Research Platform Services Blog
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by : Yuandra Ismiraldi
Having questions on how to collect and clean your data ? Lo and behold, the ResBaz team has conducted two trainings about data acquisition and data cleaning in the last two weeks. Here’s some interesting tidbits from the training just in case you missed it :
the current data acquisition training focuses on web survey tools using (Google Forms) and mobile data collection using (Kobo Toolbox). We even had a session of going outside to university square and taking pictures of building with our cellphones !
Day 2 of data acquisition training : using @kobotoolbox for mobile data collection @ResPlat pic.twitter.com/sZBXjG7g4Y
— Yuandra Ismiraldi (@iniandra)
December 1, 2015
This simulates the situation of collecting data via fieldwork - an activity where mobile data collection tools can help :)
The data cleaning training focuses on using a free, open source tools called OpenRefine. We got some technical difficulties along the way in setting up open refine, but in the end everyone get a hands on feel about how to use open refine functions such as transposing, facet, and regular experession for data cleaning.
\b[Uu][\s.:]?[Ss][\s.:]?[Aa][.:]?\b I can tell that hours of entertainment with regular expressions await…
— Ursula Smith (@syntype)
December 8, 2015
If you missed the training, we actually have another session of data acquisition and data cleaning training session as part of our Research Bazaar Conference in February 2016 ! The conference is a 3 day free conference for researchers to upskill their digital research skills - we will conduct many different courses there and you can also meet people that has used digital tools for their research.
Interested ? Registration ends today at midnight, so sign up quickly at resbaz.com !
by Paul Mignone
Last year, the Research Bazaar’s Research Product Realisation Working Group (#RPRWG) invited University of Melbourne researchers to apply for the 3D printing mini research grants. A total of 8 grants of AUD 5,000 each were awarded to support impact factor-based research (e.g., publications, exhibitions etc.) in the use of 3D printing alongside its applications across various research disciplines.
As 2015 comes to a close, it is with great pleasure to announce that the majority of RPRWG grants have successfully concluded, producing high-quality research outcomes that can be accessed via figshare digital object identifiers (DOI). A big shout-out and congratulations to our first RPRWG grant recipients!
DOI: https://dx.doi.org/10.6084/m9.figshare.1613539
#Resbaz #RPRWG Presentation 1: Chris Bolton (@rrdLab) talks #3dprinting of optics #PrintedOptics http://t.co/u849sHhNO6
— Dr. Paul J. Mignone (@PJMignone)
February 26, 2015
DOI: https://dx.doi.org/10.4225/49/565BD0B122FC4
#Resbaz #RPRWG Presentation 2: Varsha (@vpilbrow1) talks #3dprinting of primate teeth #greatapedentalscoringsystem http://t.co/MbpKGGthoD
— Dr. Paul J. Mignone (@PJMignone)
February 26, 2015
DOI: https://dx.doi.org/10.4225/49/565BE1B42CB89
#Resbaz #RPRWG Presentation 3: @Optiskel_Ravi and @DarcyZelenko talk #3dprinting optimisation techniques #optiskel http://t.co/0YcYHmh2W3
— Dr. Paul J. Mignone (@PJMignone)
February 26, 2015
DOI: https://dx.doi.org/10.4225/49/5654E2D94C260
#Resbaz #RPRWG Presentation 4: @kennyleopard shows us how #3dprinting can help us understand beauty #totouchbeauty http://t.co/lpkJRJ50LA
— Dr. Paul J. Mignone (@PJMignone)
February 26, 2015
DOI: https://dx.doi.org/10.6084/m9.figshare.2009034.v1
#Resbaz #RPRWG Presentation 5: @DrLachie discusses the #3dprinting of his #opensource microscope design #parasight http://t.co/rJTqibnFnT
— Dr. Paul J. Mignone (@PJMignone)
February 26, 2015
DOI: https://dx.doi.org/10.4225/49/5653BB1E9FAF2
#Resbaz #RPRWG Presentation 6: @AmandaCLNg talks the #3Dprinting of MRI gel phantoms #3DMRIPhantom http://t.co/MZT9wzWoKd #openmedical
— Dr. Paul J. Mignone (@PJMignone)
February 26, 2015
Guest post by engineering student Mr.Tony Zahtila. Tony is now employed by Veolia thanks to his ResBaz experience.
Hi! I’m Tony and I was a part of the ResBaz CAD teaching team for 2015.
The CAD skills I learnt as a part of the program have since been helpful in creating virtual constructions of the work I do. The best part of using CAD in my work, it’s how cheap my mistakes have become. Sketching up my work and creating a 3D model allows me to visualise what I’m trying to build in the workshop. If I’ve miscalculated a length, or overlooked a geometry, I just change the design specs and I’m ready to build. A nice short-cut to the laborious task of finding what I’ve ordered doesn’t actually assemble.
The software is far-reaching and I can see applications for CAD skills in many fields. If engineers are to become digital blacksmiths, doctors can become digital plumbers. Organs can go flying around on the monitors of health professionals, all towards a better understanding of our bodies, or a doctor’s slightly-alarming idea of fun.. 3D models of the human body would allow for an alternative to the difficult to obtain cadavers with exploded views of our bodies, as well as clarity, versatility, and interaction that’s just not possible with the traditional textbook.
There’s many variations of CAD software and the form it finds itself in use with engineers is not necessarily what the software will look like to other professionals. Pulling and stretching apart, dividing into blocks, sculpting towards roundness, and smoothing coarse materials to see their altered appearance, all of these things can be achieved with CAD software as the focal point.
I believe that the way of the future is interaction between until-now disjointed fields. The distinct lines between medicine, engineering, law, commerce, art, carpentry, and so on, they’ll blur. Communication between the fields will continue to grow as an integral skill. It’s not compulsory that you have an interest in becoming a CAD expert to gain from the course. Knowing the fundamentals will put you in good stead to clearly communicate with a CAD professional who can advance your work. An artist could have a realistic expectation and understanding as to the how their aesthetic piece could be re-worked into a digital symphony of polygons. The possibilities for experimentation are there and very accessible.
The ResBaz team are very friendly and it’s as much a sharpening of CAD skills for students as it is a festival of ideas between people who see the world with different lenses. I was challenged when I heard a visual artist, who had been taking the course and exchanging ideas as part of the group, ask whether it would be possible to ‘pull out’ a corner of a model. To visualise what was being described, imagine pinching some Playdoh and tugging on it to see how it stretches. I’d never thought of this in my exact and neat world of CAD use, I’d hitherto seen CAD as more of a program for making machine recipes.
ResBaz is a fun and engaging environment. People are very friendly and I was able to get along with all the smiling faces and people who were excited to share their own work and to learn from others. I’d highly recommend the CAD course to both people who want to develop their skills into a powerful technique to add to their repertoire, as well as, people who want to understand the basics so they are aware and able to work in a team with CAD professionals.
By Errol Lloyd
Hi all!
Yes, I’m catching up on my Dr Who.
I’m Errol and I’ve just joined as the ResCom in the new Data Vizard stream, which is dedicated to getting researchers sharing, communicating and collaborating through visualisations on the web.
Worth a dance I reckon.
During the day I’m a neuroscientist. I work in systems neuroscience, which broadly tries to work out how the brain and mind work. In this introspective era, it’s an undoubtedly big scientific question, with the added curiosity of potentially connecting, through a cohesive understanding of the mind, the mechanistic sciences with politics and art (see Susan Langer for more).
Specifically, I use the visual system as a means to study the brain. This is because vision involves nearly half our brain. We densely sample the world along a number of dimensions—wavelength, energy, space, time — simultaneously. And over many inter-weaving iterations, we integrate and contrast multiple streams of information to finally develop an understanding of our world.
Dali, Head Exploding
Soooo, why data visualisation then? Well … "vision involves nearly half our brain. We densely sample …etc … an understanding of our world”. Vision is kinda our brains’ thing and probably instrumental to understanding, discovery and science.
Even Plato is surprisingly on point on this, calling vision the cause of the greatest benefit to us, having ’created the art of number and … given us not only the notion of Time but also means of research into the nature of the Universe’. (Plato, Timaeus, 47a)
I see our aim as being to go further, to break the ‘collaborative ice’ by having researchers tell the story of their research to the world. As Alice asked “what is the use of a book … without pictures or conversations’’, so we ask what’s the use of research without visualisations and open data?
Us researchers are bad at the communication thing, and it hurts not only ourselves and our standing in society but science and research generally. By tapping into the brilliant little abstract visual computer in our brains, visualisations can not only summarise and make navigable and comprehensible otherwise boring or impenetrable data, but can also capture the essence of a topic or question and close the understanding gap so many of us find hard to bridge. Visualisations can tell our research stories.
And what if we all put them on the web? That might even be a little magical.
Also, eye candy is eye candy:
2001: A Space Odyssey
Glad to have joined the gang!
Errol Lloyd.
Hello! Lovely to meet you all, I hope you’re having a pleasant day and the procrastination hasn’t gotten too far out of hand just yet (how many hours on tumblr now? Just the 5? Don’t worry, this counts as research!). My name’s Meredith and I’m a brand new Research Community Coordinator for Research Platforms.
At the moment I’m in the midst of one of many drafts (and redrafts, and redrafts) of my Masters by Research thesis. Although the question: “so, what’s your thesis on” inspires fear and terror in any researcher’s heart, and has led to the collision of hummus and guacamole with many a well-meaning party-goer’s face, I will attempt to answer this for you now. That’s how much I love you, Research-Platforms-Tumblr-Reader, I love you with all my keyboard. Everyone knows, that’s what true love is.
It (my thesis, not the keyboard-heart metaphor) is on a poem called Aurora Leigh, published in 1856 by a one Elizabeth Barrett Browning. Here she is, looking a tad grumpy:
She had good cause to be back in 1856 - women didn’t have a great time back then, and, not to put too fine a point on it, don’t really now. I am interested in the long history of feminist writing and poetry, which is what drew me to the poem (Aurora Leigh, for those in the back row who nodded off during the last paragraph) in the first place. Here’s a picture of the poem because I hear tumblr works better with pictures:
After reading it (which I highly suggest, though it is quite long), I thought to myself “Why do all the women in this story keep imagining themselves drowning or dissolving?” Answering this key research question has unlocked (get it? key? unlocked? genius) insights into the way that Elizabeth Barrett Browning was continuing the revolutions of Romanticism and demanding liberty for women. There are gems hidden away in this poem that are incredibly relevant today, grab some cheese and a glass of red and I’ll discuss it with you until the cows come home.
“But Meredith!” I hear you interject in a tone of admonishing accusation and thinly veiled contempt “Whatever could possibly bring you to the Research Bazaar? Surely you just sit up there in your ivory tower, reading dusty old poetry books and chuckling away to your half-crazed self?” Well, dear reader, first of all let me thank you for reading this far down the post, and for the attention that your spirited interjection must have demanded.
Let me also tell you that it’s not so much an ivory tower as a crumbling edifice of cost-cutting, casualization and dire employment (or lack thereof) predictions over here in the humanities. It’s also a place where innovation and thought happens to thrive, so of course when I was introduced to the intriguing Research Platforms I was drawn in by curiosity and a vague idea that computers might not be our enemy, but instead offer possibilities.
Research Tools Speed dating was my first taste of Research Platforms. At this event I learnt that - shock! - you don’t need to store all your references in one big Word Doc! I am now a devout Zotero user, and am currently leading workshops on nifty programs like Gephi and Omeka.
Gephi is going to be particularly useful for my research because as long as you or I spend on Facebook and email, Elizabeth Barrett Browning spent writing letters. They can be an absolute joy to read, just try out a quick key-word search in this online database: http://www.browningscorrespondence.com/
Anyway, Gephi is a program that lets you visualise networks until they look like beautiful, lit-up spider webs like this one from the Gephi website:
Gephi is usually used to visualise social networks, gathering data from facebook, twitter, instagram, tumblr and the like. My big idea, which seems really quite obvious now, is that social networks have been going on for a lot longer than we’ve had this crazy thing called the internet - and EBB’s prolific letter writing is just one example of that. Here’s a lovely painting from about that time by Jean-Baptiste Greuze titled The Letter Writer (I think it’s from 1800 or 1806, but if any of my art history friends wish to correct me on that I’d welcome the input!):
Ah, the ancient art of the nip slip… anyway, during the Romantic and Victorian eras letter writing, exchanges of calling cards, and other social networks skyrocketed and I think Gephi could be a great program to help researchers figure them out. It can also be used to map the social networks created within stories, like this one about the characters in James Joyce’s Ulysses (you’re better to view it on the author’s blog, along with handy hints on visualizing networks with Gephi http://literaturegeek.com/2013/09/09/bloomsday2013results/ ):
I’m also beginning to learn Omeka, which is a program that allows users to create digital archives or exhibitions. It’s particularly useful for museums and galleries to display lots of artifacts, documents and artworks. Put it this way: if Indiana Jones had Omeka, he could have just uploaded the Cross of Coronado into his Omeka exhibition and it all would have been fine.
And on that somewhat rambling note, I’m off to enjoy this sunny Friday afternoon. It’s been fun, oh my dearest Tumblr-Reader, and for you to have made it all the way to the end! You have a special place in my heart. Feel free to drop me a line and chat about poetry, Gephi, Omeka or whatever pops into the lovely mind of yours. Bye!
by Pip Karoly
A couple of weeks ago I ran my first MATLAB course (yay me!). The week was a blast and we had a diverse group of researchers. Our attendees wanted to use MATLAB for all sorts of reasons and data. Someone wanted to model water levels and storage capacity of tanks. Someone else was interested in saving the parameters of lots of different neural stimulation experiments. It was awesome to meet you all!
And now a big shout-out to all our amazing helpers –
especially our new recruits. As always, we could not have done it without you.
I will now proceed to name (read embarrass) our lovely lovely MATLAB team.
@Yamni – our newest MATLAB ResCom. If you’re lucky she’ll make you a cup of chai and serenade you
@Parvin – Is a superstar of computational neuroscience. In between coding she’s also the secret weapon of the EEE soccer team.
@Warda – Currently working on a MATLAB course specifically for fMRI data, Warda is a gun at signal processing and can talk for hours about the Wiener filter.
@Liz – She started out in the beginners course not long ago herself and is now one of our most reliable and on-the-ball helpers!
@Artemio – Artemio used to teach MATLAB back home in Mexico, these days you might spot him riding round Brunswick or hard at work in the neuroscience department
@Greg – Maybe its cos he’s from another hemisphere, but Greg has a unique way of looking at your MATLAB problems. He’s also a gun when it comes to computational modelling.
@Ewan – Ewan is known for his MATLAB big-data skills and as a connoisseur of free t-shirts. Some describe him as benign, but when it comes to debugging your code he’s as mean as they come.
@Daniel – Our verbose friend from across the pond, ex-IT Daniel has ALL the experience in MATLAB. He’s my go-to-guy when I feel like getting a bit philosophical about code.
And of course my fave gal @Kerry – where would we be without her? Kerry is the super talented, fun and oh-so-excellent presidente of the data wranglers. I reckon she might even become presidente of MATLAB some day.
Pippa, Daniel, Greg & Kerry at Tsubu at the end of the MATLAB course
But my absolute fave part of the course was ending at Tsubu for drinks and a code challenge. If you’re reading this blog you probably already know that here at ResBaz we believe in social-coding, and you can find us at Tsubu every Thursday at 3pm.
Last Thursday we trialled our first ever MATLAB-Codathon at Tsubu. And it was so much fun that we’re doing it all again on Thursday 17th of December with a Christmas theme (sweaters optional).
So what is codathon? It is an afternoon to practice your MATLAB skills by completing code challenges. You can check out the challenge from last week here. Come by yourself or with a group - either way it’s a fun way to meet other researchers who are learning a new language too. And every challenge you complete will earn you some free swag and a drink on us!
Your first challenge is to type this into MATLAB
load(‘handel’)
sound(Fs,y)
Feeling christmassy yet? Then grab your laptop and head to Tsubu next Thurs for our Christmas CODATHON. Also it’s almost holidays and do you really need an excuse to get out of the office?
See you there!
We’ve just finished teaching our first-ever data visualisation course!
It was lots of fun and we’ve all learned a lot!
As always, this wouldn’t have been possible without the support of our trainers and helpers (@robrkerr, @pjkaroly, @maegul, @harrietgl, and @alistairwalsh)! Thank you, you are magical!
We ended the course looking at some real data!
Starting with a 10 minute brain-storming session, we decided on a good way to visualise the data and then discussed the more technical things around the implementation of such an idea.
And we would like to do this on a regular basis!
Once a month, we’ll have a space that you can take your data to. We can then brainstorm together about nice ways to make it look good. Afterwards, we’ll stick around to actually implement it!
And everyone’s welcome to participate and contribute, even if you don’t bring data, there’ll be heaps to learn!
The Research Bazaar’s ResPlaty mascot has many guises. The patron of the Humanities and Social Science team is Data Vinci. Like her namesake, Data Vinci is multi-talented - whether it’s collecting survey data, analysing text, creating maps, visualising networks or typesetting documents, this Renaissance ResPlaty has it covered!
Our training activities reflect the range of our interests. As part of Research @ Library week, we took a trip down to the VCA to deliver training in Omeka to some of the VCA’s students and some keen members of the library staff. Here’s what librarians Ruth McConchie and Sophie Kollo had to say about the experience:
The Omeka workshop was one of the highlights of our Researcher@Library Week. It was really fun and hand-on experience, with Fiona teaching us one element, then letting us run free testing out the platform with our own material and projects. Fiona helped us to think through the design of our Omeka pages with Post-its, which was really useful for those who hadn’t designed a website before. Because we are librarians, we were very excited to learn about the Dublin Core metadata standards behind Omeka and the ability to add in fields like attribution and copyright conditions. We are going to use our new skills to build a website to showcase the incredible collection of Architectural Atelier drawings from the University of Melbourne’s Cultural Collections.
Image ‘Green Eye of the Yellow God: Design for filmset’
We also teach Python’s Natural Language Toolkit, a spin on Python that’s designed especially for those who work with large bodies of test. Most recently, we taught NLTK to a small group of researchers from the Humanities and Social Sciences, who were working on everything from Tony Abbott’s Facebook page to citizen participation in policy design. We explored ways to import and analyse texts, including study of features of formal and informal language and trying our hands at web scraping and extracting data from PDFs (with mixed results).
See, I said we were multi-skilled!Graphing in nltk! @FCTweedie, satisfying both the literature and stats nerds in the room @ResPlat pic.twitter.com/lo0JLaYf2r
— Kim Doyle (@kim_doyle1)
November 16, 2015
Keep your eye out for our upcoming trainings in collecting and cleaning data and making maps. And of course we’ll be there in force at the Research Bazaar conference. Because like that other da(ta) Vinci, we believe:
The noblest pleasure is the joy of understanding
It’s true. After nearly two years lingering at the multi-coloured delights of the Research Bazaar, it’s time to load up my camels and set out on the next phase of my journey. And, inasmuch as any of us knows where we’re going, I’ve got my next destination planned - Data Science at the Australian Ballet.
When I joined the Research Bazaar family in February of 2014, it was a much smaller group. I already knew Flanders (@DFFlanders), of course. We’d organised GovHack together in 2013. And that’s a lesson right there. You find great people all over, but volunteering with someone is an opportunity to really get to know them. And a big event is a real test of someone’s mettle.
I knew that Flanders moves fast, makes stuff happen, and is always generous with the credit and the spotlight. These are great characteristics in a mentor and made me excited to join his next adventure.
While I’ve frequently felt like I’m running hard to keep up with the technical side of the job, there’s no doubt that I’ve learned a huge amount about coding and managing data. Did I mention that I’m going to be a data scientist? With a degree in Ancient History and four years of experience in policy, this career progression is perhaps unexpected. But in the last two years, I’ve learned and taught Python, CartoDB, and Omeka and played with a host of other digital research tools. More importantly, I’ve gained confidence in my ability to figure things out. I’ve often joked that if you can survive legal Latin, you’re bullet proof. It turns out that code is just another language and that, once you’ve recovered from the shock of something unfamiliar, it can be picked apart in similar ways.
Building a new program and looking after a growing team are demanding tasks. I’m still learning to delegate and to ask for help. I know it’s important to accept that no event is perfect and trust that my team is there and will do a great job.
There’s no doubt, leaving the ResFamily is going to be the hardest part of the move. I’ve been privileged to work with a wonderfully diverse group of people, who are all incredibly smart, committed and creative. We’ve been given a freedom to play and explore in our work, which is rare. I’ve learned a lot technically, but also about building community, working in a team, and leading a complex program. Watching the team gain skills and confidence has been incredibly rewarding and I’m genuinely proud of what we’ve achieved together.
I’d be lying if I said there aren’t problems I’m relieved to be leaving behind. The pressure on postgraduates and early career researchers to deliver great research, publish, teach and build their professional standing is only going to increase as research jobs become more scarce. It seems we’re just starting to have conversations about mental health in research and there’s no doubt that it’s a tough environment. It makes me sad that there are such high personal costs to pursuing research. And I’m frustrated by how slowly recognition of the next generation digital research we’re supporting seems to be spreading in some areas. I hope to see greater flexibility in the ‘academic’ career path, with more value placed on both the technical skills and breadth of experience that come from different types of work, in coming years.
I love research and I still believe that there’s nothing better than being in the room when the ideas are firing, so I have no doubt that I’ll swing by the Research Bazaar again in future. And the lessons I’ve learned here will stay with me, wherever I go.
Below is a recap of the recent 3D Slicer training workshop.
If you are interested in attending a 3D Slicer workshop, the next one will be held as part of the Research Bazaar 2016 conference, a free 3-day intensive event (Feb 1-3rd 2016) for researchers at all stages in their careers (Honours, Masters, PhD, Post-Docs, ECRs and so on) to engage with the wider community and learn new digital research skills.
Simply follow the links below to sign up and select 3D Slicer as your first preference from the available teaching streams. This conference will be an amazing experience for all, and will include a great range of social activities, fun and games.
Have a question? Check out our FAQ: melbourne.resbaz.edu.au/resbaz2016. Apply at resbaz.com/melbourne.
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The 3rd ever 3D Slicer for Beginners workshop was held at Melbourne University last week. 15 enthusiastic participants, one lovely Helper, and a guest appearance from Objective 3D made this workshop both interesting and informative. This workshop the very recently released version 4.5 of 3D Slicer.
For me, this workshop was my most intimidating. The turnout was double that of the previous workshop I held in August, and triple that of my very first workshop in July. This increasing turnout shows increasing awareness and interest in this kind of software around Melbourne University and beyond.
Participants came from a range of academic backgrounds, including Anatomy and Neuroscience, Agriculture and Veterinary Sciences, Electrical and Electronic Engineering, Nanofabrication, Psychology, Physiotherapy, and even video game design.
Jasamine Coles-Black, an MD research student in vascular surgery at Austin Health, kindly volunteered to be a helper at my workshop, after having attended the previous two 3D Slicer workshops.
Ben Darling, the National Sales Manager for Objective 3D, kindly offered to bring along some 3D printed anatomical objects to show off some of the abilities of advanced 3D printers like the Connex 3, which offers multi-material printing, “from rubber to rigid, transparent to opaque, neutral to vibrantly colored and standard to biocompatible.”
@Ben_J_Darling giving us a hand at @LouWerff’s fantastic 3D slicer image processing training @resplat #3dprinting pic.twitter.com/HF97jRbNmL
— Dr. Paul J. Mignone (@PJMignone)
November 24, 2015
For the majority of the workshop, participants were taught the steps required to generate 3D surface models of anatomical features from DICOM datasets such as MRI and CT scans, for 3D printing and visualisation purposes.
Image: A 3D volume rendering of a brain that has been isolated from an MRI scan of a patients head.
Feedback from the workshop was very positive. The below interactive graph displays the score out of 5 that participants (who filled out the end-of-workshop survey) gave for a number of different questions.
The majority of participants felt that the material covered in the workshop was relevant to their research/interests, and many of them intend to continue using 3D Slicer in the future.
If you have any questions or comments, don’t hesitate to contact me. You can email me at louisevanderwerff@gmail.com and tweet me @LouWerff.