Research Platform Services Blog
Month
Hello all,
My name is Louise and I am the newest member of the Research Bazaar team, having just started as a Research Community Coordinator with the team at Research Platform.
I’m very excited to be joining the @ResBaz team with @ResPlat; running digital skills workshops for researchers! Hello all!
— Louise van der Werff (@LouWerff)
May 11, 2015
After completing a Bachelor of Science and a Bachelor of Engineering (Materials) at Monash University in 2008, I went on to do a PhD in collaboration with Monash University, CSIRO, and Smith & Nephew. During my PhD I developed novel multi-component composite fibres with thermochromic behaviour. In other words, they changed colour with temperature changes (think mood rings in fibre form). Tuned to work in the physiological temperature range, these fibres were created as a potential method for thermal mapping of wounds beds, via their incorporation into bandages.
Later down the track, I was involved in a Researcher in Business program within CSIRO, helping Australian medical devices company Anatomics develop their porous polyethylene surgical implant material PoreStar. Outside of academia I have pursued my own developing interest in 3D printing by purchasing a Makerbot Replicator 2X, combining my knowledge and interest in polymer processing with my passion for DIYing and craft. With this new and exciting piece of hardware I taught myself some rudimentary 3D modelling skills and combined 3D printing with silicone moulding, epoxy resin casting, and general crafty inspiration to come up with some cool new products I now sell online and at markets under the brand name Wordosaurus Text.
a. my Makerbot replicator 2X, b. a treble clef 3D model in MakerWare c. a silicone mould of the 3D printed master shapes d. A final epoxy resin cast.
I have joined the ResBaz team at Research Platforms to develop awareness and run training sessions relating to medical image processing, in particular the generation of 3D models from medical scan data in the DICOM file format. DICOM image files are produced by a range of medical imaging equipment, (MRI, CT, PET, XRay etc), and consist of a series or stack of cross-sectional image slices across a region of interest in the body. By combining these slices a 3 dimensional representation of the body can be generated.
Generating 3D models of anatomical features from DICOM image files can be beneficial in multiple scenarios. Physical 3D prints of anatomical features such as bones may be used for teaching or training purposes, for the planning of a complex surgery to reduce overall theatre time and risk, and for the creation of implants custom designed and fit to a particular patient. The “3D Printing for Medical Applications” seminar (#3DMed), held on the 14th of April this year, highlighted many applications in which this functionality has been harnessed, and how it could be harnessed in the future.
The software around which the training will be designed is 3D Slicer, an open source community platform with a wide range of capabilities. It’s modular nature provides flexibility and the ability to add on new functionalities as required. It’s interactive visualisation capabilities includes the ability to display arbitrarily oriented image slices; segment, label features and generate colourmaps, and render 3D models of desired anatomical structures.
Screenshot taken within 3D Slicer from inbuilt example dataset ‘CTChest’
As this training course is in the very early stages of development, there is ample opportunity for community input and feedback in regards to the content of the material covered. This course is intended to provide researchers and medical staff with valuable and relevant image processing and 3D modelling skills. If you feel you would benefit from this course, or if you know somebody who might, please feel free to contact me to discuss your requirements, at louisevanderwerff@gmail.com, or tweet me at @LouWerff.
Are you using MATLAB for your research and have the feeling that your code could run faster? Come along to a free information session to learn about how you can use the MATLAB GPU toolbox to easily accelerate your applications (Tuesday, 2 June 2015 from 10:00am to 11:00am). We encourage you to come along even if you don’t have a GPU, since we may be able to support you through cloud based computing.
This short overview will help you work out if the MATLAB GPU toolbox will work for your applications. There will be free follow-up workshops with smaller groups of people to help you adjust your code for use with the MATLAB GPU toolbox. These follow-up workshops will be discussed further at the information session, and tailored to your specific needs.
For more information about the event, and to sign up, check out the event page here.
By Damien Irving.
Over the past few weeks we’ve been thinking about how best to provide support and assistance to the global network of ResBazadors (local site hosts) in the lead up to ResBaz 2016. In particular, we know from previous experience that global communities eventually hit the “timezone barrier”. Half the world is asleep at any one time, so as an event grows it quickly becomes impossible to run a meetup that everyone can attend.
We’re so excited to announce that @MozillaScience are going to help coordinate #ResBaz2016! http://t.co/qj3bKAuVTe
— Research Bazaar (@ResBaz)
May 26, 2015
Organisations like Moziila Science Lab and Software Carpentry often hold the same meeting twice to cater for different timezones, but the audience on some of those calls gets so large that it’s hard to have the detailed one-on-one conversations that we’re looking to cultivate. Taking inspiration from mozsprint, we’ve therefore decided to run a continuous 24-hour call on the last Thursday of every month. Anyone who is interested or involved in organising a ResBaz event can call in to hear the latest news and to ask questions about running their own event. Members of the global coordination team will do shifts on Google Hangout to ensure full coverage of the 24-hour period, and notes from all conversations will be taken in the ResBaz gitter room.
So many great conversations happening in the new @ResBaz @gitchat room! https://t.co/9dMAAaAHuz pic.twitter.com/qVuJtQkf1g
— Damien Irving (@DrClimate)
March 16, 2015
This month’s call starts at 8am on Thursday 28 May on the east coast of Australia (i.e. AEST) and will then make it’s way around the world (the Google Hangout link is here). To help you figure out what time that corresponds to in your part of the world, here’s the shift times in UTC (this site is great for making timezone conversions):
The only pause in the conversation will be from 10-11am AEST for the Mozilla Science Lab Australasia Community Call, which we figured would be of interest to ResBazadors in Australia and New Zealand. The major topic of conversation will be the ResBaz cookbook, which will eventually contain all sorts of information and advice for ResBazadors. We’ll be hacking on the cookbook during mozsprint, so if you’re participating in that event we’d love your assistance!
Earlier this month, I had the fantastic opportunity to visit the Victorian Institute of Forensic Medicine to discuss the opportunities that 3D modelling and 3D printing can provide for professionals in the field of forensic science. While the historical list of scientific fields being misrepresented by non-scientific groups continues to grow, I cannot help but feel for the forensic science field.
Popular TV shows like CSI have misrepresented forensic science to the point that the even our own Victoria Police has to get involved in expectations management! This impact on public perception is also known as the CSI effect, which can effect jury members during trail. At the same time, when I got to the VIFM, a very small part of me was hoping for a David-Caruso-like detective to start dropping some classic one-liners…
Alas, it was not meant to be. Nevertheless, I was still in for a pleasant surprise when I got to the institute. My reason for being there was to expand the awareness of Resbaz’s #3DMed initiative, which aims to build and up-skill the medical community in digital and data-science tools such as programming languages, 3D modelling and 3D printing techniques.
VIFM Communications officer Ms Andrea Hince has been a strong advocate for VIFM collaborating with #3DMed, so much so that she offered for her colleague, Dr. Chris O’Donnell to present at our recent, highly successful 3D Printing for Medical Applications Seminar. His fascinating presentation on the use of 3D Printing in forensic science applications can be viewed below.
We had over 100 medical professionals attend the seminar early last month. When I started my presentation, I was equally surprised to see roughly 50 forensic science professionals at the presentation. Not only did Andrea go to amazing lengths to promote the event, but 3D printing was still very new to the forensic science field, with almost all attendees having never used a 3D printer before.
My presentation gave a brief overview of my adventure into 3D printing, how it impacted my research (for the better) and how it’s opening up new avenues into cross-disciplinary research. Combined with small, carefully targeted amounts of research funding, 3D printing technology is able to produce high-quality and innovative research outputs. Our RPRWG projects are testament to this strategy.
I also got to see some of the facilities at VIFM, including toxicology and the MRI room. While I was amazed to see some parts of a technologically impressive scientific field, it was also a sobering experience given the work mainly involved the ‘ex-situ’ analysis of someone that has recently passed, and usually under bad circumstances.
I left the facility with a new appreciation for the forensic medicine field. The potential for 3D printing in forensic science applications are immense. With the MCRIP bid to build a new innovation centre now submitted, we hope to be in a better position to collaborate with researchers in this space. A big shout out to Ms Andrea Hince on all her efforts in organising a fantastic presentation and visit!
Very excited to welcome @paulmignone to Vic Institute of Forensic Medicine to give a lecture on 3D printing #3dmed pic.twitter.com/QekS6z5q65
— Shinjuku Thief (@Hincerooney)
May 12, 2015
Log in to your Omeka account, add some data, attach files and share with the world. Easy, right? Not so fast!
As any researcher who collects data knows, organising it so that it can be interrogated usefully takes forethought. So at the recent Omeka workshop we ran here at the Research Bazaar, we started with hands off keyboards. Instead, participants were asked to create their collection on postit notes, then group the ‘items’ into collections and attach descriptive metadata. In some cases, it emerged that something such as a location was better as a collection of items rather than an item in its own right. In another cases, an artist was entered both as an individual, so that she could be represented as part of an exhibition, but also formed part of the metadata as creator of her works. By exploring how to arrange physical objects before jumping into Omeka, workshop particpants already had an appreciation of the importance of metadata and organising data.
@robbiefordyce @FCTweedie @parrotluke Yo, dawg!
— Omeka (@omeka)
May 5, 2015
Particpants came from a range of disciplines, from fine art to archaeology and included both professional staff from the library and archives and research students. The diversity of the participants reflects the flexibility of Omeka as a tool. It’s ideal for handling images but also makes a great database for other types of objects, from films to fish!
We’re exploring the possibilities of Omeka as a tool for managing cultural data collections as part of a year-long pilot in conjunction with the library. The resources from the workshop are available here. Thanks are due to ANDS, who funded the development of the workshop materials as part of our Data Carpentry program. And huge thanks to Lachlan Musicman, whose help in unsticking and reassuring participants on the day was invaluable!
Which blog posts from the last month had the most readership? We list our top 3!
1. “I didn’t feel silly about asking questions” by Isabell Kiral-Kornek.
Isabell reflects on our MATLAB workshop for women - offering insights into why it was done and how to helped!
2. “Introducing Text Mining (and Myself)” by Daniel McDonald
Daniel shares the wonders of NLTK, Text Mining and some of his research!
3. “#3DMed Wrap-Up” by Paul Mignone
Paul highlights the best moments of our “3D Printing for Medical Applications” seminar - held at Carlton Connect’s Lab-14!
BACK BY POPULAR DEMAND!
Due to the huge success of the female oriented workshop that we ran in May this year, we are proud to announce that we’ll be holding a beginner’s workshop, open to all researchers.
MATLAB is one of the standard tools in science & engineering. It is an extremely versatile high-level programming language that allows you to do pretty much anything: from controlling hardware to recording, analysing, and visualising data. And the best thing is that you can test small parts of your program immediately.
During the workshop, you will get a basic introduction to MATLAB’s user interface and then learn about basic programming concepts that allow you to write programs to read in and analyse your own data.We will cover how to write and use scripts, loops, functions, and conditionals.
Know your way around MATLAB, or want to refresh what you learnt last time? Then contact us to join our awesome team of helpers.
Find a more detailed explanation, dates, and schedule here and make sure to sign up! (This workshop is limited to 30 attendees.)
See you there!
Comments rolling in! See bottom of this post for ‘declarations of support’ :)
Over the past 3 years, the University of Melbourne has been experimenting with 3D printing as a technology which can help support researchers in making their ideas a reality (aka, “proof-of-concept” or “rapid prototyping”). We’ve worked with over 2500+ people in this 'community experiement’:
We are now asking you to help decide if we should carry on with this experiment, or more importantly which part of this experiment you see as being most valuable to you!?
Below you will find a link to a draft proposal we are putting before you the research and entrepreneurship community[2]. We are asking for those of you who are interested in 3D printing (using it in your studies, researcher or entrepreneurship) to 'sign your declaration of interest’, along with comments for how you think we can make 3D Printing work for you.
PROPOSAL FOR 3D PRINTING PLATFORM AT UNIMELB, (please read this link then leave your 'declaration of support’ below): http://go.unimelb.edu.au/6q9n
If you wish to leave detailed comments on sections of the proposal please do so on this living draft (Note: your comments will be published openly): http://go.unimelb.edu.au/2n3n
Thanks for your consideration and continued participation in the research community at the University of Melbourne.
[1]= Please RSVP October 9th and 10th for the #3DShow 2015: 3D printed car race, Shark’s Tank, Latest 3D Printers and much more!
[2]= As the Research Community Manager for the University of Melbourne I’ve promised to always be as open and transparent as possible so as to assure inclusion for all researchers regardless of age and/or stage of their studies.
Written by David F. Flanders, Research Community Manager, University of Melbourne https://dfflanders.wordpress.com/2013/07/16/research-community-manager-university-of-melbourne/
Dr Shane Battye: “I’ve been using 3D printing for a year now to create prototype microscope and robotic parts - see www.pathobin.com. Anyone now has the ability to rapidly prototype concepts from the drawing board in an affordable way.”
Paul Mignone: “Having achieved a 95% cost reduction in costs and lead times with my own research, I support 3D printing’s potential to help researchers produce lower-cost research outputs in lower time frames.”
Kae Sato-Goodsell: “I support the 3D printing programme at Melbourne University as it will give access to students and community to explore the possibility to research and try-out their ideas. The equipments is limited to most of the population due to the price and availability of support so it is greatly appreciated by the community. It is truly great that the programme is open to public, not just for the students but the people who teach them. It will be good to expand it to quick and quality scanning and small metal printing in the future – that will bring more opportunities to try-out great ideas.”
Kerry Leonard Graduate Researcher: “3d printing clearly represents the most exciting new method of production and manufacture for our future. As an artist, the potential of attempting new artworks which in the past have suffered from the limitations of budget and traditional structure, I am now able to consider possibilities totally unrealistic before 3d printing.”
Tommy Carron: “3D printing will bring value to the University and wider community by providing the tools and skills for research and industry. This is an exciting field that is moving from niche experimentation into the mainstream and will affect all our lives. The University of Melbourne is position to be the leading innovator and default choice for students and researchers who work with 3D scanning and printing.”
Mr Bruce Ferabend: “3D printing allows for a quick fabrication of designs and prototypes. This is invaluable for showing others and testing concepts along with fabricating equipment.”
From Charles La Trobe College “For the past few years, 3D printing has became a global phenomenon. From design to manufacturing has changed. 3D printing is cost-effective, environmentally friendly and easy to do. It is something important yet so simple. I’m a high school student. I love creating gadgets and assets. 3D printing has been a fantastic way of making my ideas into a prototype then a reality.
"It will provide a way to physically view items created in virtual reality”
“Potentially very useful for producing 3D models for education as well as parts for photographic gear for production of education material”
David Parris: “"Allows prototyping at reasonable cost. Is a disruptive technology that students and graduates should be fluent in.”
“3D printing helped me with my courses, and is definitely going to help me in future studies!”
Freddy Navas: “I fully support 3D printing for research and entrepreneurship activities to develop rapid prototypes of ideas, making it possible to refine product development, and further refine concepts.”
Dr Philipp Nauer: “As part of my research in soil microbiology I I investigate the complex internal structure of termite mounds, and develop innovative sampling equipment for soil gas. For me 3D printing is the ONLY way to get my parts manufactured at reasonable costs, as they are complex and low numbers. 3d-printing facilities at UoM would greatly increase development time and quality! In fact, every lab should have a 3d printer, just like a normal printer, to replace off-the-shelf parts and manufacture custom-designed parts for specific experiments!”
Dr Paul McMillan: “I am happy to provide my support to the proposal for a 3D printing platform at the University of Melbourne. It is essential that this capability is available to the staff & students at the university. In biological research, the visualisation of complex structures can be used as both a teaching and research tool. As manager of the Biological optical Microscopy Platform, I am also interested in custom building components (such as stage inserts or sample holders) for our microscopes.”
Djordje Dikic, CEO of SwatchMate: “As a company built around product development, we would not exist if we didn’t have access to the incredible 3D printing facilities of the University.”
Dr. Stewart Ryan: “I strongly support this important initiative to increase access to practical 3D printing technology and training on the University of Melbourne campus. This will be of great benefit to both my research activities and clinical surgical service for my RHD students and pet owning clients.”
Dr. Varsha Pilbrow: “I am using 3D printing to develop hand-held dental plaques for doing research in human evolution. The plaques help by providing standardization of research approaches and improving inter-observer repeatability. They add to the methodological rigour in palaeoanthropological research.”
Jas Johnston: “3D printing has been an important part of architectural prototyping and model making allowing the creation of physical representations of complex geometries and algorithmic design processes. This technology is now reaching the point where 3d printing is being used to print full scale architectural elements and buildings. It is vital the Uni Melb maintain and advanced understanding and interrogation of this technology to be a part of the design revolution that technology like this enables.”
Dinesh Kantheti: “It’s the future of research that will democratise innovation. Will become integral to research”
Nathan Clisby: “3D printing is an extremely promising tool for mathematics and mathematical physics. For educational purposes, appropriate 3D models can make it much easier to communicate difficult mathematical concepts, while for research purposes a good 3D model can be a great aide in developing intuition.”
Vikas Thondapu, MD: “3D printing technology heralds significant and potentially generational advances in the field of cardiology and implanted medical devices. Access to this powerful tool as a researcher will likely translate to clinical advances and improved patient care in the foreseeable future.”
Rohan Workman (Carlton Connect): “3D printing is critical to early stage prototyping for entrepreneurs and the more activity the better. I’m keen to see this program fully supported.”
Ioanna Ioannou: “3D printing could be very useful in surgical education. Trainees could be provided with a 3D printed models of body parts capturing various anatomies and pathologies. These models would be useful in teaching surgical approaches, or even practicing surgical procedures (depending on the availability of appropriate materials)”
Simon Young: “This is the future.”
Maxine Lee: “3D printing is shifting the landscape for entrepreneurs who can now bring their ideas to life in a convenient and accessible fashion (from design to manufacturing). Startup founders can now also benefit from lower prototype and production costs.” “
Michael Kuiper: "3D printing has been immensely valuable for visualization of molecules in the life science. It provides tangible models of protein complexes not easily explained in 2 dimensional media.”
Gil Rind: “3D Printing is a valuable potential tool for combining engineering and medical research, allowing for better medical surgical planning for preclinical experimentation, prototyping of useful tools and cheap alternatives for many research projects, and enabling of proof of concepts before paying for certain tools or devices to be manufactured in higher quantities.”
Linda Le: “Creativity opens up many opportunities”
Nick Pollard: “Innovation and involvement in 3D Printing at The University of Melbourne is very important for research projects in the various relevant faculties. It adds a whole new efficient method for prototyping and for even teaching concepts to students.”
Cameron Nicol: “I have now entered the workforce now and in my first few months 3D printing has played a massive role in allowing me to rapid prototype design and test them before progressing to more common forms of manufacturing, and in the not to distant future I dare this final step may not even be necessary. The same advantages can be seen in research and entrepreneurship. In fact I used 3D printing extensively in my final year project.”
Tara Elizabeth Cook: “I use 3d printing as part of my doctoral research in the Visuals Arts at the VCA&MCM. 3D printing is a wonderful tool for artists as well as a practice in itself within the Visual Arts. 3D printing is rapidly proliferating contemporary art globally and becoming a commonplace part of artistic production today. Having a 3D printing platform will assist the university in maintaining research excellence, innovation and relevance.”
Antonio Gonzalez, PhD: “I can’t talk for everyone but in my case, it has provided me with a new field of critical enquiry that art historians might follow in a few years, once the stigma attached to 3D printing is vanished. Also, itwould be very usefu for art schoalrs to think more about the aesthetic possibilities that 3D printing can offer to students.”
Recap of the MATLAB workshop for female researchers
We recently ran our first workshop that was advertised as being primarily for female researchers. We did this to encourage more women to unlock their programming potential!
There is a worrying
gender gap in IT. And the idea that this may translate to researchers’ programming ability is not too far off. This may influence the potential of research, the possibility of getting published and even help launch a successful academic career.
So we decided to run a workshop that was primarily for female researchers, run entirely by female trainers and helpers. Luckily all the best MATLAB users I know are the women around me, so finding helpers wasn’t a problem. But we also had fantastic volunteers from other areas. Aliza Wajih (@awajih08), Anita Ponsaing, Amy Parker Watson, Philippa Karoly, you were all amazing!
The workshop was quickly booked out - with a waiting list that was as long as the number of spots we had offered!
18 of the 27 researchers who signed up attended (we will need to work on that ratio). 17 women and one man, who we were able to offer a last-minute spot due to the drop-out.
Kerry (@kerry_halupka) and I (@isa_kiko) had a great time teaching this course. We seemed to get everyone engaged and received some lovely feedback over the four days.
Naturally we wanted a more formal way to find out if female-only workshops are necessary in order to engage women, so we designed a survey.
Our first question was:
This workshop was advertised as a “MATLAB for female researchers”. I would have felt equally comfortable signing up for a course described as…
Responses were given on a scale from 1 (No way) to 5 (Totally) and 12 women filled out this part of the survey.
In a perfect world, we would have hoped that there’d be no difference between signing up for a course advertised for “female researchers” and a course advertised for “researchers”. Even though the gap wasn’t too big, it was still there. However, a quick fix to encourage more women to come might be to simply run workshops “for beginners” instead.
We then wanted to dig a little deeper, asking participants to tell us about the atmosphere, which everyone who had been to another workshop before (8/13) agreed, was excellent. So we asked:
If there was a difference, what caused it?
The overwhelming majority attributed the good atmosphere to the small groups and our excellent helpers and instructors <3, with two attendees mentioning that they thought having a workshop for women and specifically run by women made all the difference.
However, when we asked:
What did you like about having a workshop that was primarily for women?
we got some interesting feedback:
“I didn’t feel silly about asking questions”
“I can communicate with many talented women researchers”
“The ‘feeling’ of the course is different”
“It was great, no attention seeking men”
“Female teachers”
“Everything. Having women as demonstrators was also very empowering. Having women who seem just like me, and are examples and role models, and are demonstrating that the material is easy to use, was fantastic.”
So while our survey shows that we might be ok advertising for beginners, we also found that our attendees genuinely enjoyed a space that lacked the usual gender dynamics.
And last but not least, I myself really enjoyed this course. I met brilliant women who weren’t afraid to ask questions and who seem to have become good friends over the course of the workshop.
I think we’ll keep running these in the future. But I’m also interested in finding more ways to encourage other minority groups to attend our workshops and feel like they have a safe space to learn and improve their programming skills. Please share your ideas about how to do this with me!
By Damien Irving.
At the close of the inaugural Research Bazaar conference back in February, we announced our desire to make it a multi-site event in 2016. By running multiple ResBaz’s simultaneously we’ll be able to reach more researchers and create more buzz around the event, which will hopefully translate into increased sponsorship opportunities (keeping the event free is a priority) and also increased exposure of the fact that researchers are crying out for quality training in the latest digital research skills.
Over the past few months we’ve been blown away by the amount of interest we’ve had from not only universities in Australia and New Zealand, but also throughout North America and Europe. While each individual ResBaz site will have a great deal of autonomy, when we made the announcement we had envisaged that we’d provide some central coordination and assistance to help new sites with planning, logistics and general advice. This would have been achievable for a handful of sites scattered around Australia and New Zealand, however tens of sites from all over the globe is a little beyond our capacity! Enter Mozilla Science Lab. The team from MSL were fantastic supporters of ResBaz 2015 and they’ve agreed to be the central coordinator for ResBaz 2016. Given their experience running large and globally distributed events (e.g. MozSprint), we’re absolutely thrilled that they’ve jumped on board. Our next community call for the global network of ResBazadors (yep, that’s what we’re calling the hosts at ResBaz sites) will be later this month, but in the meantime jump on the ResBaz Gitter room to keep up-to-date with the latest happenings and/or contact us at research.bazaar@gmail.com if you’d be interested in becoming a ResBazador!
We also have @MozillaScience science at the bazaar! Come chat to @kaythaney & @billdoesphysics #ResBaz pic.twitter.com/cXeuvbRqyg
— Research Bazaar (@ResBaz)
February 17, 2015
Law is probably one of the most book-bound disciplines in the academy. “Reading law” is what lawyers call practical legal training. Lawyers love the idea of bookshelves filled with identically bound volumes of law reports. Sure, legal researchers use library databases and e-journals – but more often than not, we download and print out the pdf before taking notes by hand and writing up our research for publication in hardcopy.
In short, legal research is ready for a digital revolution. After all, law is text and text is data and data can be mined, mapped and manipulated. And so enter Resbaz. Research Platforms Services, in conjunction with Melbourne Law School’s Graduate Researchers’ Association, recently ran a workshop to introduce legal researchers at MLS to a range of digital tools to support legal research endeavours.
The workshop was organised around four stages of legal research: collecting material, managing and analysing data, writing and sharing. Daniel McDonald introduced text mining for lawyers, and the potential for Python and Natural Language Toolkit to analyse large volumes of text such as judgments, legislation, or representations of law in the media. Lachlan Musicman demystified databases and Fiona Tweedie explained collaborative writing with Authorea and creating digital exhibitions using Omeka. I took the opportunity to spruik my global maps charting every national constitution ever written, created using CartoDB. Finally, Dejan Jotanovic encouraged us to stop lurking on Twitter and start communicating our research to the rest of the world.
Now @heyDejan debunks some myths of social media for researchers - check out #auslaw or #auscon! pic.twitter.com/ic6C18A64h
— Research Platforms (@ResPlat)
April 28, 2015
And the reaction from legal researchers? For some, it was the first time they were exposed to so much tech talk, and naturally it takes a while to become familiar with new languages and concepts. (Now we know how non-lawyers feel when we use incomprehensible legal jargon!) For others, this brief introduction opened up exciting new directions for legal research, or for learning new skills and doing research more efficiently. So while nothing will replace the close reading that lies at the core of legal research, digital tools can provide legal researchers with the means to take legal research down new pathways, to collaborate across disciplines and to communicate our research to new audiences in new ways.
Anna Dziedzic is a PhD student at Melbourne Law School and a recent convert to social media and mapping.
Anna shares her research journey from word doc to interactive @cartoDB map with a little help from us! pic.twitter.com/xHAu04c3bd
— Research Platforms (@ResPlat)
April 28, 2015
The insane popularity of Software Carpentry workshops in Melbourne along with the rise of newly trained Instructors from our Train-the-trainer program has made it increasingly difficult for all of us to keep track of workshops being run in Melbourne.
It’s important for us all to be aware of when and where workshops are being run. All of us are approached by different groups wanting workshops run for their institutions, but we’re only a limited pool of people, most of us who are working on PhDs. Since we all work together to instruct at each other’s workshops, we also need to work together to make sure we have time to instruct, and aren’t getting burnt out.
Although we do have a Software Carpentry mailing list for Australia, it’s easy for information to get lost in long email chains, and especially hard to collaborate on specifics like dates instructors and helpers are available. I was mulling this problem over in a meeting with COMBINE, a student group who have taken the lead in organising several workshops since ResBaz, and Harriet Dashnow suggested we create an Etherpad. Etherpad is a collaborative document editing program, which is used extensively during Software Carpentry workshops to promote interactivity between students.
Interested in helping out at a @swcarpentry workshop in Melbourne? Join our etherpad to volunteer! https://t.co/N93ZfhmhKN @ResPlat #ResBaz
— Scott Ritchie (@sritchie73)
May 1, 2015
This has proven to be an overwhelmingly successful experiment. Since publicly announcing our Melbourne-workshops etherpad last week, five workshops across three institutions have begun being organised. Instructors have begun putting their names next to various workshops to volunteer their time and expertise, and workshops further down the pipeline have even had helpers come onto the etherpad to volunteer their time! Best of all, no email chains!
Interested in helping out at a Software Carpentry workshop in Melbourne? Come volunteer your time as a helper on our Melbourne-workshops etherpad!
In the lead up to our successful Research Bazaar conference we put in a lot of work to develop lesson materials for the R stream. At the time, the R instructors in the Software Carpentry community were all using their own lesson materials because the centralised teaching materials were a literal translation from the Python materials, which were not representative of R one would encounter in the wild. Although there had been a lot of talk about developing better materials, no one had taken charge.
We had run several R workshops in the previous year, cobbled together from various sources, and were determined to get useful R materials ready for ResBaz. We chose to develop teaching materials around the Gapminder dataset, a rich dataset containing data on the life expectancy, population, and GDP per capita for every country since 1952. It’s also perfect for teaching R: it has a mixture of data types, is easy to understand, and you can run some statistical models to ask interesting questions. Additionally, there has been a lot of interest from the R Software Carpentry community in developing materials around this dataset.
An example plot from our popular ggplot2 lesson.
Since ResBaz, our lessons have been used by COMBINE, a national organisation for students and early career researchers in computational biology and bioinformatics, for a workshop ran in April for the Department of Biosciences at the University of Melbourne (The Biosciences department wrote glowing report of the experience in their newsletter!). Prior to the workshop, Harriet Dashnow, Dr. Phillipa (Pip) Griffin, and Dr. Noel Faux, our newly trained Software Carpentry Instructors from COMBINE, did some further development on the materials based on feedback from ResBaz.
Last week, our lesson materials were officially adopted by the Software Carpentry R community, who will be collaborating to further improve the materials. We’re looking forward to contributing to this development, and running even better workshops in the future!
Interested in viewing or contributing to the R lesson materials? View them here, or submit a pull request to the Software Carpentry GitHub repository here.
*by [Daniel McDonald](https://twitter.com/interro_gator)* Hullo everyone, I’m Daniel McDonald—a PhD student in Linguistics/Medicine here at the University of Melbourne. My thesis looks at how language use changes over the course of membership in an online support group for bipolar disorder. My background is in stock-standard linguistics—think syntax trees, cardinal vowels, Oxford commas, and wugs. Increasingly, though, my research has led me down the computational path. Because the dataset I’m using in my thesis is over eight million words long, I realised I’d need to do a bit of automatic text wrangling and number crunching to get the job done right. Like many others before me, I headed straight to Python as the language of choice. It fits a grammarian like a glove (enter a Python session and type `import this` if you want to understand why). After a couple of months, I was thoroughly hooked: I’d written [my first library](https://www.github.com/interrogator/corpkit), and irreparably damaged my relationship with my sub-editor brother by proclaiming that Python ‘could probably automate like half your job’. Anyway, recently, I’ve been helping out the Research Platforms gang, writing materials and giving free lessons to postgrads with the inimitable Fiona Tweedie (@FCTweedie) about the juicy intersection between Python, words, grammar and discourse.
NLTK training starts, @FCTweedie & @interro_gator introduce the course #resbaz @ResPlat @ResBaz pic.twitter.com/2kB0Utq8dz
— Lachlan Musicman (@datakid23)
April 16, 2015
Fiona, my trusty co-pilot, begins our lessons by stressing a particularly fundamental concept in text analysis: that language is data, just like stats—that you can learn things about the world by manipulating and interrogating it. We’re both passionate about this idea, actually: we sometimes repeat it like a bit of a mantra.
What’s interesting is the radically different way in which the Humanities- and STEM- folk in the classrooms react to this idea. Humanities students often roll their eyes a little … ’well, of course language is data’. They’ve never thought otherwise, and are often in our classes because they want training in analytical tools. The people from STEM, however, often seem to have their minds blown, and immediately invent whole new areas of interdisciplinary study to cope: ’My god—are—are you saying we can run Wikipedia articles through a DNA sequencer?!’.
These awesome and opposite reactions to a basic fact about language go a long way to show you the complementarity of totally different branches of research, and totally different kinds of researchers.
In our classes, half of the students come to us having known since birth the difference between integers and floats, and why you can’t parse HTML with regular expressions. These students are wonderful: they can help the others understanding the meaning of a famously vague Python error message, or fix an unexpected encoding error on their instructor’s MacBook if need be (thank you thank you thank you).
The other half of the students bring to the table a totally different kind of knowledge about research: they understand exactly why we shouldn’t conflate a word with the thing it denotes, or mix formal and functional theories of language willy-nilly.
Opposites attract, worlds collide, cliches abound, and many hands make light work: as a group, we’re always far more than the sum of our parts. An interdisciplinary classroom is a superhero, whose only weakness is deadlines.
For those that missed the hugely successful 3D Printing for Medical Applications Seminar (#3DMed), seven of the eight fantastic talks presented at #3DMed were recorded and are now available. Talks covered a range of medical-specific, 3D printing topics, including surgical planning, implants and prosthesis, bio-printing applications, commercialisation of medical products, imaging techniques, forensic medicine and bio-visualisations. A summary of each talk can be viewed on our live notepad.
The last three presentations, including the panel discussion can be viewed here. Please click here for the first part.
Enjoy!
For those that missed the hugely successful 3D Printing for Medical Applications Seminar (#3DMed), seven of the eight fantastic talks presented at #3DMed were recorded and are now available. Talks covered a range of medical-specific, 3D printing topics, including surgical planning, implants and prosthesis, bio-printing applications, commercialisation of medical products, imaging techniques, forensic medicine and bio-visualisations. A summary of each talk can be viewed on our live notepad.
The first four of these presentations can be viewed here. Please click here for the second part.
Enjoy!
By Damien Irving.
I’ve been avoiding David Flanders for the past few weeks. For those who’ve never met Flanders, he is the innovative brains behind the hugely successful Research Bazaar conference (ResBaz) that was held in Melbourne earlier this year. A whole bunch of sites in Australia, New Zealand, North America and Europe have already put their hands up to host their own ResBaz conference in 2016 (Feb 1-3), so David asked if I’d help him coordinate the global expansion of the event.
I’m trying to finish my PhD this year, so naturally my first reaction was to run for the hills. But then I got to thinking – if running this event becomes a massive burden on any single person, then we’re doing it wrong. This isn’t our event. It belongs to the whole international community, which means we can (and should) spread the load amongst that community. This post summarises my thoughts on how we might go about doing that. I’m hoping it will be a conversation starter, with a view to consolidating the plan at the next ResBaz community call (28 May).
General leadership and oversight
From conversations I’ve had with Flanders, I know that so long as ResBaz (or opportunities for digital research skills training more broadly) is successful, he couldn’t care less whether he’s the front man or not. Having said that, in these early stages I think it’s very important that he does take a central leadership role. As is often the case when Flanders has a good idea or takes on a lead role, he calls on his team of Research Community Coordinators at the University of Melbourne to help make things happen. I’ll be the one helping out for ResBaz 2016.
Website and online presence
Obviously one of the most important tools for coordinating a global event is a website. Ours doesn’t need all that much content (just a pitch to potential hosts, a list of requirements and advice for hosts, a pretty map showing all the sites, etc), but it does need to look slick and professional so that it impresses potential hosts and sponsors.* The Mozilla Science Lab were fantastic supporters of ResBaz 2015 and are all about helping researchers thrive on the open web, so I’m hoping they’ll take the lead on the website. They have a great deal of experience running globally distributed events (e.g. mozsprint), so I’m also hoping they’ll have some great ideas on how we can use the web to link up the ResBaz host sites.
We also have @MozillaScience science at the bazaar! Come chat to @kaythaney & @billdoesphysics #ResBaz pic.twitter.com/cXeuvbRqyg
— Research Bazaar (@ResBaz)
February 17, 2015
Survey
An important outcome from ResBaz 2015 was the researcher survey that was included in the registration process. We had over over 450 applicants fill out the survey, which allowed us to capture all sorts of great information about the digital research tools and skills researchers are currently using and seeking to learn. Our sample size will grow enormously with the global 2016 event, so I’m hoping the Software Sustainability Institute will lead the design and implementation of the survey and also the analysis of the data it collects. They have a great deal of expertise in this area and were also strong supporters of ResBaz 2015.
Simon from the Software Sustainability Institute (@SoftwareSaved) - building & using better software #ResBaz pic.twitter.com/iVloio37qk
— Research Bazaar (@ResBaz)
February 16, 2015
Quality assurance
It’s fair to say that most of the formal classes delivered at the various ResBaz 2016 sites will be taught by Software Carpentry instructors using the Software Carpentry teaching materials (when I say Software Carpentry I also mean their sister organisation Data Carpentry). This was certainly the case at ResBaz 2015 (where we essentially ran three Software Carpentry workshops simultaneously) and it was a key factor in the success of the event, because it ensured that the quality of the classes was high. Software Carpentry instructors undergo formal training before they teach and the materials have undergone years of community development, which means the classes are the state-of-the-art in computing education. Software Carpentry also helped us run an instructor training course in Melbourne during the week prior to ResBaz 2015, so there were lots a newly qualified instructors around to teach and help out.
I haven’t asked them yet, but I’m hoping that Software Carpentry might consider running a couple of live training events (and perhaps also an online course for people who can’t get to the live trainings) in the lead up to ResBaz 2016. We’ll also need Software Carpentry’s help in encouraging their global network of workshop organisers to consider running a workshop as part of ResBaz 2016.
For non-Software Carpentry classes, we’ll need to have a think about quality assurance. We have global brand to protect, so we want to make sure participants get a great learning experience when they attend ResBaz.
We’re here at @swcarpentry instructor training at @unimelb getting ready for #ResBaz! pic.twitter.com/jsH8Uj0EAl
— Research Bazaar (@ResBaz)
February 11, 2015
Community
Flanders has put together a group of interested ResBazadors (yep, that’s what we’re calling ResBaz hosts) who had their first community call a few weeks ago. These calls will become a monthly thing and will be the place for ResBazadors to get the latest information and also to ask questions and receive advice on running their event.
If you’ve got any comments or feedback on this proposal, please jump on the ResBaz gitter room and let us know!
* There’s an existing ResBaz 2016 website that was thrown up just to make sure there’s something up on the web, but it’s pretty ugly (in my opinion) and has to go.
As part of Research Bazaar we thought there would be space to provide generic IT consultation for attendees about good solutions to their problems. As someone with twenty years experience in IT, the most constant issues I’ve seen have been solutions that were inappropriate, hard to maintain for the end user, expensive, not fit for purpose, have (often expensive) vendor lock in, or a combination of all of these problems.
By no means do we ever think we could solve everyone’s problems, but non computer scientists are often unaware of the tools and systems available to them, or have no way to judge the value of the advice or quote that they are given.
To be fair, often people expect a lot more than they can afford, have no idea of the complexity or cost of implementation of their ideal solutions, or even the language with which to describe what they want.
This is something that Research Platforms are perfectly suited to provide, and I was lucky enough to be asked to be one of those consultants.
In the first ever running of this consultation, there was a queue almost immediately.
There was an atmospheric scientist that was looking for better open tools, in particular for presentations - “how can I replace PowerPoint”. I offered LibreOffice’s InPress originally, but that had been tried and wasn’t wanted - too much like PowerPoint. So I pointed her to Reveal.js a web based alternative that is as beautiful. Not something I’ve used a lot, but @stevage uses it for his mapping presentations that have toured the country and it seems a good fit.
Another, a bioscientist, was in the R stream, but was looking to expand their repertoire. It’s hard to go past Python and shell. They are both excellent tools in their own right, and my knowledge of large scale supercomputing (thanks Pip@bio!) is that a rudimentary in shell is almost mandatory. Shell can be a long slog, but it is worth it. The concept of stringing a lot of small, single purpose, utilities together can be hard to understand at first, and the admitted arcane interface is intimidating, but it is powerful and most can get away with a small understanding and a dozen commands.
Python is much easier to get up to speed with, is as ubiquitous as shell, and with a hour or two of research and testing, incredibly powerful scripts
I was surprised how much of the advice needed was web related. I had three people ask about websites for their projects. This is a multidimensional problem.
First and foremost, most researchers and teams, especially those seeking grant money, can over think their needs and wants before consulting a web developer. In the last five years, the number of people that have asked me for a site that includes the phrase “kind of like Facebook” and then followed it up with “we have no money” is reaching into the dozens. Here is the hard truth - Facebook has been built over a decade with billions of dollars, and includes work by psychologists, some of the planet’s brightest developers and millions, then billions, of users.
Find a consultant to talk about what you need first. They will help narrow your needs into at most four or five deliverables that will make it easier to work out what you need. For as little as $1000 you can have a pretty decent - not gorgeous, blue collar - data entry system that will collect your data, your data will be well modelled and there will be an API that will provide you with the scaffolding required to hang other applications off it. A supercharged spreadsheet, for want of a better analogy.
The speed of development will provide you with a good feedback mechanism so quick and easy tweaks can happen without breaking the fundamentals. This has two distinct positive outcomes - the developer(s) will have a greater understanding of your needs, and your users will have greater agency of the built software.
From that base you will be able to build further applications on top. Building websites is an iterative process (thanks Flanders!), so the smaller each part or deliverable is, the easier it is to make them work together well. Rome wasn’t built in a day, as they say.
The next most important thing to remember, and this goes to the heart of Research Platform’s raison d'etre, is that open is always better than closed. When a company wants to charge you $2 million for a site, it must be understood that there is a high likelihood - in the realm of 99% - that you will be locked into that provider for life. If they don’t perform to expectations, you are left with sunk costs that can’t be recouped if the project isn’t open. Proprietary code that is unavailable, often poorly commented and incomprehensible if available, and highly specialised is a lock in that no one can escape. When you use open tools and platforms - like Django, Ruby on Rails or Drupal, you have a plethora of companies available to you should you decide you need a new provider, or even want to just employ a small team of developers yourself.
Finally, there are often pre-made systems - like Omeka, CKAN, Zooniverse, Tumblr, MapBox/TileMill - that are free and will get you 90% of the way to where you need to be. They are open, often free, and will reduce your costs significantly.
From the other perspective, it is important to remember that web development is done by teams of people that are highly experienced and that doesn’t necessarily come cheap. Design and user experience, in particular, are fiscally expensive, back end and development support will be tax your time and mental understanding of what you want to achieve. You will be asked to think slowly and clearly, and if you are on a budget, you may need to think hard about “must haves” versus “desirables”. You will be asked to think hard about your problems in a way that can be translated into what can be achieved. This is an ongoing process, and often involves a distillation of big ideas into smaller, achievable ones. The consultants aren’t dismissing your greater goals or dreams - they are thinking about the possible, the plausible and the achievable. Patience is required from both sides. But if you can save yourself a bunch of headaches and $1.5 million, it’s probably worth it.
#NLTK, #django, @swcarpentry, #sharktank… it’s all happening at #HackyHour! pic.twitter.com/pCGYjnBd38
— Research Platforms (@ResPlat)
April 30, 2015
Research Platforms offers a weekly meetup - the Hacky Hour, Thursdays, 3pm at the University of Melbourne’s Tsubu, where you can get advice about your project. If you think your project needs a web application, come down and ask us. We can’t build it for you, but we can help you think more clearly about what you need, and what it might cost. And depending on what you need, we may be able to provide you with either a quick and dirty solution or a new experimental platform that we are testing.
As a developer, we love and respect your hard work and domains of knowledge in which you outstrip us - often we are fascinated and explosively excited to help and work with your projects. We are there to help your project in our domain of expertise. Come visit us.