#HealthHack Science Day at the MCRI

By Louise van der Werff

Last week a tour was conducted through the facilities at the Murdoch Childrens Research Institute (MCRI), and I was happily invited to tag along as a representative of our little team at the Research Bazaar! The tour was organised by Dr Marguerite Evans-Galea (Maggie), a scientist specialising in neurogenetic diseases, for the winning team members of #HealthHack 2014, an initiative connecting medical researchers with software engineers to solve research problems.

The tour was focussed around some of the facilities and people involved in genetic disorder research, genome sequencing and gene therapies, a fascinating and highly complex field. Identifying genes responsible for genetic disorders and developing targeted treatments for those disorders is a mammoth task, but it looks like they have it well in hand.

The first port of call was the Translational Genomics Facility (a facility within the collaborative Melbourne Genomics Alliance), which holds some very impressive next-generation DNA sequencing equipment. The HiSeq 4000, worth a cool $1.8 million dollars, can carry out a full genomic sequence of up to 6 genetic samples in less than 3.5 days using a patterned flow cell technology, and outputs a whopping 4TB of data per run! They must have some hefty data storage capabilities at the MCRI! If not, they can always talk to Data Services here at Research Platforms Services :)

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Image: Dr Stefanie Eggers showing off the HiSeq 4000.

We were then treated to a presentation by George Charalambous from Curve Tomorrow, a six year old innovation company that has a digital health partnership with MCRI. Their mission? To create products that have a positive impact on society. Amongst other things, the team look at harnessing established technologies such as Microsoft Kinect, Google Glass and Oculus Rift for medical applications that involve motion tracking, and for simulation training (such as CPR training). They have also developed a number of iPad apps, including P.E.E.R.S (Pediatric Evaluation of Emotion, Relationships and Socialisation), which can be used by clinicians to diagnose and evaluate autism in young children, by, for example, testing their ability to match a written emotion to a facial expression in a relaxed, gamified way.

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Images: The PEERS iPad app, and a wristband that tracks muscle twitches.

Next up was Dean Phelan, a PhD candidate studying novel genes associated with cardiomyopathy. Dean is looking at methods of identifying causal genes by reprogramming patient skin cells into induced pluripotent stem cells (iPS cells) and then differentiating them into specialised heart cells for disease modelling and drug treatment screening. Did you know that differentiated heart cells start beating together spontaneously in a petri dish? I didn’t either! Luckily enough we got to take a look through an optical microscope in the cardiomyopathy lab to see for ourselves.

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Image:  Dean Phelan with his Petri Dish loving differentiated heart cells.

One of Dr Maggie Galea’s PhD candidates, Sze Hwee Ong, gave us a great overview of her research looking into cell and gene therapy treatments for Friedreich ataxia, a neurodegenerative disease that causes progressive damage to the nervous system. 

In the BLC (Bruce Lefroy Centre) Lab, we met Greta Gillies, who showed us her technique for extracting DNA out of blood samples for further analysis. It was surprisingly similar in principle to the strawberry DNA extraction experiment I remember doing as a kid. We also saw some of the freezers used  for the long term storage of tissue and blood samples, and were introduced to the concept of immortalising cell lines.

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Image: Greta Gillies speaking to the tour group in the BLC lab. 

And last but not least we met Kate Pope, a registered nurse and Associate Genetic Counsellor. She has the weighty task of working with kids with genetic disorders and their families, providing them with information and getting their consent for exploratory procedures aimed at identifying the genes responsible for their disorders, such as epilepsy. This may involve taking skin and even brain tissue samples for analysis and genetic sequencing. Dr Maggie Evans-Galea spoke of the powerful moments when Kate is able to make a phone call and break the news that the responsible gene has been identified, allowing for better and more targeted treatments for the patient.

All in all it was a fantastic and eye opening experience, but I feel we only really touched the surface of what goes on at the Murdoch Children’s Research Institute.

If you would like to learn more, Dr Marguerite Evans-Galea can be contacted via marguerite.galea@mcri.edu.au and tweeted at @MVEG001

What’s on the menu at ResBaz?

No matter your research discipline, there will be something to satisfy your research training taste buds at the Research Bazaar Conference. There will be four major teaching streams running concurrently over multiple sessions and days (i.e. each participant will sign up to one of these), plus a number of other elective classes that anyone can attend.

Stream 1: Programming and data analysis using Python, R or MATLAB
Stream 2: Research maps using CartoDB and TileMill
Stream 3: Natural language processing using Python
Stream 4: Drawing and printing 3D objects using AutoDesk Inventor
Extras: Elective classes

Programming and data analysis using Python, R or MATLAB

Researchers spend much of their time wrestling with software, but most are self-taught programmers. As a result, they spend hours doing things that should take minutes, reinvent a lot of wheels, and still don’t know if their results are reliable. To tackle this problem, we’re running a stream based on the world renowned Software Carpentry teaching syllabus.

The target audience for Software Carpentry is researchers with a basic familiarity with programming concepts like loops, conditionals, and arrays, but who need help to translate this knowledge into practical tools to help them work more productively. The syllabus covers:

  • The basics of the Unix Shell, which is the cornerstone of all programming.
  • An introduction to Python, R or MATLAB (you can pick which you’d like to learn) - functions, defensive programming, error handling, debugging and unit testing are just some of the topics covered.
  • Version control with Git and GitHub, which are the tools for backing up and sharing your code.

Research maps using CartoDB and TileMill

The research maps stream will begin with an introduction to CartoDB, which is a simple yet powerful tool that lets you visualise data onto maps. You’ll learn how to format data to make a map visualisation, and we’ll explore the range of inbuilt features that CartoDB offers and how to start customising these tools to produce a map that communicates your research data. Finally, we’ll explore more complex data visualisation and how to publish and share your maps.

After this introduction to CartoDB the mapping stream will move on to TileMill, which is a more advanced tool that has many more options for map customisation. In the TileMill sessions you’ll learn about the art of cartography and the types of data that you can access and use in TileMill. We’ll introduce you to CartoCSS, so you can customise the appearance of your map and control the level of detail that appears and create a map that you’ll be proud to publish. Finally, we’ll look at how to publish and share your creations.

The mapping stream is recommended for researchers who want to be able to create highly customised maps to illustrate their research. No knowledge of programming is necessary.

Natural language processing using Python

What do you do when you want to comment on features of the language in a large corpus of text? Python’s Natural Language Toolkit (NLTK) offers a powerful means of analysing text and provides a basis for understanding more complex text mining tools. During the NLTK sessions at ResBaz, participants will be introduced to Python and learn to apply NLTK to answering questions about text. The course will also address how to prepare texts for analysis with NLTK or similar tools. These sessions are particularly designed for researchers in the humanities and social sciences and no knowledge of programming is required.

Drawing and printing 3D objects using AutoDesk Inventor

Interested in creating 3D models as part of your research? Interested in designing and 3D printing your experiment apparatus? Participants in this stream will use AutoDesk Inventor to create basic parametric 3D models for 3D printing.

Elective classes

Genomics data workflows using Galaxy: Galaxy is an open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses.

Medical/clinical surveys with REDCap: Nowadays more and more research studies need to collect data from disparate places or people in an electronic format that facilitates their management. REDCap assists this process by providing a secure web application designed to support data capture and management for clinical or health-related research studies. Collected data can be easily exported afterwards for analysis using statistical tools. If you need or want to collect health-related data in an electronic format for your project or you need to conduct health-related surveys then REDCap is the tool for you.

Online collaborative editing using Authorea: We’re very excited to announce that the co-founders of Authorea - an academic start-up that’s fundamentally changing the way researchers write papers - will be at ResBaz to present an introduction to Authorea and a crash course in LaTeX. There will be two different electives available - one for the Humanities and one for the Sciences. Authorea for Humanies will include integration with reference managers, embedding images, and working with non-standard fonts and characters. Authorea for Sciences will explore embedding graphs and figures and including large formulae or equations. 

Introduction to the Research Cloud: The session is going to be a high level introduction to the conceptual foundations, advantages, disadvantages, and the parts of the research cloud. If you understand these then you’ll be far less likely to be bitten in your journey to the cloud: and given the scale and low price of the research cloud you will, most likely, be making that journey.

Databases and SQL: Almost everyone has used spreadsheets, and almost everyone has eventually run up against their limitations. The more complicated a data set is, the harder it is to filter data, express relationships between different rows and columns, or handle missing values. Databases pick up where spreadsheets leave off. While they are not as simple to use if all we want is the sum of a dozen numbers, they can do a lot of things that spreadsheets can’t, on much larger data sets, faster. And even if we never need to create a database ourselves, knowing how they work will help us understand why so many of the systems we use behave the way we do, and why they insist on structuring data in certain ways.

Introduction to 3D printing: 3D printing is changing the way we create, design, and manufacture objects. In this session, we’ll introduce the concept of 3D printing, take a look at it’s many applications in different industries, and visit the Engineering Workshop where you can have a first-hand look at 3D printers in action (and maybe print something for yourself!).

Social media for research: Interested in collaborations? Sharpening your academic writing? Increasing your reputability? Enhancing the public’s understanding of research? Sourcing ideas? Endorsing your publications? Well, have you considering Twitter or blogging? Step inside the world of social. In this workshop, we’ll show you how to use social media in scholarly ways - to better your research, from start to finish. You’ll be tweeting (alongside your favourite academics) in no time at all.

Critical approaches to Big Data: Research taking advantage of enormous datasets is become more and more common, both within and outside academia. While much attention has been paid to methodologies for manipulating and extracting findings from Big Data, critical discussion of the ontology and epistemology of Big Data research is only beginning to emerge. In this elective, Big Data is conceptualised as both theory and resource. After briefly sketching the current landscape of Big Data research, claims concerning the ability of Big Data to provide more objective insights, or to reveal new things about human life, are problematised. Ethical issues and ownership and control of data are also briefly discussed.

Online surveys with LimeSurvey: LimeSurvey is a user-friendly tool for creating and managing online surveys. It offers a number of templates to help you get your survey right and a single user account lets you run multiple surveys. LimeSurvey lets you create complex conditions between questions and, with MySQL as the back-end database, is also great for analysing your results once they’re in. As LimeSurvey is also hosted by the University of Melbourne, you can be confident that your respondents private information won’t be stored off-shore.

A crash course in Wikipedia editing: Increasingly, participating in online projects is an important way to grow your online profile and disseminate your research. But beware - Wikipedia editing has its own etiquette and the community will let you know if you’re doing it wrong. In this short workshop, we’ll introduce you to the fun of Wikipedia editing while helping you to avoid some of the traps along the way.

High performance computing using MATLAB: High performance computing (HPC) is traditionally complicated and involves a steep programatic learning curve. HPC 2.0 involves using any and all tips and tricks to make your existing code run faster. There are actually a number of simple things you can do to substantially speed up your code. We’re offering an introduction to *some* examples in MATLAB, including techniques like automatic vectorisation as well as new learning how to run MATLAB code on Graphics Processing Units (GPUs).

Analysing urban data with AURIN: In Part One, we will introduce you to over 1300 Australian urban datasets accessible by urban researchers containing a wealth of information on health, socio-economics, demographics and the built environment in general. Not only mash-up open datasets, but access secure data restricted for urban policy development and use a suite of online mapping and decision support tools. In Part Two we will explore specialised analytical tools that pull together diverse sources of data surrounding human settlements and combine them to reveal patterns and solve problems. We will look at how transport networks, population density and industry clustering interact at the meso-urban scale and how we might be able to create more sustainable, healthier built environments.

Image repositories with Omeka: Omeka is an image repository originally designed to help small galleries and museums to create online exhibitions but which can also be used as a research database. Omeka makes it easy to search across your collection and handles images, video and descriptive text. In this session you’ll learn the basics of Omeka, including formatting data, creating metadata, building a collection and creating an online exhibition. This session is recommended for researchers who want an easy-to-use database to manage and share their research, especially those working with cultural collections. It is ideally suited for, but not limited to, art historians and archivists. No knowledge of programming is necessary.

Python and data management in the atmospheric and ocean sciences: If you work/study in the atmospheric and ocean sciences and have a basic knowledge of the command line and Python, then do not miss this session. Damien Irving will take you through the Python libraries and data management practices that will make your life that much easier!




If you’re having trouble deciding what tool would be best for your research, feel free to send us a Tweet (@ResPlat), come down to Hacky Hour for a chat, or contact one of our Research Community Coordinators who will be more than happy to help you figure out the most appropriate tool for your data.

(Data) Drover to the Rescue!

Genomics researchers, much like cattle drovers in the outback, are increasingly having to wrangle very large datasets.  Managing herds of DNA data can be a painstakingly manual chore for researchers, yet this is where the automation of machines can make your research life easier. 

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Ergo: we are pleased to announce a new data service aimed at helping biomedical researchers working with large datasets as produced by DNA/RNA sequencing machines.  We are calling this new data service the “Data Drover”[1] and it is powered by the MyTardis system[2] and Research Bazaar[3].

The problem: DNA sequencing machines produce large datasets (terabytes in days!).  One computer server sitting next to your sequencer is not enough (nor is it secure!). You need the ability to share datasets with fellow trusted researchers, as well as utilise new analyst tools to decode the genomes; and the ability to publish your data to cite in your forthcoming research paper.  

The solution:  The Research Platforms department at the University of Melbourne is now offering consultation through its “Data Drover” service to any research group requiring a purpose built system for managing the research data produced by your sequencing machines.  We are very pleased to be using the tried & tested MyTardis research data system as the engine which automatically droves the data from your sequencing machine into well organised and described datasets.

Some of the much loved research features of the MyTardis system include:

  • Captures data off a wide variety of scientific instruments and stores it securely and privately online.

  • Allows the sharing of data securely with fellow research team members.

  • Quick thumbnail previews of experiments, images and metadata.

  • Easy-to-use web interface that offers search and “tagging” functionalities.

  • Shareable timestamped links to allow researcher outside of your team to consult on your data for declared periods of time.

  • Verify, backup and redundancy of data in University housed datacentres.

  • For good practice in research data management techniques.

  • Ability to produce DOIs of datasets for citation in your research publications once ready for publishing.

  • Plugins that allow preliminary processing, and visualising of data.

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But wait there’s more!  Our Data Drover service also builds on the MyTardis engine to help your team develop the skills to analyse your data using the latest genome tools like:

  • Galaxy Genomics workflow engine, so you can do DNA analysis which is repeatable with clearly published methods. See: an interview with a researcher using Galaxy.

  • Rstudio data analysis and research graph generator.  Helping make sure you produce graphs and plots which have good statistical analysis and error bars! see: #DataCarpentry

  • iPython Lab Notebook for doing big data analysis across multiple gene sequences. see: #SWCarpentry

In short, our new Data Drover service can help you muster your DNA data management and analysis in the most efficient way possible so you can forget about the technology and focus on the research!

How can I get involved in the Data Drover Service so I can plug my sequencing machine into MyTardis and get my team skilled-up in utilising genomics analysis tools to the best of their ability?

Please contact Dr. Andy Tseng (Lead Data Architect <andy.tseng@unimelb.edu.au > or David F. Flanders (Research Community Manager) <David.Flanders@UniMelb.edu.au>.

The Director of Research Platforms is Dr. Steven Manos <smanos@unimelb.edu.au>

Stop by our website to pick up a brochure describing our other compute and data services.

Get the latest news from our news feed: https://twitter.com/ResPlat ← if you have a Twitter account, you can also ask question live to our friendly staff waiting to help.

[1]= Data Drover is a sub-project within the VicNode (a federally funded project to provide storage solutions to suit a variety of Victorian research data storage needs) aiming to offer a simple integrated workflow between instruments and data storage.

[2]= MyTardis (http://mytardis.org) is an Open Source data management system purpose-built for managing large datasets produced by scientific instruments.  It was created at Monash University with the Australian Synchrotron in mind (see https://store.synchrotron.org.au/) but is quickly becoming the de facto multi-instrument system for managing scientific equipment throughout all labs in the University.  To know more about MyTardis and its community, please contact steve.androulakis@monash.edu

[3]= The Research Bazaar is our campaign, community and conference to help bring about the next generation of digital research skills: http://resbaz.tumblr.com/about

Image citation: images by Kate B. Dixon, reused through a creative commons license.  Thank you for sharing Kate, your pictures have helped make science more interesting!

Galaxy in the Cloud…it’s not as far as you think!

By Katie Ewing

Have you ever dealt with a spreadsheet so large (say, on the order of billions of entries) that it couldn’t even be opened in Microsoft Excel? This is a common problem for computational biologists who investigate the cause of diseases by looking for a change of a single DNA base in a huge gene.  Luckily, there’s a tool that can help make sense of all that data. Galaxy is a web-based platform designed for data intensive biomedical research, making large data sets more accessible and reproducible.  It runs as part of the Genomics Virtual Lab (GVL) on the Australian Research Cloud.

Over two days in April, the first Galaxy in the Cloud training course was held at the University of Melbourne, in collaboration with VLSCI, HABIC, and ITS Research. Participants were instructed how to launch instances on the cloud so that they can work with large data sets without using up resources on their individual machines. Researchers learned to create workflows to analyze their own data, while system administrators learned how to administer Galaxy so that they could take it back to their respective institutions.

Dejan talks to Ashley and Miriam from the Murdoch Childrens Research Institute (MCRI) about their research

So how does genomics data typically flow?  A clinician will meet a patient who has a genetic disease such as Parkinson’s or autism.  He or she will collect a sample of the patient’s DNA and then send it off to get sequenced using next generation (“next gen”) sequencing, which enables the whole genome sequence to be read digitally (meaning quickly!).  A bioinformatician will sort through the DNA bases and send the organised data back to the biologist, who is then able to identify the specific mutation that is causing the disease.

With next gen sequencing becoming more and more common, researchers are wanting to understand what exactly is IN the “black box” that they’re sending their data through. Galaxy is the bridge, or common language, between the biologists in the wet lab and the bioinformaticians in the dry lab.  As one participant said, it’s not about reinventing the wheel; it’s just about learning how to use it.

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Is this necessary? Probably not.

Data is more than just an Excel spreadsheet. It takes powerful yet user-friendly tools, such as Galaxy, to produce and share world-class research that ultimately leads to new discoveries. 

Ready to learn more? Stay tuned for upcoming Galaxy Workshops! 

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