 4253 or shlomo.berkovsky@csiro.au
Sazzad Hussain: (02) 9372 4177 or sazzad.hussain@csiro.au
H&B17
Project Title
Beating the state-of-the-art in medical concept recognition using Deep Learning
Project Description
Health data repositories often contain valuable information stored in free text which is
unstructured and ambiguous. This project will investigate if Deep Learning, a new trend in
Artificial Intelligence that uses neural networks that are several layers deep, can be used
to improve the performance of current state-of-the-art Natural Language Processing
techniques that are used to identify medical concepts in free text.
Project Duties/Tasks
The project will be divided into five phases:

Understanding the state of the art (2 weeks): The student will look at key papers
that explain the state of the art in concept identification from medical text.

Preparing the evaluation framework (3 weeks): It is important to have a
framework in place to quickly evaluate new methods on a wide range of test
collections. In this task the student will help with the design and implementation
of a testing framework that uses several test corpora.

Replicating state-of-the-art results (1 week): Using the evaluation framework, the
student will replicate some of the well-known concept identification techniques.

Designing a Deep Learning approach for the concept identification task (5 weeks):
This is the core task of the project. The student will design and implement a deep
learning approach to concept identification in medical text.

Evaluating the Deep Learning approach (1 week): Using the evaluation framework,
the student will compare the performance of the deep learning solution against
other state-of-the-art techniques.
Relevant Fields of Study
Computer Science, Information Technology and related disciplines.
Skills/Knowledge required:
 Java, algorithm development, machine learning; and
at least one of following desirable skills/knowledge:
 Natural language processing, neural networks, deep learning
Location: Herston, Brisbane, Qld
Contact: Alejandro Metke on (07) 3253 3645 or email alejandro.metke@csiro.au
H&B18
Project Title
Automated Classification of Queries to a Medical Search Engine
Project Description
Our team is developing a search engine specifically designed for medical/clinical data.
Specifically, this student project will look at applying machine learning methods to better
categorise clinical search queries into different types (diseases, treatments, test, etc.) and
then utilise these categories to improve search results.
Project Duties/Tasks

Collate a dataset of clinical queries and their categories

Develop statistical machine learning classifiers (e.g., Support Vector Machines) to
classify data of clinical queries

Evaluate the effectiveness of the classifiers

Integrate the classifier within an existing clinical search engine
Relevant Fields of Study
Computer science / software engineering / I.T. The project involves following skills:




Good programming skills (preferable in Java, Python or C++)
Knowledge of algorithms, data structures
Natural language processing
Some statistics experience
Location: Herston, Brisbane Qld
Contact: Dr Bevan Koopman on (07) 3253 3635 or bevan.koopman@csiro.au
H&B19
Project Title
A Scenario Specific Medical Search Engine
Project Description
Our team is developing a search engine specifically designed for medical/clinical data.
Specifically, this student project will adapt search results according different clinical
scenarios – diseases, treatments, tests, etc.
Project Duties/Tasks


Setup the a search engine and index a collection of medical records
Divide the medical records according to mentions of different scenarios – diseases,
treatments, tests, etc.


Adapt the search engine ranking mechanism to favour specific scenarios
Evaluate the effectiveness of different scenario specific rankings.
Relevant Fields of Study
Computer science / software engineering / I.T. The project involves following skills:




Good programming skills (preferable in Java, Python or C++)
Knowledge of algorithms, data structures
Natural language processing
Some statistics experience
Location: Herston, Brisbane Qld
Contact: Dr Bevan Koopman on (07) 3253 3635 or bevan.koopman@csiro.au
H&B20
Project Title
Visualising Medical Search Engine Results
Project Description
Our team is developing a search engine specifically designed for medical/clinical data.
Specifically, this student project will extract different clinical scenarios – diseases,
treatments, tests, etc. – from search engine results and present those in a visual,
interactive search results UI.
Project Duties/Tasks

Setup the ElasticSearch search engine and index a collection of medical records

Divide the medical records according to mentions of different scenarios – diseases,
treatments, tests, etc. – and index these separately

Extend the basic search engine results to include interactive plots and
visualisations providing summaries of the different clinical scenarios
Relevant Fields of Study
Computer science / software engineering / I.T. The project involves following skills:

Good programming skills (preferable in Java, Python or C++)

Front-end web UI skills

Web services, including REST, JSON, etc.
Location: Herston, Brisbane Qld
Contact: Dr Bevan Koopman on (07) 3253 3635 or bevan.koopman@csiro.au