R skills workshops – 13th November

Melbourne Integrative Genomics will be running a day of R skills workshops on Tuesday 13th November. These are open to all and are heavily discounted for UoM staff and students. See details below.

Note that registrations close COB today. Register now to reserve your spot.

R skills workshops

R is an interactive environment for data analysis and statistical modelling. When performing data analysis, you typically need to share your insights with others. In our morning workshop, you will learn how to share and communicate your findings with yourself and others using R Markdown. As you go further on your journey with R, you will write functions that you use to perform common tasks. In the afternoon workshop, you will learn how put these together into an R package, which makes them easier to use and very easy to share.

Tuesday, 13th November 2018

University of Melbourne

For more information about prices and to register for the workshops, please visit: https://www.trybooking.com/YSEO

Registrations close at the end of Monday 5th November.

Places are limited, register now to make sure you get a spot!

These workshops are brought to you by Melbourne Integrative Genomics (MIG) and the Statistical Society of Australia, Victorian Branch (SSA Vic).


R Markdown (morning session, 9am to 12:30pm)

Presented by: Patrick Robotham & Nick Tierney

For a scientific report to be completely credible, it must be reproducible. The full computational environment used to derive the results, including the data and code used for statistical analysis should be available for others to reproduce.

R Markdown is a tool that allows you integrate your code, text and figures in a single file in order to make high quality, reproducible reports. A paper published with an included R Markdown file and data sets can be reproduced by anyone with a computer.

After completing this course, you will know how to:

Create your own R Markdown documentCreate figures and tables that you can reference in text, and update with – your dataExport your R Markdown document to PDF, HTML, and Microsoft WordUse keyboard shortcuts to improve workflowCite research articles and generate a bibliography

We may, depending on time, also cover the following areas:

Change the size and type of your figuresCreate captions for your figures, and reference them in textCite research articles and generate a bibliographyDebug and handle common errors


Building R packages (afternoon session, 1:30pm to 5pm)

Presented by: Damjan Vukcevic

You have developed a new statistical method. Now it is time to share it with the world.

The methods that actually get used in practice are those with readily available and user-friendly implementations. Writing and disseminating software is therefore a key skill for modern statisticians, one that is generally not taught widely. This course aims to fill the gap.

The R software environment is widely used for statistical analyses. One of its distinguishing features is the extensive range of R ‘packages’, which anyone can write and share via the internet. This used to be an intimidating process but modern tools have made it simple.

We begin our course with how to write a very basic package, and then show how to include documentation, examples and data. Further topics include: an efficient development workflow, managing relationships between packages, sharing your packages with others, and easy ways to manage packages (finding, installing, upgrading).



COMBINE positions open

Do you want to be more involved in the COMBINE community? We are excited to announce that nominations for 2019 COMBINE positions are now open! Joining the COMBINE committee is a great way to improve your leadership skills, build your confidence and help the Australian student community (and it also looks great on your CV!).

COMBINE aims to create a vibrant Australian bioinformatics and computational biology student community but to do so we rely on the work of a group of student volunteers. If you would like to help us build this community please consider nominating for a position in 2019. In return you will get an opportunity to develop a range of important skills and exposure to the inner workings of a national society. If there is something you would like to see COMBINE do or an event you would like to see us run this is your chance to make it happen!

Please see this post on our website for more details of the available positions, their roles and responsibilities and how to nominate (combine.org.au/2018/11/05/2019-nominations/). If you know someone who would do a great job but might not apply themselves please nominate them and we will contact them to confirm they are interested. Supervisors, please discuss this opportunity with your students and encourage them to apply, they might be interested but uncertain about nominating without your support!

The current committee is more than happy to answer any questions so if there is anything you would like to know please contact us at combine@combine.org.au.

Kind regards

The 2018 COMBINE committee

P.S. Registrations and poster abstracts for this year’s symposium are still open. Come join us in Melbourne for what should be an excellent day of student presentation!


Public Event – Keeping under 1.5°C: are we doing enough to avoid dangerous climate change? Thursday 11 October, 6:00pm to 7:45pm at Univ Melb

Public Event – Keeping under 1.5°C: are we doing enough to avoid dangerous climate change?


Prof Ove Hoegh-Guldberg, Director of the Global Change Institute (GCI) and Professor of Marine Science, The University of Queensland (Co-Author of the IPCC Special Report Global Warming of 1.5°C)

Prof Ross Garnaut AC, Professorial Fellow in Economics at the University of Melbourne, Chair of the Energy Transition Hub and President of SIMEC ZEN Energy

Prof Robyn Eckersley, Head of Political Science, School of Social and Political Sciences, plus Climate and Energy College, University of Melbourne

Dr Sarah Perkins-Kirkpatrick, Senior Research Associate and ARC Future Fellow, Climate Change Research Centre, UNSW





Have we missed the opportunity to avoid dangerous climate change? Australia has already experienced over 1°C of warming with an increase in extreme heat events and severe bushfire weather.

What actions need to be taken to get on track to avoid a greater than 1.5°C future? If we don’t act, what could our future climate look like?

To coincide with the launch of the IPCC Special Report Global Warming of 1.5°C, as well as the 10 year anniversary of the Garnaut Climate Change Review 2008 (updated in 2011), the Australian Meteorological and Oceanographic Society and the University of Melbourne Climate and Energy College present a panel of experts to discuss the implications of this important report for Australia and the World.

Thursday, 11 October 2018 
6:00pm to 7:45pm
Kathleen Fitzpatrick Lecture Theatre
Arts West 148 Building 
The University of Melbourne, 
Parkville, Victoria

High Performance Computing Courses 11 and 18 October at Uni Melb

The University of Melbourne is offering three courses in October to help new and experienced researchers make use of the high performance computing facilities.

* Introduction to Linux and HPC

Thu. 11 October 2018 10:00 am – 3:00 pm

If your desktop system is too slow for your “big datasets” or the problems too complex, High Performance Computing (HPC) is the tool you need. At the University of Melbourne we have one general purpose HPC systems, Spartan, which is available to researchers. This introductory course will provide an overview of this systems and the Linux command-line, how to write Slurm script so you can submit data or task parallel jobs, and with plenty of “hands-on” examples of running with research applications. Bring a laptop and a desire to learn about supercomputers.

Register at the following URL:


* Shell Scripting for HPC

Thu. 18 October 2018 10:00 am – 3:00 pm AEDT

Basic job submission scripts in Slurm allow for the allocation of resources and computation in batch mode. However these job submissions can be made even more powerful and flexible with a working knowledge of shell scripting and more advanced Slurm commands. This course assumes knowledge of the ‘Introduction to High Performance Computing course’ and describes more advanced Linux commands, regular expressions and regex tools, various shells, the use of variables, loops, conditional statements, the incorporation of shell scripting knowledge in job submission scripts, and autogenerating scripts with heredoc. Please bring your laptop and a desire to make your supercomputer job submission scripts even more powerful.

Register at the following URL:


* Parallel Processing with HPC

Parallel processing is how applications can scale to deal with large datasets and complex problems. In this course, an initial revision of parallel job submission on Spartan and parallel extensions available in some applications leads to a consideration of HPC system architecture and the various limitations and bottle-necks in parallel processing. This is followed with an introduction to the two core approaches in parallel programming, shared memory and distributed memory, using OpenMP threads and MPI message passing routines. A number of programming examples and opportunities for development are provided. Please bring your laptop and a desire to learn the basics of parallel processing.

Register at the following URL:


Microbiome Analysis with QIIME2 @ Monash Uni, 14-16 November, 2018

Workshop: Microbiome Analysis with QIIME2

Registration now open!

Micromon (Monash MNHS), in conjunction with the EPHM Lab (Monash Engineering) and the School of Biological Sciences, would like to invite you to register for our upcoming three-day workshop and symposium. A half-day symposium will provide selected attendees with the opportunity to talk briefly about their work in a relaxed atmosphere with a combined question and discussion session. A half-day theory-only session will cover sample processing, DNA extraction, amplicon-based sequencing library construction, and Illumina next-generation sequencing and associated QC. The following two days will include a hands-on workshop covering, data analysis and best practices using the QIIME2 data analysis package, presented by contributing authors of the QIIME2 package. The workshop will be held in Monash University’s newest building, Learning and Teaching (https://www.monash.edu/lt-building#).

  • Date: 14-16 November 2018
  • Price: $350 (ex-GST) per person (includes lunch and two refreshment breaks each day)
  • Location: Learning and Teaching Building (Room G31), 19 Ancora Imparo Way, Monash University, Wellington Road, Clayton

Visit the Micromon website for more information and for registration.

Email:  scott.coutts@monash.edu
Phone: (03) 9905 8592


Microbial Ecology-Environmental Microbiology in Victoria

Microbial Ecology-Environmental Microbiology (MEEM) in Victoria


What: Microbial Ecology-Environmental Microbiology (MEEM) in Victoria (4 ECR speakers, 3 PhD speakers; afternoon tea, post meeting social event)

When: Thursday 27th September, 2018 from 14:00-17:15

Where: La Trobe city campus, 360 Collins Street , Melbourne (Room: 360C-2.10).

Why: Promote communication/collaboration for those interested in microbial ecology, environmental microbiology, evolutionary microbiology, and related disciplines

Sponsor: Australian Society for Microbiology

Organisers: Assoc Prof Ashley Franks (La Trobe); Dr Chris Greening (Monash); Prof Linda Blackall (Melbourne)
RSVP: Please email chris.greening@monash.edu by Friday 21st September if you are coming

Cost: nil



2:00 pm: Intro and Aims – Microbial Ecology-Environmental Microbiology in Victoria

2:10 pm: Dr Jennifer Wood (La Trobe University / Swinburne University of Technology) – Trait-based predictions of microbial community assembly and function

2:35 pm: Heyu Lin (School of Earth Sciences, University of Melbourne) – Investigating the potential for mercury methylation by marine microaerophilic bacteria (tentative title)

2:50 pm: Nagalakshmi Haleyur (Department of Biotechnology and Environmental Biology, RMIT University) – Bioremediation of oil-contaminated soils (tentative title)

3:05 pm: Dr Eleonora Chiri (School of Biological Sciences, Monash University) – Microbial methane oxidation across six orders of magnitude


3 30 pm: Afternoon tea – Sponsored by Australian Society for Microbiology VIC Branch


4:00 pm: Dr Matt Neave (CSIRO Australian Animal Health Laboratory) – Diversity, global distribution and genetic potential of prevalent symbiotic marine bacteria in the genus Endozoicomonas

4:25 pm: Ashley Dungan (School of BioSciences, University of Melbourne) – The anemone Exaiptasia pallida as a model to explore probiotics for climate resilience in corals

4:40 pm: Dr Rebekah Henry (School of Civil Engineering, Monash University) – Who’s Poo? Application of microbial community data for understanding faecal contamination in recreational water

5:05 pm: Discussion on MEEM communication


5:15 pm: Drinks – Go to local bar afterwards


Imaging and Modelling of Cellular Life Symposium – Biological Optical Microscopy Platform

A reminder that registration is open for the Biological Optical Microscopy Platform Imaging and Modelling of Cellular Life Symposium.

This symposium will highlight research that uses high-end imaging, quantitative image analysis and mathematical modelling methods.

  • 1-5pm, Friday 14th September
  • Peter Doherty Institute Auditorium, The University of Melbourne
  • Registration: Free and open to all. Please register here.

We have now completed the program and the speaker list and titles can be found below. Our plenary address will be given by Prof. Mark Ellisman (UCSD). If anyone would like to meet with Prof Ellisman, please email Vijay Rajagopal (vijay.rajagopal@unimelb.edu.au).


Time Presenter Title
1:00 Leann Tilley CryoEM: Imaging the conformational dynamics of the malaria parasite proteasome
1:25 Staffan Persson Quantitative analyses of the actin cytoskeleton in plant cells
1:50 Kathryn Stok Multiscale imaging of musculoskeletal mechanobiology
2:15 Vijay Rajagopal The cardiomyocyte under the mathematical microscope
2:40 Afternoon tea
3:10 Puxue Qiao A spatio-temporal model and inference tools for longitudinal count data on multicolour cell growth
3:35 Janet Keast Mapping the visceral connectome
4:00 Mark Ellisman Revealing Secrets Hiding in Plain Sight: Recent Advances in Multi-scale Multi-modal Imaging


Paul McMillan | Manager, Biological Optical Microscopy Platform

Faculty of Medicine, Dentistry & Health Sciences

Room N803, Medical Building,

The University of Melbourne, Victoria 3010 Australia

T: +61 3 9035 3021 M: +61 400 975 760 E: paul.mcmillan@unimelb.edu.au

www.microscopy.unimelb.edu.au | facebook | twitter

Introduction to R Workshops – 11th September and 13th September

Introduction to R Workshops

Tuesday Sept 11th and Thursday Sept 13th 9:00am-5:00pm

Learn how to use R for data manipulation, analysis and visualisation.
R is commonly used in many scientific disciplines for statistical analysis and its array of third-party packages. The emphasis of this one-day workshop is to give attendees a strong foundation in the fundamentals of R. No previous knowledge is required.

September 11th: REGISTER NOW
September 13th: REGISTER NOW

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