THE UNIVERSITY OF MELBOURNE
ADVANCED RESEARCH WORKSHOPS IN
NEUROSCIENCE
A series of advanced, hands-on workshops for PhD students will be available during 2015.
These workshops will offer students the opportunity to develop skills in key areas that they
identify to be directly related to their research project. Each program has been designed by
the Workshop Leader to provide a comprehensive, small group experience.
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Advanced Research Workshops in Neuroscience
www.neuroscience.unimelb.edu.au
Program
There are 6 workshop programs offered in 2015. These are detailed within this document.
WORKSHOP
Magnetic Resonance Imaging
WORKSHOP LEADER
Professor Roger Ordidge
Human Pluripotent Stem Cells in Neuroscience Research
Professor Martin Pera
Fundamentals of Ion Channel Function in the Brain: Associate Professor Steve Petrou
Intracellular and Extracellular Recordings
Fundamentals and Future of Advanced Live Cell Imaging
Associate Professor Andrew Metha
Advanced Workshop in Human Genetics
Introduction to Bioinformatics for Neuroscientists
Associate Professor Justin Rubio
Dr Victoria Perreau
There is no cost to attend the workshop programs.
Application Process
The timeline for the application process is as follows:
Applications Open:
Friday 6 March 2015
Applications Close:
Friday 18 April 2015
Successful Applicants Notified: Monday 18 May 2015
Very limited places are offered for each workshop program. Expressions of Interest are to be
submitted on the form provided, together with your CV, by COB Friday 18 April 2014.
Please send your EOI and CV to the following email address: research-mni@unimelb.edu.au
For any enquiries, please email: research-mni@unimelb.edu.au
Melbourne Neuroscience Institute
For further information about the Melbourne Neuroscience Institute, please visit our website:
www.neuroscience.unimelb.edu.au
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Advanced Research Workshops in Neuroscience
www.neuroscience.unimelb.edu.au
Advanced Workshop in Magnetic Resonance Imaging
The aim of this workshop program is to educate students in the principles of MRI, the design of the
MRI scanners and use of contrast to distinguish between abnormal and normal tissue. The focus will
be on imaging the brain. A scanner will be used to explore MRI contrast differences between various
liquid samples.
It is envisaged that this course will provide a solid foundation in MRI for current PhD students
involved with MRI research.
Presenters: Professor Roger Ordidge and Dr Brad Moffat.
Workshop format: 18 hours total.
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Topics to be covered in a series of one-hour lectures (3 per week) will include:
o Classical description of Nuclear Magnetic Resonance
o Excitation of the MR signal by resonance
o Spin relaxation behaviour: T1 and T2 Spectroscopy
o MR signal detection and processing
o MR image formation
o MRI hardware
o Spin-echoes, gradient-echoes and production of image contrast
o Understanding MR sequences using K-space
o Echo-Planar Imaging, artefacts, and MR safety
o Fast imaging using FLASH, contrast agents
o Flow and angiography
o Diffusion- and perfusion-weighted imaging and functional MRI.
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Two one-hour tutorials covering multiple choice questions discussed as a group.
Hands-on demonstration of T1, T2 and Diffusion measurement in liquid samples (2 hours).
Analysis of T1, T2 and Diffusion parameters from acquired data (2 hours).
Proposed timeframe: August to Sept 2015, over 6 weeks, up to 3 hours per week.
Prerequisites: VCE qualification in secondary maths, physics or chemistry (or all).
Professor Roger Ordidge
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Advanced Research Workshops in Neuroscience
www.neuroscience.unimelb.edu.au
Advanced Workshop: Human Pluripotent Stem Cells in
Neuroscience Research
The aim of this workshop program is to familiarise participants with the application of human
pluripotent stem cells to problems in neuroscience, including the study of brain development,
functional genomics, and disease modelling.
Presenters: Professor Martin Pera and Dr Anna Michalska.
Workshop format: 28 hours total.
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6 x 1 hour tutorials
2 x 1 hour literature review
4 x 5 hour workshops including:
o Pluripotent stem cell propagation, maintenance
and characterisation
o Stem cell genetic manipulation and
differentiation
o Functional investigation of differentiated cells.
Pre-Reading will be provided to students.
Professor Martin Pera
Proposed timeframe: 1 – 4 September 2015
Prerequisites: Tissue culture experience
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Advanced Research Workshops in Neuroscience
www.neuroscience.unimelb.edu.au
Advanced Workshop: Fundamentals of Ion Channel Function
in the Brain: Intracellular and Extracellular Recordings
This program will introduce students to theory, methods and approaches for the expression and
analysis of ion channels using two electrode voltage clamp and extracellular fields using
multielectrode arrays. This program will cover:
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Theoretical lectures on “counting ion channels” and source of extracellular currents
Whole cell electrophysiology using automated two electrode voltage clamp recording in
Xenopus oocytes
Analysis of cultured neuronal networks using multi-electrode arrays.
Presenters: Associate Professor Steven Petrou and Dr Chris
Reid.
Workshop format: 36 hours total.
 2 x 6 hour theoretical workshops
 3 x 8 hour practical sessions
Pre-Reading will be provided to students.
Proposed timeframe: July 2015
Associate Professor Steven Petrou
Prerequisites: Interest in biophysics and electrophysiology. A
basic knowledge of electricity from high school or first year physics would be help students get the
most out of the course.
This workshop is limited to 6 students. Priority will be given to students who wish to apply this
knowledge to their PhD studies.
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Advanced Research Workshops in Neuroscience
www.neuroscience.unimelb.edu.au
Advanced Workshop: Fundamentals and Future of Advanced
Live Cell Imaging
The ability to visualise the minutiae of biological structures has underpinned our knowledge about
plants and animals. New methods continue to evolve, pushing beyond the diffraction limits imposed
by the physical nature of light itself, to increase the microscope’s scientific prowess.
In a mixture of tutorials and hands-on workshops, workshop participants will be introduced to the
theory and practicalities of advancing microscopy techniques that allow cellular-level resolution, invivo and super-resolution of in-vitro biological samples. The program will cover:
 Imaging of live human retinal cells using adaptive optics: View your own photoreceptors and
make movies of individual red blood cells as they course through your capillaries
 3D Structured Illumination Microscopy (3D-SIM): Sample illumination techniques, combined
with point fluorescence and image processing
 Localization microscopy techniques: photo-activated localization microscopy (PALM) and
stochastic optical reconstruction microscopy (STORM). Photo-switchable proteins
embedding in samples are exploited such that the locations of single molecules within a cell
can be determined
During the course of the workshop, the potential for hybrids of these methodologies will be
emphasised. Workshop participants will become cognisant of emerging technologies to improve
spatial resolution of live-cell imaging while keeping tissue/cells viable, and gain valuable hands-on
experience as they discover the limitations, and future possibilities, of these techniques.
Pre-reading material will be provided well in advance of the program.
Presenters: Associate Professor Andrew Metha and Dr Paul McMillan.
Workshop format: 17 hours total
 2 x 4 hour tutorials (round-table format).
 3 x 3 hour hands-on workshop sessions with equipment for each of the above techniques.
Pre-Reading will be provided to students.
Proposed timeframe: October – November 2015.
Prerequisites: None
Associate Professor Andrew Metha
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Advanced Research Workshops in Neuroscience
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Advanced Workshop: Human Genetics
The aim of this workshop is to educate students in the principles of human genetics and to illustrate
how it can be leveraged to reveal fundamental aspects of disease biology and translated into clinical
application.
With a mixture of tutorials, wet- and dry-lab practical sessions, it is envisaged that this workshop will
equip students with knowledge that can be applied to their own
projects and research endeavours.
The workshop will focus on:
• Genetics and human disease – gene mapping and statistical
interpretation
• Techniques in human genetics – genotyping, DNA
sequencing and gene expression analysis
• Genomic databases – SNPs, GWAS and regulatory
information
• Integrative genomics and systems biology – concepts and
analytical techniques
• Translational genomics – applications in drug development,
precision medicine, genetic risk prediction and diagnostics
Presenters: Associate Professor Justin Rubio and Dr Michael Inouye
Associate Professor Justin Rubio
Workshop format: 22 hours total
 5 x 2 hour tutorials (round table format)
 3 x 4 hour practical sessions.
Pre-Reading will be provided to students.
Proposed timeframe: October 2015.
Prerequisites: This workshop will assume a basic knowledge of human genetics and/or
bioinformatics to undergraduate level.
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Advanced Research Workshops in Neuroscience
www.neuroscience.unimelb.edu.au
Advanced Workshop: Introduction to Bioinformatics for
Neuroscientists
Bioinformatics is a diverse field and this course will provide an intensive introduction to selected
basic analysis methods and data types commonly used in bioinformatics, with a particular focus on
neurosciences. The course is aimed at bench researchers with no programming skills.
A selection of tools and databases useful for researchers in the Neurosciences will be demonstrated
during the workshop. Topics proposed are listed below, however the topics may be changed at the
request of the group:
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SNPs, genotyping and disease
Protein sequence alignment, domains and motifs
Using the Allen brain atlases
Expression analysis using microarrays and RNAseq
Finding and analysing experiments in Gene
Expression Omnibus
 Co expression analysis of on line data using Gemma
 Analysis of complex traits and phenotypes in
GeneNetwork
 Protein Interactions and networks
The course is structured to include defined tutorials using
example data. However, students will also be supported at
an individual level to apply analysis skills to their own
research questions of interest and encouraged to present
their findings to the group at the end of the course.
Presenters: Dr Victoria Perreau, Bioinformatics core
manager and Dr Noel Faux and Dr Andrew Fox
Workshop format: 20 hours total contact time in 10 weekly
2 hour small group workshops.
Additional 20 hours (minimum) outside workshop hours,
for completing workshop activities and individual support.
Dr Victoria Perreau
Total 40 hours commitment.
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Advanced Research Workshops in Neuroscience
www.neuroscience.unimelb.edu.au
All software used in the workshop is freely available and instructions for downloading and installing
will be provided where necessary.
Proposed timeframe: Course commencement will be between June and September 2015, actual
dates are to be decided.
Prerequisites:
 A good understanding of molecular biology, including gene structure, transcription and
translation is essential.
 Applicants who articulate a biological question, relevant to their research area, that they
think might be approached from a bioinformatics stand point will be preferred. This is
because the student’s own research interests will be used as examples in tutorials wherever
possible and students will be expected to present their own analyses to the group at the
conclusion of the workshop.
Familiarity with using genome browsers and the types of data used in genome browsers is required.
It will not be covered by the course. Tutorials for genome browsers are available on line:
UCSC genome browser: http://www.openhelix.com/ucsc
Ensembl genome browser: http://www.ensembl.org/info/website/tutorials/index.html
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Advanced Research Workshops in Neuroscience
www.neuroscience.unimelb.edu.au