Have you ever wanted to type some mathematics in a document?
During a meet-up on the 5th of September, 2018 we discussed how to typeset mathematics, using LaTeX and JavaScript. Keep reading to learn how, and to view some beautiful examples (including animated rainbows!)…
Do you want to use mathematics in your documents? Join us tomorrow afternoon to learn how, using LaTeX and JavaScript!
Register for free: https://t.co/2w4Ec1CnMS
…see examples, learn tips & tricks, and ask questions while enjoying light snacks and beverages with the community! pic.twitter.com/YIv2nzVN1C— Meirian (@MeirianLT)September 4, 2018
LaTeX is a programming language for high-quality, beautiful typesetting. TeX was originally released by Donald Knuth in 1978. As a mathematician himself, Knuth was motivated to create something which allowed one to type complicated mathematical formulas in a professional-looking manner. As a result of his efforts, the ability to typeset mathematics in LaTeX is a major strength.
Anyone who has studied mathematics or statistics will know that the notation is plentiful. LaTeX allows for the many symbols you may desire to use, whilst presenting them in a clear and beautiful way. So many symbols are available that there is a 338 page Comprehensive LaTeX Symbol List. But when it comes to finding the symbols you need, I recommend using Detexify by Kirelabs. This tool allows you to simply draw the symbol you’re looking for, then it will identify it and tell you which command and package to use!
During the meet-up we created a LaTeX document which was abundant in examples of mathematics notation and formulas. You can view the document on Overleaf.
Once LaTeX had been introduced, Errol then gave an excellent presentation on the inclusion of mathematics on the web. Read on to learn more and see his animated rainbow equation!
Thanks to @maegul for your presentation on #JavaScript during our meet-up today on Mathematics in your Documents at @ResPlat! Your use of emoticons, rainbows and animation captured everyone’s attention! pic.twitter.com/h5B33B7ZdM
— Meirian (@MeirianLT)September 5, 2018
One of the great things LaTeX has given to the world is its mathematics or equation typesetting syntax. Not just because LaTeX is great and powerful, but, because this typesetting syntax is now a standard across many different kind of software.
This is especially the case when it comes to web pages. Go to the wikipedia page on the normal distribution, and see all of the mathematics typesetting. Copy one of the equations and paste it into a text file … what do you see? (Spoiler alert … LaTeX).
All of this works because when it comes to the programming language called javascript, which powers all of the interactivity and animation of the web, there’s a principle which has shown to be true again and again: ‘anything that can be made in javascript will be made in javascript’. The web is everywhere and everyone uses it all of the time. Which means javascript has to do its best to be everything to everyone. And so, LaTeX mathematics can be done with javascript.
If ever you find yourself wanting to write a blog, create a simple web page (which is easier than you might think), or share your Jupyter or RMarkdown notebook or create an attractive interactive data visualisation or publication for your research, know that javascript has got your back when you need to show some mathematics.
Beyond blog writing, you may be wondering why you should be interested in javascript and making web pages. There are two responses to this. First, with the Observable Notebook, it is now easy to learn and get started. Check out the tutorials at the home page and just start playing. Second, unlike any programming language you’ve learnt, javascript is built to normal programming things like crunching numbers, as well as graphics. This means you can make interactive publications, like this notebook on predator and prey population dynamics.
Or, you can just make rainbow equations:
#javascript + LaTeX = Awesomeness @observablehq https://t.co/V7KTWx3IlL pic.twitter.com/b1VfXhJxXV
— Errol Lloyd (@maegul)September 6, 2018
If you’re interested to learn more, take a look at this notebook of mine, which demonstrates LaTeX, interactivity, using Observable, and making interactive graphics with javascript.
This blogpost was created by Meirian Lovelace-Tozer (@MeirianLT), and Errol Lloyd (@maegul) who are Research Community Co-ordinator and trainers at Research Platforms Services (@ResPlat).
Why would you want to learn Numpy? Well I guess I can start by telling you why I learned it!
I don’t often admit this, But I started as a Matlab user (gasp!). Needless to say it is an excellent product, but sadly in many professions, it is quite a bit too expensive. So I found myself looking for an open source replacement. Also, I wanted to learn Python because it got along well with the GIS programs I often use.
However there is a bit of a learning curve: In Matlab you can easily do vectorized mathematics or matrix mathematics on two vectors of data like so:
And that is hella convenient! The maths look like maths!!!
Now, when I first started using Python, I was told that it was basically like Matlab so I tried to do some basic vectorized operations:
That is not what I wanted!!
Python will actually concatenate, or splice, the two lists together into one list, instead of adding up the items. This is because lists can store any type of data or python object, so Python wouldn’t necessarily know how to add up each item in the list like we saw up there… hmmm A bit frustrating!
Thank you for your realism Borimir. Now a Python Purist would use a list comprehension, which is basically a quick one liner loop creating a new list
**Opinion: **There is a lot of riff raff around the math up above, which makes it a bit harder to read and comprehend, plus, if we accidentally have a non number in our inputs, python will flag an error right?
Well luckily people wayyyy smarter than I have addressed my concerns, and have created the Numpy Library in order to make maths look like maths again in Python:
As you can see above, we can turn any list we want into a numpy array for analysis, it just follows one major rule:
Numpy Array Rule 0 - All data in it are coerced into the same data type,
that way python knows how to add the elements together (and do other mathematical operations)
But wait there is more!
Because of the above rule, Numpy arrays are much more efficient than lists at storing large data sets of numerical data, and cycling through them than a list
Numpy arrays can be multiple dimensions, representing geographic data, 3-D data, and any sort of multidimensional data set
….AND Numpy arrays are used to feed data into a variety of other data science packages like Pandas, Scipy, Scikit-learn and plotting libraries
So how do I Numpy?
Well I am a Geomorphologist, which is a fancy term for an Earth Scientist who spaces out so much on car rides they wonder why that hill over there is a particular shape.
#realgeomorphologyquestions - answer - It’s very pointy
I literally study the shape of the Earth’s surface. In many cases, the data describing the earth’s surface, and the factors changing it, can be described as a “raster” (basically photograph with pixels)
where we lay an imaginary grid on the earth’s surface to separate it into even sized squares, and store a value (say elevation) representing the value averaged over that square in the grid. Here is some 2 metre by 2 metre resolution LiDAR elevation data as an example:
Note, there is a bridge crossing the river from north to south in the middle,see if you can spot the road fill! The darker red colors represent lower elevations, and therefore old (and current) river channels. I could stare at this stuff all day. That’s why we in the biz call it LiDAR crack… because it is physically addicting to a Geomorphologist!
And with a 2 dimensional Numpy array, i get a lean efficient fast way to to analyse my LiDAR data using open source software, and figure out why that river switched places up above!
But wait there’s more!
if I am feeling really fancy, I can use a third dimension representing time slices of lets say a flood simulation, and make a movie of the water velocities (note matplotlib helped here as well)
SO Are you ready to calculate smarter not harder? Then check out our course material here come on down to our numpy workshops (see calendar) and learn how to crunch the numbers with Python
Cheers,
Jon
At the recent Omeka Meet-Up, we opened up discussion to include all things Digital Humanities.
Over three fantastic presentations and several provocations around data, Humanities research and cultural collections, the group developed a range of responses, provocations and ideas for future projects.
To kick start things we first had a discussion about what we mean when we use the term ‘data’ in the Digital Humanities space. Are we referring to text? Images? Digitised materials? Or simply everything involved in research? Questions around ontologies and silenced voices also came to the fore as did thoughts about the future of infrastructure in Digital HASS.
Julianne Bell then gave a fantastic presentation on a project she is working on as part of the Digital Studio Graduate Internship program, entitled Execution Ballads of Pre-Modern Europe. Developing this project with Dr Una McIlvenna from the School of Historical and Philosophical Studies, Julianne has encountered an array of challenges and discoveries around presenting and narrating cultural materials with Omeka.
The project has developed a database on execution ballads (cheaply printed songs about crime and punishment dating from c. 1550-1900) that includes hundreds, if not thousands of items. These are partly in textual form (transcriptions of lyrics, notes on historical context, dates of publishing, etc), partly pictorial (images of the pamphlets and broadsides, images of historical figures who feature in the ballads, etc), and some audio recordings. Until recently, this has been stored in a MySQL database on Heurist software. The intern project is transferring and setting up the database correctly in the content management software Omeka, as well as adding to the database.
Here’s a breakdown of the project:
And the methods and approaches taken in customising Omeka to fit the parameters and requirements of the project:
Following Julianne, our excellent Omeka ResLead Alex Shermon spoke about his work on an Omeka site that is part of a broader project within the University of Melbourne looking at Sir Redmond Barry.
This project brings together cultural and legal history, biography, philosophy and a wide range of curation and collecting practices.
Here’s the official description from the Lives Lived with Law Journal edition:
“We see ‘Lives Lived with Law’ as drawing into relation the scholarly experiences of disciplinary technique, and the experimentation over time with style and forms that help to show what the conduct of lawful relations can be between peoples, between everyday and official experience of law, as well as between Indigenous and Anglo Australian laws.” (Genovese, Rush, McVeigh. Lives Lived with Law: An Introduction, p.2)
According to Alex, “Jurisography is the hip new rebranding of legal biography.”
Working under Carole Hinchcliff (who is collaborating with several academics from the Melbourne law school), Alex has set out to examine the fragmentary sources and forms of legal theory involved with Sir Redmond Barry.
Title: The trial of Ned Kelly
Subtitle: Newspaper illustration
Date: 1880
Keywords: people, biography, Bushranger, trial, illustration, media
Record creator: Department of Information
National Archives of Australia
Alex writes how, “Sir Redmond Barry (who, by the way, has an apple named after him) got a lot done and left a pretty big legacy. Aside from the apple thing, he helped found the State Library, The National Gallery, and the University of Melbourne (He would have loved the sheer boring monotony evoked in the brown brick monstrosity named after him).”
“In law he was the first standing counsel for Aboriginal people, and famously sentenced Ned Kelly to death just days before he himself died. Barry shattered over Melbourne when he died. The task then for the Jurisographer, is to pick up these pieces and present them in a meaningful way. That’s where Omeka came into our project. It is allowing us to relate contemporary instances of Barry (statues and bookcases) with his own digitised publications, such as the important addresses he made at circuit courts and his annotations in statute volumes.”
Alex presenting his talk:
Mitchell Harrop from SCIP then delivered some timely and useful information about Omeka and Web Archiving - a topic we’ll be coming back to very soon as there is increased need for and interest in researchers being able to maintain and present their work on Omeka into the future.
Stay tuned for the next Omeka event. We have something very exciting in the pipeline which will, once again, consider dynamic scholarly workflows that connect Omeka with other digital research tools.
For more information, get in touch with our Community leader, Tyne!
Humanities, Arts and Social Sciences researchers are often faced with big questions when it comes to planning and orchestrating their data-related projects.
Our recent Omeka workshop took some of these questions and challenges head-on by considering the research ‘life cycle’ that comes before and after using a web-publishing platform.
While Omeka is free, flexible and very easy to use, there are serious and important considerations that must be undertaken before embarking on a research project that has a visual exhibition component.Full house for @omeka workshop today @ @ResPlat with 2 excellent ResLeads, Alex & Daniel! pic.twitter.com/OEGCcZT0MR
— Tyne Daile Sumner (@tynedaile)July 26, 2018
What kind of story do you want to tell?
Who is your audience?
How will the project or site be used?
What kinds of items will be included in your project?
What kinds of features do you want? Will they enhance the research?
Who will be contributing to the project?
Is the project sustainable?
In the workshop we explored provocations such as these. We trialled this new approach to gain insights into the kinds of questions that HASS researchers ask at the outset of their projects as well as some of the barriers that they face and how these might be overcome. The result was an engaging and thought-provoking discussion around not just Omeka but Digital Humanities research outputs more generally.
Jared Winton opened the session by canvasing some of the key recommended steps when starting out in a HASS research project that involves collections and data. Jared is the Data Collections Manager at Research Platform Services. ResPlat offer a range of research-specific infrastructure. In the workshop we had a brief look at Mediaflux - just one tool among many for managing digital assets.
We then looked at Omeka in the context of a data management plan and considered how best to set up a project. Although Omeka is designed with non-IT specialists in mind, it’s nevertheless important to seek out expert help in the early stages of a large research project.
Omeka can handle large archives of metadata and files (over 100,000 items), and is extensible by publicly available plugins and themes. Users can populate an Omeka site by adding items individually or by ‘batch,’ using data migration tools such as the OAI-PMH harvester, and CSV, EAD, and Zotero importer plugins. Omeka accepts and stores all file types, including: images, video, audio, multi-page documents and Pdfs, and Powerpoint presentations.
Our fantastic ResLead Daniel then gave a demonstration of just one way in which a large dataset can be imported into Omeka. Daniel’s example was the Actors Database on IMBD, which he used as a case study dataset.
Using a Python tool (Pandas) to wrangle the data into shape, Daniel showed us the steps that could be taken to transform a pre-existing database for display in Omeka.And here’s a shot of today’s guest presentation by Daniel on preparing data for @omeka. @ResPlat pic.twitter.com/whcasijEql
— Tyne Daile Sumner (@tynedaile)July 26, 2018
Finally, one of the most important parts of conducting research that uses Digital Humanities methods or tools, is being able to connect with the relevant experts.
Here at Melbourne University, two of these resources are:
Research Integrity Training (RIOT): covers the principles of research integrity and their application to the planning, conducting and reporting of research.
Managing Data @ Melbourne: an online program that guides you through the process of writing a data management plan for your research project. It has been developed for graduate researchers, early career researchers, and information professionals.
There’s lots going on in the world of Omeka at the moment.
We’re working on making “Preservation and portability” better via #DataCrate. Eg, this export from Omeka: https://t.co/t6OVtuKMKV @omeka https://t.co/Yd8ce7l3jI
— petie (@ptsefton)July 30, 2018
On the 3rd of August, 2018 we held our first LaTeX meet-up!
The purpose of this event was not only to showcase some exemplary LaTeX documents, but also to give attendees the opportunity to ask their burning LaTeX-related questions, and learn some tips and tricks. We saw examples of including images in LaTeX, a recipe book, academic posters, and slide presentations. Keep reading to hear about each of these, and to access some great templates…
Do you use LaTeX? Come along and meet other LaTeX enthusiasts tomorrow afternoon for a special event! https://t.co/mvtMQ5sLDZ
…ask questions, learn tips & tricks, and see some exemplary documents while enjoying light snacks and beverages with the LaTeX community! pic.twitter.com/d0gLBm8dN5— Meirian (@MeirianLT)August 2, 2018
After some quick introductions and once everyone had settled in with some tea and snacks, Ben began the meet-up with his presentation on preparing illustrations and images for inclusion in a thesis using LaTeX.
Ben also discussed the following frequently asked questions:LaTeX handles images slightly differently to many other applications. The DPI setting in the image is ignored and the size of the image will be based on the DPI of the document if no other size parameters are included. There are no rules for adding images, thesis instructions including required DPI settings are rare. For the sake of consistency I recommend you resize your images to match the size that they will be reproduced at… There are a few ways of including figures with vector objects (with or without images as well) in LaTeX. From a technical support perspective I look for methods that provide the best quality with the fewest problems… – Ben Kreunen @OzBigBen
Next, Brian presented his Mother’s recipes coded in LaTeX. The detail of his presentation was not about code specifically, but about communication with audiences and working with teams.
When we write we often write to ourselves, as my Mother did. We may include shorthand, not fully explain ideas presuming others have already grasped them and more importantly, we may not be actually addressing our audience or have a clear idea who they are. Pitch your ideas at the knowledge set of your presumed audience and explain all concepts that would be unclear to this audience. Make sure the flow of the document is logical and leads the reader to the conclusions that you intend.
Also, working with teams on documents — as this one was — has it’s own difficulties and complexities. This was created with an online editor/UX coder, a typesetter/graphic layout person and a recipe checker. As it was a labor of love it was difficult to assign deadlines. However, when working with a team who have specified areas and content to deliver it is a good thing to specify both job demarcations and time-lines in which to deliver the work. Deadlines and clarity around what a person is to do helps them deliver and, while it may be some pressure, people generally perform better knowing the limitations. – Brian Boyce @innerversitysou
You can view the template Brian created for the cookbook on Overleaf.
Fantastic #latex meetup tonight with three awesome speakers @OzBigBen, @innerversitysou and Tom, each sharing their experiences with the tool. #resplat #unimelb #research pic.twitter.com/WGrVJfTmWI
— Research Platform Services (@ResPlat)August 3, 2018
Meirian also showed examples of slide presentations which were created in LaTeX.These included his Ph.D. thesis, a presentation, as well as a set of lecture notes for a subject he is teaching. Particular attention was given to creating a poster in LaTeX using the baposter template designed by Brian Amberg.
This link contains a sample poster created using the template, the documentation of the template, as well as a LaTeX primer with sample code to get things rolling. – Thomas Wong
The document class for creating presentations is beamer. There are many options for layouts and colour schemes to choose from; some of these are displayed in the beamer theme matrix. I recommend reading the ShareLaTeX guide on beamer for some great help and tips when creating your own presentations in LaTeX! There are also a variety of templates available online to help you get started. – Meirian Lovelace-Tozer @MeirianLT
Would you like to come along to a future LaTeX workshop or meet-up, and get involved?
I encourage you to sign up to upcoming events on Eventbrite. Please also check out our website for more information, or contact me if you have any questions.
It is time for us to grow our ResFamily again! Do you love science and research? Are you the one all your friends/colleagues come to for their typesetting solutions? Can you explain technology eloquently and kindly to the grumpiest professor? If you answered YES to any/all of the above, then Research Platform Services invites you to apply for our Junior Research Community Co-ordinator position in 3D Printing and TinkerCAD!
The successful applicant will grow their respective communities through regular workshops and meetups. Maintaining an online presence is also an essential part of the job. You would also be expected and supported in organising events within your communities, as well as Research Platforms-wide events such as the famous Research Bazaar conference. You can find out more about the Research Bazaar community in the first pages of our new publication: The Digital Research Skills Cookbook.
Please see the below links for a detailed position description for the role, including how to apply. Get in quick, applications close COB 16th July, 2018.
3D Printing & TinkerCAD Position Description
Julianne Bell is an intern employing Omeka in her current project. She is working on a project with a rich database of Pre-Modern Execution Ballads.
Julianne is a second year PhD student in Cultural Materials Conservation at the Grimwade Centre at the University of Melbourne. Her thesis is on the management of the deterioration of plastics in museums from an Arts and Science perspective. She is one of 11 interns at the Digital Studio. She is working on the project ‘Execution Ballads in Pre-Modern Europe’, supervised by Dr Una McIlvenna, Hansen Lecturer in History at the University of Melbourne. Dr McIlvenna has collected an impressive range of original data on ballads in early modern and nineteenth-century Europe in a variety of formats.
Julianne Bell
‘The project was my first experience with Omeka’, said Julianne. ‘I was a little daunted at first to learn a brand new program, but I found that Omeka has such a user friendly interface… After the training session that Tyne led, I was able to start developing the database almost straight away’.Julianne is keen to use these skills in the project: ‘it relates directly to what I’m doing for the internship project… The project includes textual data, images, sounds, as well as items such as people, locations, and events and it’s all really easily collated and managed together’. Julianne sees a number of benefits to using Omeka, ‘while you develop the database, you’re also developing the public facing output at the same time. That seems like getting two jobs done at once.’What’s in the box… categorising and digitising objects for the @digitalstudioUM @omeka training @tynedaile @ResPlat pic.twitter.com/zvFY5ANte4
— Kim Doyle (@kim_doyle1)May 28, 2018
Dr Stephen Giugni
OAM Associate Director, Research Platform Services.
Making sense from data, the data deluge, big data, sharing data, publishing data, data, data, data….
Research is increasingly becoming a data driven activity – but data is only the starting point of our research journey. Valuable in its own right, but that value increases as we bring understanding to our data, to interpret it, to combine it with other sources of information to enhance its ability to unlock the mysteries of our universe, our environment, our social interactions, our ability to make better decisions.
This issue of our newsletter explores the ways that the University of Melbourne research community are using our data management tools and platforms to bring life and meaning to data. Something as simple as grouping or graphing data can provide enormous insight into aspects of human endeavour. For example, we can explore data by bringing together collections to create an exhibition that can bring a focus on an area of research, or we can provide a platform to explore possibilities. Join us as we explore the world of data.
Dr Stephen Giugni
OAM
Associate Director, Research Platform Services.
w: http://research.unimelb.edu.au/infrastructure/research-platform-services
Professor Rachel Fensham
Assistant Dean, Digital Studio
The Digital Studio is delighted to be a part of the Research Platform Services community. The Studio is a collaborative space in the Faculty of Arts supporting researchers working in the digital humanities, arts and social sciences. We are building a community of digital humanists here at the University through a diverse range of programs and activities, including an internship scheme tackling research data challenges for more than 10 projects. These projects range from organising the textual data of execution ballads in Omeka to data scraping and network analysis of Twitter content. We are also collaborating with industry partners such as Regional Arts Victoria, Creative Victoria, Lucy Guerin Inc, Digital Heritage Australia, and ACMI-X.
The Studio itself is a technically resourced workspace in Arts West which hosts seminars, visiting fellows, training and laboratory sessions, and project exhibitions. In semester two, we are excited to be hosting a Visiting Fellow from Leeds University, and will be working with Research Platforms, and other partners SCIP and Researcher@Library, to host data curation, training and workshops. We will also be presenting a Digital Heritage seminar series that explores cutting edge practices and issues in the Galleries, Libraries and Museum Sector.
Keep an eye on our events page or sign up to our email newsletter to find out what’s happening in the Studio. Or if you’re a researcher working on a digital HASS project feel free to get in touch via email digital-studio@unimelb.edu.au.
Professor Rachel Fensham
Assistant Dean, Digital Studio
by Emilie Walsh
The best part of working for Research Platform services as a CAD and 3D printing ResCom*, is that I get to meet researchers working with 3D in all disciplines. Reagan has been helping with my trainings for a few months now.
Awesome first #fusion360 training yesterday with @JongEric & @reaganks! So good to see interest in #CAD for a variety of #researchers! @ResPlat @unimelb pic.twitter.com/AvGo3O0Hfu
— Emilie Walsh (@emilouwalsh)1 May 2018
If you are interested in learning 3D modelling yourself, come to my next training:
https://fusion-360-july-2018.eventbrite.com.au
Reagan graduated from his Master in Engineering last year and is now working on an exciting project using his skills in 3D modelling and 3D printing!
Reagan Kurniadwiputra Susanto
Tell us about your background and experience at the University of Melbourne ?
I did Bachelor of Science majoring in Bioengineering Systems and Master of Engineering majoring in Biomedical Engineering. During my undergraduate studies, I was quite active in Indonesian Student Association both in the University of Melbourne and in the state of Victoria. However, during my master’s degree, I was more focused on my academic skills and tried to do something more relevant to my field. I joined the Melbourne University Racing team as a Junior Engineer on the Low Voltage team and also participated in Student Ambassador Leadership Program from the School of Engineering.
Tell us about your interest in 3D printing?
It was all started from a subject called Biomaterials, where I have to design a spinal implant for people with specific lower back problem. I had to 3D print the implant and vertebrae with 1:1 scale to visualise the results. This has caught my interest on 3D printing since I can hold something that I designed myself and it was very quick and cheap. Straight after that subject concluded, I bought myself a 3D printer to kick-off my journey in learning and playing around a printer.
I have find that 3D printing is very well supported by the online community. I have teach myself with some very useful skills though some online resources:
- Make Anything - it’s a creative works channel, he posted a lot of fun and functional things, very very inspiring
- Makers Muse - 3d printing reviews, tutorials, etc., he’s Australian and quite popular amongst 3D printing community
- RCLifeOn - mixed of 3D printing, Remote Controls, drones etc. but his 3D printing works are very creative and functional
I am quite interested in utilising 3D printing for rapid prototyping. For example, creating a box for electronics, a rig to simulate breathing, a bracket to join mechanical structures, and a custom-made holder for a very specific purpose.
Reagan breathing box! Gif of the first prototype
3D printing is definitely not the best tool, but knowing how to utilise the technology in combination with other techniques will definitely create something unique and interesting.
Reagan’s Second prototype of the breathing machine.
What skills did you learn during your Master?
Basically general engineering skills like programming and project management as well as something more specialised like electronics, signal processing, 3D modelling/printing, and medical device commercialisation. Throughout the degree, I also learn organisational and leadership skills through student clubs.
Reagan helping out during one of my Fusion 360 training.
So you graduated! Tell us about your current project?
I am working on a MedTech Startup developing a respiratory rate monitoring system for hospital patients. Currently, we are at a very initial stage where we still developing the product and the commercialisation plan. We hope to get the device to the market and helping clinicians to save their valuable time. This device could also potentially reduces hospitals costs related to adverse events.
How the skills learnt in research can be apply to industry?
The technical skills are definitely useful during device development. The skills will help to make a proof of concept and reduce significant cost in development. The most important skill is the problem solving skills that any researcher gained from its training, at least it helps me to be able to prioritise and make important decisions!
If like Reagan you are interested in 3D modelling and 3D printing come to one of my workshop and learn CAD with researchers from all disciplines. Check our calendar of training here:
https://www.eventbrite.com.au/o/research-platforms-services-10600096884
*ResCom : Research Community Coordinator
Neil Killeen (Research Platform Services), Donna Hensler and Nicolette Freeman (VCA Film and Television)
The University of Melbourne’s VCA Film and Television is Australia’s longest continuing film school. Its high-value (historical, cultural, research, teaching), 50-year old Student Film Archive was originally only stored on transient and largely inaccessible media such as celluloid film and magnetic media.
The VCA took initial steps many years ago to digitise and preserve their collection, however it wasn’t until 2015, with the approach of the school’s 50th birthday that the Film School was able to start the process of digitising 50 significant film titles to celebrate and promote its uniquely historical moving image collection. That same year, the archive was recognised as a Cultural Collection by the University. This was achieved based on a Significance Assessment, which made the case for the archive’s value and research, teaching, learning and engagement potential. A digitisation investment grant from Film Victoria then enabled a cultural partnership to be entered into with ACMI, who took on the digitisation of the celluloid films in the collection.
Subsequently, in 2017 and 2018, and facilitated by a grant from the Australian National Data Service (see http://www.ands.org.au) the VCA, Research Platform Services (ResPlat), and commercial partner Arcitecta (supplier of the Mediaflux data operating system - see http://www.arcitecta.com) have since transformed the digitised films into a highly-curated, meta-data rich film archive, accessible via a specialised and re-usable Audio-Visual Archive Portal operating in ResPlat’s Mediaflux data management platform. This work is an essential part of the on-going process to ensure maximum University, National and International use of- and leverage from this important collection. Most recently, this visual showcase has received a further grant from the University’s Student Services Amenities Fund which will further enhance the interface and functionality.
The picture shows a box of digitised USB drives which are being uploaded and the screen shows a few of the films via the current AV Archive interface. Films are stored in 3 formats: the master (JPEG2000 – preservation quality), the mezzanine (Pro Res 422 - for editing and exhibition) and the H.264 proxy for streaming via web browsers. Interface functionality includes the ability for users to upload films, view films, upload associated artefacts such as stills, store rich descriptive meta-data, create playlists and tag film segments for later discovery and viewing.
Neil Killeen, Wei Liu (Research Platform Services), and Andrew Leis (Bio 21)
The era of big data is truly upon us and a current example of this at the University of Melbourne is the new Cryogenic Electron Microscope situated in the Bio21 Facility. This instrument is now fully operational and capable of producing up to about 14TB per day. More typically, it produces a few TB per day. It is expected that in 2 years time, there will be a fleet of these electron microscopes producing about 0.5 PB of data per week!
Major challenges for all organisations operating large-data generating instruments include where and how to store data long term, how to get data efficiently to that storage, and how researchers will access and process that data. The cost burden of storing data, typically for a minimum of 5 years, is very substantial and new paradigms involving pre-processing and discarding of data will be required.
Over the last 6 months, Research Platform Services (ResPlat) has worked with the Electron Microscope Platform (led by Assoc. Professor Eric Hanssen) to handle the data from this first instrument. The system in place, which is reusable for other instrument contexts, utilises ResPlat’s primary data management platform (DMP) built with Arcitecta’s Mediaflux system. The DMP operates in the University’s main data centres and data are streamed to it in quasi real time from a workstation (which also does some pre-processing) located with the electron microscope.
Figure 1 - The upload pattern
The upload software client is generic and reusable. The data is uploaded directly into a ‘project’ accessible by (only) the research team acquiring the data. Data may be stored in the project transiently or persistently (for long-term management).
The researchers can then access their data in a multitude of ways from the DMP as seen in Figure 2. The DMP offers a very flexible multi-protocol environment so that users can pick the method that works best for them. Whilst it is possible to create fast networks connecting instruments to the data centre, users of instruments like this may be from anywhere (e.g. other Australian institutions or international). Therefore, a challenge for delivering data to users is the fact that their network throughput may be quite poor.
Figure 2 - The download pattern
In Figure 2, the user represented can log in to the DMP. However, we have also developed download solutions where shareable links are despatched to researchers who don’t have accounts (perhaps a one-off use). For big data, ResPlat has developed shareable links that don’t download the data directly (also available) but download a “download manager” which itself fetches the data restartably and in parallel.
Finally, the pattern above in FIg.2 is largely a ‘copy out’ pattern. This means the data are duplicated and this just adds to the time and cost burden, especially for big data. ResPlat are exploring ideas around ‘in-situ’ access (like SMB but more scalable) so that users of say, a High Performance Compute facility can access their data directly in the DMP and compute on it. In this way, data can be stored and managed, as well as directly integrated with processing environments, so as to minimise time and costs.
In recent years, digital Humanities, Arts and Social Sciences research has enjoyed a surge in interest, critical attention, promotion and funding.
One offshoot of this growth is the Digital Studio Graduate Internship Scheme. At the end of May, the recently-selected Digital Studio interns attended a workshop on Omeka, an open-source web publishing platform for the display of cultural heritage objects.
In addition to learning the ins and outs of building a basic Omeka site, the interns generated detailed and insightful discussion around such topics as: copyright, provenance, research data management, graphic design and digital curation.
Several of the interns are employing Omeka in their current projects. Recent months have seen exciting new updates by the Omeka team. Most recently, the release of Omeka S has responded to the growing need for HASS researchers to connect across collections and repositories. Omeka S is a next-generation web publishing platform for institutions interested in connecting digital cultural heritage collections with other resources online. First released in November 2017, it has already been widely adopted and developed by the Omeka community..@ResPlat’s @tynedaile talking metadata with the @digitalstudioUM interns pic.twitter.com/iUV1Hkcgq7
— Kim Doyle (@kim_doyle1)May 28, 2018
Beyond the Digital Studio Internship program, there is also lots of exciting work happening in the Omeka-space. Last month Research Platform Services ran a meetup focused on displaying 3D objects online with Omeka. In the coming weeks, there will be more opportunities to discuss the latest developments in the online cultural collections space with a meetup to explore ‘Omeka and Copyright’ as well as a workshop on Research Data Management as relevant to the online display of HASS research.
To hear more about these exciting events and opportunities or to sign up, get in contact with Dr Tyne Sumner, our Senior Research Community Coordinator at ResPlat.
Tyne runs trainings and events to support Omeka as well as a range of other initiatives designed to increase engagement in digital HASS research at the University of Melbourne and beyond.
Tyne is also involved in consulting and engagement work on the exciting new Humanities, Arts and Social Sciences Data Enhanced Virtual Laboratory (HASS DEVL). The HASS DEVL is a national collaborative project that aims to lower the barriers to entry for digital infrastructure to support HASS research, increase interoperability between existing platforms and deliver skill-building opportunities across the HASS sector.
Get in touch with Tyne if you’d like to know more about the HASS DEVL project or to be involved.
Sign up for the next Introduction to Omeka training here.
We have spoken to PhD candidate Emad Alghamdi from the School of Languages and Linguistics about his research project.
What is your PhD Research Project?
I am trying to answer a deceptively simple question: what makes a video complex or difficult for language learners. My study of that question is very challenging at many levels, for one, I am dealing with a dynamic and multifaceted type of data, videos.
What prompted you to choose this research topic?
Before starting my PhD, I worked as an English teacher for non-native learners for almost six years. As a teacher, I came to know that students like to watch videos and they learn much from watching videos. But whenever I looked for videos on the Internet, it was always a challenge to find videos that are not too difficult for my students. The process was tedious and time-consuming and I always wished that if there was an automated tool that can help me find the right videos with less effort. So I decided to take up the challenge and build one for myself and for all language teachers and practitioners.
What are some of the challenges you have faced or overcome in your research project to date?
With the aim of developing a prediction model of video complexity, I searched for an approach that could help me make sense of the data (videos) and I found Machine Learning to be the most appropriate approach for the task. But Machine Learning is an emerging and active field and it is very challenging to keep up with the recent approaches and techniques.
Another challenge I faced is that I could not find a video dataset that I can play (experiment) with. So I built a video dataset myself and thought I overcame my biggest challenge. Not long after I started analysing my data, I knew I had a very challenging problem on my hands. Hopefully, I’ll get through the analysis phase soon.
What digital tools do you use to use to help analyse your research data?
To remind you, I am analysing videos (a lot of them) which are generally made of three components: language, picture and sound. I use different tools for each component. At the moment, I am focusing on analysing the language component using advanced NLP tools such as TAACO, TALLES, and Coh-Matrix.
I am also using many great Python libraries for data pre-processing, presentation, and visualisation such as NumPy, Pandas, Matplotlib, and Seaborn. For building ML models, I have been exploring Scikit-learn and TensorFlow.
Have you attended any workshops at the university to learn how to use the digital tools you need?
I am SO fortunate to be a resident at Digital Studios where all fascinating workshops and seminars are happening. I have learnt a lot from attending those workshops and others organised by Research Platform Services. I recommend every student to benefit from such wonderful workshops. You never know what doors these workshops may open to you.
Sweave and knitr are engines for generating reports with R which are elegant, flexible, and fast dynamic. Sweave is a package in R that enables integration of R code into LaTeX or LyX documents. Developed by Yihui Xie, knitr combines features from Sweave with other add-on packages to enable integration of R code into not only LaTeX and LyX, but also Markdown, HTML, bookdown and other document types.
Access the documentation on knitr at yihui.name/knitr.
On the 30th of May, 2018 we held a meetup to introduce the R community to knitr and Sweave, and showcase some of their applications. During the event, R-markdown, HTML, LaTeX and bookdown examples were presented. Keep reading to hear about each of the presentations given at the event!
Ready to make elegant and replicable documents with all you R-data-analysis in it? Come to our R-meetup to find out how! @ResPlat @MeirianLThttps://t.co/2UsKZFSDw7
— Pablo Franco (@jpablofranco)May 17, 2018
Meirian began the event by introducing Sweave and knitr, and demonstrating how to easily create a R-markdown document in RStudio.
R-markdown enables you to create documents that contain all your code and results, making your data analysis entirely reproducible. However, R-markdown can do much more than that! It allows you to create a script with all your data analysis pipeline, which you can play with as you try different statistical or visualisation methods. The great advantage, as opposed to standard R-scripts, is that you can add text amongst your code to create amazing documents that you can personalise with just a few clicks! Pablo Franco @jpablofranco
There are a few useful cheat sheets available online. I recommend this one, because it outlines the steps to produce your own R-markdown document.
After viewing a demonstration, participants were then encouraged to create their own R-markdown document, and challenged to reproduce the following example:
The *mean* car speed was `r mean(cars$speed)`mph.
The mean car speed was 15.4mph.
We’re having a wondeRful time learning #knitR with @jpablofranco at @ResPlat pic.twitter.com/SbksF32iQi
— Meirian (@MeirianLT)May 30, 2018
Next, Pablo gave an example of how to create HTML files which contain R code. To demonstrate, he shared an example he had prepared.
Participants had hands-on experience on how to modify the document to generate three types of reports:At the end of the exercise, we were able to create amazing html files that included interactive plots (using the plotly package) and even good-looking regression tables (using stargazer and pander packages). – Pablo Franco @jpablofranco
- Show everything on the script: A document that shows all your code and output. This is excellent for reproducibility, and great for sharing with collaborators.
- Show only results: A document that shows only the output from your analysis. Also great for sharing with collaborators.
- Show only the relevant parts: Choose what pieces of the code and which outputs to show. Not everyone is interested in the complete process. This functionality allows you to personalise exactly what you want to share.
LaTeX is a programming language for high-quality, beautiful typesetting. Tim showed us how we can also create beautiful documents in LaTeX which contain our R code.
One of the best parts of having a science degree is the way it empowers us in our mundane lives outside of academia. When a housemate needed clarification about how much they should pay each fortnight in rent and bills, I helped them out with a beautiful and reproducible expenditure summary using Sweave, version controlled with Git. Sweave smushes together R and LaTeX in the spirit of “literate programming” as espoused by Donald Knuth. – Timothy Rice @resnomicon
Tim’s budget is now hosted at notabug.org/cryptarch/budget.git
If you would like to learn more about typesetting your R code in LaTeX, I recommend the tutorial on ShareLaTeX.
@resnomicon from @ResPlat showed us how he saved some $$$ by keeping a budget in #Sweave and combining the powers of #rstats and LaTeX! ✌#candid pic.twitter.com/zlqm5OLvte
— Meirian (@MeirianLT)May 30, 2018
Finally, we saw another impressive application of R documentation from David, who had created a bookdown project, which was itself an R tutorial!
Several R packages have been developed to take advantage of R’s RMarkdown functionality, and one of those is bookdown. bookdown lets you compile a series of RMarkdown files (with a couple of bookdown specific ones for formatting) into either a traditional book as a pdf or, as in my case, a website. Using materials I had developed for a beginner R workshop as an example, my presentation showed the general structure of a bookdown project, how to compile it into a book/website, and how to make use of GitHub’s gitbook functionality to host my course material online as a website free of charge. bookdown serves as an accessible middle ground between basic RMarkdown documents and full blown LaTeX documents, and with the ability to embed R code it becomes a viable option for writing up your thesis! – David Wilkinson
You can check out the result of David’s hard work online here. The corresponding bookdown project can also be viewed, on GitHub.
This blogpost was created by Meirian Lovelace-Tozer, who is a Research Community Co-ordinator and LaTeX trainer at Research Platforms Services @ResPlat.David also impressed us all with his #rstats tutorial, which he developed with the #bookdown package! Thanks for helping attendees with their first #knitr experience @ResPlat pic.twitter.com/vHcWTV3lyL
— Meirian (@MeirianLT)May 30, 2018