Liam P. Spurr, Mathew P. Watts, Han M. Gan and John W. Moreau (EMRI Member). Biodegradation of thiocyanate by a native groundwater microbial consortium. Peer J; DOI 10.7717/peerj.6498
“…Amid the controlled chaos, coral geneticist Madeleine van Oppen stands like a coach directing her team. A doctoral student from Van Oppen’s lab at the University of Melbourne in Australia approaches with an update. One species of coral appears ready to spawn sooner than expected. “That’s not helpful,” Van Oppen declares. She strides to a large aquarium, reaches in up to her elbows, and lifts out a basketball-size piece of coral. “Move,” she orders, marching past to deposit her load into a small bucket of saltwater, in order to isolate the coral and to avoid accidental cross-breeding.”
EMRI affiliate Katarina Damjanovic will deliver her PhD Completion seminar on Friday 8th March – see details Katarina Damjanovic Completion Seminar 8Mar19.
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).
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 firstname.lastname@example.org.
The 2018 COMBINE committee
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,
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:
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.
Phone: (03) 9905 8592
Number of posts found: 41