Research Platform Services Blog
Month
By Yamni Mohan
Hello! My name is Yamni and I am a data-wrangler. I am the newest Matlab research community co-ordinator at research platform services.
I was recently called dragon-lady by a friend and at first I was a bit uncomfortable with it. I have since then decided that I really like this title. It is particularly relevant that I bring this up in this blog post because from here on, I am going to talk about dragons. If I am a dragon-lady, then my data is my dragon. This parallel may seem absurd but I believe it is quite accurate. Below is a list of all the ways data is similar to dragons.
Both data and dragons come in all sizes and forms.
Types of Data:
http://www.howtoprogramwithcoldfusion.com/coldfusion/wpcontent/uploads/2013/09/variables.jpg
Types of dragons-
When you have ideas, having data supporting your ideas, like having dragons on your side can be empowering.
Here is what it
looks like when your data doesn’t support your conclusions.
http://www.huffingtonpost.com.au/2009/12/08/will-fox-news-enforce-its_n_384612.html?ir=Australia
Here is what it looks like when your dragon doesn’t support your conclusions:
You gotta admit, both will sting a little.
Both data and dragons can be legendary.
A legendary dragon:
the_hobbit_the_desolation_of_smaug_1920x1080
Legendary data:
I am going to tell you the story of Vagusstoff- literally translated to Vagus juice. Vagusstoff, also known as acetylcholine, was the first neurotransmitter discovered. Not only do neurons secrete it to communicate with each other, it is also the neurotransmitter which exists in the nerve muscle interface (neuro-muscular junction). Acetylcholine is secreted by the vagus nerve and when it is present, the heart slows down. Legend has it that its discoverer Otto Leowi conceived the experiment to show that information transfer at the neuro-muscular junction was mediated by neurotransmitters in his dream. He then immediately headed to the lab and conducted an experiment to collect data. If you are a little squeamish, you can easily skip the next paragraph which describes the experiment.
Leowi had a frog heart beating in a saline bath (the heart tends to beat for a while even when taken out of the body). He stimulated the vagus nerve and watched the heart slow down. He then collected the fluid immediately surrounding the heart and applied it to another frog heart in a saline bath devoid of any of its original connections. To his delight (I wasn’t there but I presume he’d be delighted), he found that this process slowed the second heart down showing that neuro-muscular communication occurs with the aid of chemicals.
https://en.wikipedia.org/wiki/Vagusstoff#/media/File:Vagusstoff2.png
Loewi’s legendary data settled the question of how information transfer occurs at the neuro-muscular junction at that time, but it is one of my all-time favourite because it was so simple and elegant and to the point.
Having read all the similarities between data and dragons, you maybe wondering what I am doing here. I am a PhD student in the department of Optometry and Vision Science and I use Matlab for all my data analysis.
Why Matlab you may ask?
Like many scientists, I fell unwillingly into the programming world, 2 months before my Masters thesis was due. Honestly, I picked Matlab because the software I was using could export Matlab files and I had access to Matlab. As a beginner, I also found the user interface pretty simple to work in given the limited amount of time I had. Of course, my love for Matlab has increased alteast 10 fold since and I will swear by its ability to allow you to extract meaningful information from your data.
Why Vision Science?
This is a harder question for me to answer because it is hard to pin point one particular reason. That there is a system that takes in a lot of simple inputs and compiles these inputs in a manner that allows us to make sense of the world around us in any meaningful way is an incredible feat. Armed with my keen Matlab skills, I would like to contribute a little towards understanding how the visual system does what it does.
Here at Research Platform services, I hope to further your Matlab skills and help you wrangle your data dragons. So dragonlads and ladies; if you ever want to discuss your data or dragons with me, please contact me at ysmohan@unimelb.edu.au or tweet @yamnimohan
I am Yamni: PhD Candidate, Dragon Lady, Data Wrangler.
By Isabel Zbukvic (PhD Candidate, ResPlat Intern) @isabelzbukvic
Research is going virtual. Journals and reference managers are moving online, academics are increasingly using Twitter to connect, and blogs are a legitimate way to find out about new publications and cutting-edge technologies. I joined the ResPlat team 4 months ago to manage the online presence for a mid-career researcher, Dr Jee Hyun Kim. Let it be known: I am not a marketing or IT graduate. I am a neuroscience PhD candidate. When I started this journey my tech skills did not go much beyond searching PubMed through the library website. But I have since built a solid Twitter following, created a Wikipedia page, learned how to create social media graphics, and mastered managing multiple social media channels simultaneously.
At ResPlat, we believe in the power of the internet to increase the impact of research by reaching more people in more places. We also believe that “cyber-citations” (such as how many times an article has been mentioned in blogs, cited in Wikipedia, or shared on Twitter) reveal the impact of a paper. Traditional citations are currently the most widely recognized measure of research impact. However, there is an emerging approach to measuring impact that captures these online forms of credit. This method uses alternative metrics, or AltMetrics.
“Altmetrics expand our view of what impact looks like, but also of what’s making the impact.” - J. Priem, 2010. Altmetrics: A manifesto.
The advantages of using AltMetrics in addition to citations alone is A) their speed (online feedback takes mere hours compared to literally years for traditional citations to accumulate) and B) their ability to capture diversity. By representing your research as it appears across a wide range of online platforms, AltMetrics builds a more detailed, informative picture of your true impact.
I want to share what I’ve learned about increasing your web presence to help make it easy for all researchers to increase their online impact and thereby improve their AltMetrics score. As the academic world moves increasingly online, AltMetrics about your online impact are being used by a growing number of institutions to measure and report the attention and engagement surrounding their research outputs. Going forward, they could be used to help inform decisions on hiring, grants, or tenure. Of course improving your online presence is not just a matter of increasing your AltMetrics score for its own sake. Getting yourself out on the WWW is also about connecting with other researchers, engaging with the public, and telling the world about the incredible work you’re doing.
Wikipedia: Embrace your inner gnome
Not all internet trolls are evil. In fact, Wikipedia survives and thrives on users known as WikiGnomes. These are the people that build, approve (or reject), and edit the pages of this tome. To increase your citations across Wikipedia (which increases your AltMetrics score), you must become a WikiGnome!
For me, learning the ropes of Wikipedia was a learning curve. I’ve never coded, so seeing the other side of a webpage was something similar to dissecting my first rat in Mr. Gannon’s Year 9 biology class: terrifying, fascinating, and completely enthralling. For anyone who likes reading articles to find the best place to add their own citation (i.e. every academic ever), Wikipedia editing is seriously addictive. Thankfully, you do not need coding skills to be a WikiGnome! Wikipedia has a very handy feature called VisualEditor that makes it possible to make changes in situ – this means you can edit directly onto your page of choice, in plain English, with the click of a button. There are definitely some glimpses into the realm of web code, especially when you’re starting a page from scratch: fear not! Once you get the hang of it (and there is SO much information in Wikipedia on how to use it, unsurprisingly) you will be gnoming with the best of them.
Twitter: Find your unique voice in a choir of 320 million
Twitter is your most powerful tool for creating personal connections with both academics and the public, as well as the people that bridge the scholar-everyday-human gap (like bloggers and journalists). There are many personal benefits to increasing your social media presence as a researcher (and you can read about them here, here, and here). I want to tell you about what’s worked for me.
First, you need to find your voice. This will be what you Tweet about, as well as your tone. I suggest choosing two topics: your major and your minor. Your Twitter major will naturally be your own research. Keep it broad, so you can easily Tweet to both academics and the public. For instance, Jee’s research involves using rodent models to study the neurobiology of extinction learning. This can broadly be classified as research about memory (hence, @About_Memory). This is easy to communicate for both scholarly and lay followers. Your Twitter minor will be something that represents something more personal, like your funny side, your family life, or your love of internet cats. Jee’s minor still relates to research but is more about the personal experience of being a young woman in academia, the trials and tribulations of “the system”, and advocating for #womeninSTEM. Tweets that earn the most engagement for Jee are usually those directed at academic followers rather than the general public. I suspect that as her following grows, this may change - Jee gets at least a couple of new followers every day, so time will tell.
On that subject, when you first start using Twitter, it may feel ridiculous sharing content with 0 followers. My advice for these early days is to persevere! Start by following people in a similar field. There are several hashtags that you can search to help you find others in the research community (like #acwri #scholarSundays #ECRchat #phdchat). When you follow a user, they usually follow you back. Once you have a few followers, the Twitterverse will open up. Trust me.
My top 5 Tweets for @About_Memory (provided by Twitter Analytics)
Instagram: Become an artist without cutting your ear off
Yes, Instagram is a valid platform for researchers. And no, you will not need to perfect your duckface (although the occasional selfie can’t hurt). Instagram takes advantage of the fact that humans are primarily visual creatures (which also explains why images on Twitter receive more engagement than text only). Instagram is now also the #2 social media following Facebook in Australia, with over 5 million active monthly users. It’s is a wonderful way to share all kinds of images: figures from papers [see A1], infographics about your field, or quotes from yourself. Ok, so quoting yourself has a bit of the royal ‘we’ about it. But there is no better way to tell the world about what you do than by putting it in a great font, on an eye-catching background. After all, you’re the expert! Use a simple, free tool like Canva to create images of your own pearls of wisdom. And using a social media manager (see below) means you can post them all to Twitter at the same time. Double happiness.
Image made for @drjeehyunkim on Canva, using a histology image from my own collection
Social media manager: Streamline your operations
Many of us wish to be more savvy with social media, but feel like time won’t allow it. Totally fair! I felt the same when I started. I won’t lie, you absolutely do need to commit at least a few hours per week for your online presence to have real effect. Luckily there are several tools around designed to save you time. These platforms (e.g. SproutSocial, Buffer, Hootsuite, Feedient) allow you to manage all your social media channels from one dashboard. You can schedule your posts in advance, and your manager will automatically publish the content at the most appropriate time. This means you can sit down on a Sunday afternoon, and schedule all your Twitter, Facebook, and Instagram posts for the week (or even more). Genius.
I wonder how many academics have an ‘eat now’ reminder set in their phone so they don’t forget lunch
It’s been a wild ride learning the ropes of building a web presence. I’d say the biggest challenge has been the times when I’ve put content out there and it hasn’t received much engagement. In those moments it does feel a bit like you’re yelling into the abyss. But for me, the instances where I’ve engaged in live conversation with researchers on the other side of the planet about a new technique or the joys of publishing a paper make all those trying times worth it.
We know that many scholars use Twitter to discover the work of other researchers. The people who fund our work (i.e. the public) deserve to know how we’re spending their money. Young people need inspiration from more diverse community leaders, like women, people of CALD backgrounds, and members of the LGBTQIA community. The internet gives us an equal platform to do this. And moving forward, more academic institutions are more likely to acknowledge our online engagement using AltMetrics. I say, the time is now to start making your impact.
Appendix
A1. Never post unpublished figures on the internet. If you didn’t know, now you do. Anything you post on the web (including Instagram, Facebook, Twitter, your blog, anywhere!) is considered published material. That means journals won’t accept it – and your university may not accept it as part of your thesis.
by Aliza Wajih
Hey Everyone!
It’s ResBaz time again! If you have chosen the Inventor stream for your ResBaz conference or if you just would like insight into inventor this should be a good read.
So, What is inventor?
Inventor is a 3D CAD software offering professional-grade tools for 3D mechanical design, documentation and product simulation. If you are doing research on a product that you would like to design and possibly have manufactured, Inventor is the tool you would use to design it!
Its application is largely in engineering. This software helps you easily handle large assemblies and automates advanced geometry creation for intelligent components. You can design using sheet metal, plastic parts, steel frames and rotating machinery as well as tube and pipe runs!
However animation tools and free-form modelling make it a great software for art and free-hand design too!
Freeform Modelling View
Who is this class for and what do you expect to learn?
This class is for beginners! Don’t worry if you’ve never used 3D modelling software. We will go through it at a pace that will keep everyone on board! If you’re a fast learner there will always be more exercises to keep you busy.
In our class we’ll be going through basic design element. We will look at how to take a 2-dimentional drawing & make it a 3D model! We will also look at how to work with multiple parts and make more complex geometries further on in the course. We will conclude the session by learning how to do some free-form modelling, as well as 3D printing our final products!
It is going to be a guided session with plenty of helpers and plenty of fun - hope to see you all there!
Let’s bring our inventions to life with Autodesk Inventor!
Here is a rough timetable we will follow! See you all there :)
By Platy the Wrangler and Kerry Halupka
Howdy partner, I’m Platy the Wrangler, and I’m here to show y’all how to round up your data. You’re in the West now partner, it’s a wild world out here. If you want the full shabam I reckon you oughta listen to this while reading this here post.
Y’all better keep them voices down though ‘less you want to get stampeded by a herd of wild log files, those little critters surely can spook easy. They sneak up on you too, when you’re not looking, then suddenly there’s hundreds of ‘em, bearin’ down on you, all needing to be cleaned and processed, but all the while they’re multiplyin’.
Out here we got a lot of data, but we also got tools, yep they’re some gosh darn powerful tools too y’hear. Got ‘em for simulations, computations, analytics, algorithms… There ain’t no data we can’t wrangle. If you’ve got data needs wranglin’, you’re already one of us. We gotta stick together out here – there ain’t no knowing next time you gotta herd your data into the Publication Pen, and if you ain’t got tools behind you, you’re gonna have a mighty tough time y’hear.
Out here we got a few mainstay’s, you know the type – got that slow drawl that puts them critters at ease, can spot a code bug a mile away, always with their clicker finger at the ready to subdue it. Yeah, they’ve been around long enough to know you never stop learning.
There’s Alistair “Magic Fingers” Walsh. They call him that ‘cause there ain’t nothing he can’t do with a keyboard and some code. Some say he even knows how to make his data analysis more intelligent with what he calls “machine learning”, heavens to betsy that’s some fancy stuff there. They say sometimes he even scares the code bugs into submission with his damn near perfect critter impression, we caught it on film here, but I don’t like to look at it, scares the bejeezus outa me.
Alistair “Magic Fingers” Walsh
Fastest lasso-arm in the land belongs to Yamni “Annie Oakley” Mohan. If you let that smile fool you even for a second you’ll be wrapped up in no time. Most people only make that mistake once. If you’re on her good side though, and if you’ve got any sense in ya you will be, she can show you all the cleverest tricks of the trade. MATLAB-mountain is where she’s at, see that colossal peak out there in the distance?
Yamni “Annie Oakley” Mohan
It can get pretty wild out here, but Dan “The Man” Sandiford never loses his cool. The way he deals with them critters you’d think he was out for a Sunday stroll. Some say he used to be a snake charmer in the east, they say that’s where he picked up his mean Python skills. Others say he used to be a bee keeper, that’s why he can keep his cool an’ quit the trigger finger trembles even when his code is covered in bugs.
Dan “The Man” Sandiford
Hear that yee-haw over past MATLAB-mountain? That there is Pippa “Calamity Jane” Karoly. Some folks say she can read minds just by lookin’ at you. Between you and me, those rumours are actually half true, she also needs a computer and an EEG though. We all thank our lucky stars she’s on our side, them powers would be damn near god-like in the hands of the critters.
Pippa “Calamity Jane” Karoly
Some among us travelled vast seas to be here, none are more revered or feared than Scott “Dread Pirate” Ritchie. You’ll know him by that steely gleam in his eye and his catch-phrase: “Rrrr me harties, use R!”. He’s been here for longer than I can even remember, steerin’ us all in the mystical ways of R.
Scott “Dread Pirate” Ritchie
This lot are wild as they come though, gotta be wild to take on the perils of the west day after day, yep, they be crazy. That’s why our little sleepy town has Sheriff Kerry “Crazy Eye” Halupka. Woah nelly does she have her work cut out for her. But if you’re new in town she’s the one to talk to, she’ll set you up with one of them wild wranglin’ geniuses for a lesson. They’ll have you swingin’ that lasso with the best of ‘em before you can say “there’s a snake in my boot”.
Kerry “Crazy Eye” Halupka
Sun is settin’ now though, in an hour the glow of your screen will be the only light in this perilous landscape. Head in to town an get yerself set up, make sure you sign-up for a lesson quick smart, or email if you’ve got some more questions. Remember y’all, we got stick together out here, data can be wild and ruthless, but if you want to learn to control it you’ve come to the right place.
They see me wranglin’, they hatin’
We’ve been teaching R workshops for over a year now at the University of Melbourne, and one thing we’ve noticed is the disparity in skill level among workshop attendees. Researchers generally fall into one of two catergories:
Absolute novices: those who have heard of R, but have never touched a programming language before.
Regular users: those who are using R in their research, possibly on a regular basis. They can modify scripts, and have a general understanding of the language basics, but want to extend their knowledge.
Those who fall into the first category fit the Software Carpentry attendee archetype. The novice materials work well for them. The latter group typically find the novice materials too basic, and end up quickly bored and tune out. However, like the absolute novice they have never encountered programming concepts, and have never written their own function, nor understand for loops.
Early last year we recieved a request to run a workshop for a group of quantitative ecologists at the University of Melbourne. The organiser, Saras Windecker had attended a novice workshop previously, found the material too basic, but had appreciated the best practices and programming concepts. Together we sat down, and came up with a rough outline for some of the extension material she thought her group would find useful, and taught a two day workshop themed “effectively working with data”. A write up of the workshop can be found here
Learning about functions with @JovMaksimovic at the @swcarpentry @qaecology workshop! @ResPlat #ResBaz pic.twitter.com/kmT8aGesjC
— Scott Ritchie (@sritchie73)
July 7, 2015
Since then, we’ve typed up our notes from the workshop into the Software Carpentry lesson format, and can now present you with intermediate materials for regular useRs.
Just like the novice materials, the lesson spends a lot of time covering the staple programming concepts taught by Software Carpentry:
At a faster pace, we also expose attendees to more advanced concepts and R specific material that gets missed out in novice lessons:
apply family of functions.data.table and reshape2.data.table and plyr.foreach loops.R markdown.We have contributed these lessons to the Software Carpentry community, and hope that the community finds these materials useful. We look forward to hearing about intermediate and advanced R workshops in the future!
by Aliza Wajih
It is hard to believe that a small community that started with just 4 initial CAD trainers we have managed to reach a number of over 15 in just under one years!
After our successful Autodesk Inventor training session in August, we successfully made our way into the Engineering Community at the University of Melbourne by working along side professor Colin Burvil.
CAD Training in August 2015
In our training session we trained six of professor Colins’s most brilliant students who then went on to teach postgraduate students of their cohort! (talk about the snowball effect!)
It makes me very happy to say that the course notes designed by Paul and I were used by the new trainers to teach the Inventor course! In other words our Autodesk inventor CAD curriculum was used to compliment the Masters and Bachelors course work for design subjects offered by unimelb!
This year we were able to help both postgraduate and undergraduate engineering students to develop their projects using Autodesk Inventor by holding a number of weekly drop-in sessions in August and September. Our popular drop-in sessions allowed students to gain knowledge of CAD as well help them refine their projects. Some outstanding work was produced, and here is just a snippet of it!
Gearbox exploded diagram by Vincent, Bentley and Aston!
All students who came to the drop-in session and hacky hour were given access to our notes. We not only received great feedback but also requests for holding more training sessions!
This year, at ResBaz, I will be working with a few of our graduate trainers as well as other students from professor Colin’s class!
My New CADventurers!
I hope this year the CAD community continues to rise exponentially, just the way it has been going! Watch out for more future events and trainings!
We have a mascot, and it’s a platypus. Wikipedia says: “The unusual appearance of this egg-laying, duck-billed, beaver-tailed, otter-footed mammal baffled European naturalists when they first encountered it, with some considering it an elaborate hoax.” But be assured, our choosing of ResPlaty (yep, that’s its name) is no hoax.
Much like the semiaquatic egg-laying mammal, our team is a hybrid of sorts - offering a diverse range of skills and tools for all research types. ResPlaty, a technophilic researcher, thus has the power to change its look based on these desired research skills and tools.
Upon donning a pointy hat, ResPlaty transforms into a data vizard - armed with the ability to cast data visualisations on the web (specialising in tools such as D3 and CartoDB).
Where there’s wild data to manoeuvre around ResPlaty becomes a seasoned data wrangler - lassoing the numbers and performing kick-arse data analysis (R, MATLAB, Python).
Looking to create, build and explore the 3D world? ResPlaty the CADventurer has you covered! You’ll be 3D modelling and printing in no time (3D Slicer, TinkerCAD, 3D Printing).
And if burrowing into the web is what you’re after, ResPlaty the data miner will help you collect and play with all the text data your heart desires (NLTK, spreadsheets, surveys).
Of course, ResPlaty has a more ‘social’ side too, and takes the form of data vinci - allowing us access into the data-driven worlds of the humanities and social sciences.
And then there’s Rosie. She keeps us on our toes so we don’t forget the importance of research diversity - not just between departments and faculties, but within our ResBaz community too!
Why have these mascots? Because when reaching out to our community with such a variety of tools and skills to offer it helps to find something (or someone) to identify with - a role to plant your feet into, a hat to wear. ResPlaty and all its eggs, beaks, tails, costumes, accessories, skills and talents will therefore play a large role in the upcoming Research Bazaar Conference!
Which ResPlaty will you be meeting?
At a typical academic conference keynote presenters will talk about their research. While that’s all well and good, what you don’t get to hear so much about is their story. How did they get to where they are today? Why are they so passionate about what they do? We’ve picked three of the most interesting people we know in research and have asked them to present a “keystory” instead. Here’s a little about each of them:
Dr Fiona Tweedie | @FCTweedie
Data Scientist, The Australian Ballet
“Ivory towers and revolving doors”
After falling in love with the Roman orator Cicero in first year, Fiona Tweedie completed a PhD in Roman History at the University of Sydney. During her candidature, she taught Ancient History and Latin as well as working as a tour guide in Rome and Pompeii. The trials of Roman Law and getting groups of school children safely up and down Mt Vesuvius persuaded her that she is indestructible.
Post PhD, she left the Academy and worked in research and policy for the NSW and Australian governments, where she struggled with the tyranny of dot points while relishing weekends free of the feeling that she should be writing. Meanwhile, she moved to Melbourne and began volunteering with Open Knowledge Australia and discovered the world of hackathons. In 2014, she joined Research Platforms Services at the University of Melbourne to bring a humanities flavour to a science-heavy team. She spent two years building up the Digital Humanities capacity at ResPlat while wrangling an increasingly complex training program.
Fiona now works at the Australian Ballet as their first in-house data scientist, where she is combining her loves of data and culture.
Ri Liu | @riblah
“Finding truth, beauty and purpose in data”
Ri is a data visualiser who uses design and code to paint narratives of structural inequalities. In her work, Ri focusses on expressing data in novel ways and exposing social injustices; from creating art out of motion captured dance data, to exploring the gaps between men and women around the world.
In 2015 Ri’s Close the Gap project was a finalist for the UN Human Development Data Visualisation Competition and was awarded an honourable mention in the Kantar Information is Beautiful Awards. Her work has been featured in various online and offline publications including Fast Company, Wired UK and The Washington Post.
She has worked on projects for Google, Facebook, Foreign Affairs, The Conversation, The Nation, Popular Science and Pew Charitable Trusts.
Although lacking in substantial academic qualifications, Ri is a researcher in spirit, guided by curiosity in her work and a motivation to contribute a net positive to the world.
Dr Tseen Khoo | @tseenster
Co-Founder of The Research Whisperer, Convenor of the Asian Australian Studies Research Network (AASRN)
“Why am I here again, and again?”
Tseen can’t seem to work out what she wants to be when she grows up. She has swapped between academic and non-academic roles four times in her career so far, and is constantly lured back to academia by the idea of doing research.
As a PhD student, she helped found a national research network – the AASRN – that has become the peak body for the area of Asian Australian Studies internationally. She is currently still the research network convenor, and has previously been a University of Queensland Postdoctoral Fellow (2001-2004) and Monash University Research Fellow (2004-2010). Tseen has landed a couple of major grants, various minor ones, and published on critical race studies (particularly focused on Asian Australian cultural production and politics), early career researcher experiences, and academic research and funding cultures.
While working as a research grant developer at RMIT, Tseen created and runs The Research Whisperer (a recognised research culture and development blog) with Jonathan O'Donnell. She is a former editor (and current editorial board member) for the Journal of Intercultural Studies, founding editorial advisor for Peril (an arts and culture magazine), and has been recently appointed to the editorial board of Australian Universities’ Review.
At the moment, Tseen is a lecturer in research education and development at La Trobe University. She wears many social media hats, and is a zealot about the value of building digital networks to create communities for collegiality, personal support, intellectual sharing, and access to great memes.