Research Platform Services Blog
Month
By Steve Bennett
A major theme in digital history projects is transcription: turning digitised copies of old manuscripts, public records, diaries, newspapers, film reels or audio tapes into text that can be studied. If the original material is typeset and the digitisation is good quality, then OCR software can work. But what about this:
Scripto is a neat interface that ties a content management system - Omeka, Wordpress or Drupal - to MediaWiki, the software that drives Wikiedia. The CMS manages the digital images, audio or video files, while the wiki handles the task of multiple people simultaneously editing transcriptions and keeping previous versions of each transcription.
It’s a bit fiddly to install and configure (you need to install Apache, MySQL, Omeka, MediaWiki and Scripto…) so I’ve created an automatic deployment formula using SaltStack: salt-scripto
It’s currently being trialled by Dr Nick Thieberger, a linguist and digital humanist at the University of Melbourne. He works on projects such as transcribing and analysing the Daisy Bates Collection, an incredible survey of West Australian indigenous languages from the early 1900s.
If an online transcription tool could be useful to you, please get in touch.
By Damien Irving.
Following the success of our first ever Software Carpentry bootcamp late last year, we’re planning to run quite a few more in 2014.
To kick-off the year, we’re teaming up with COMBINE to deliver a Python bootcamp for the bioinformatics community. The first session is on Tuesday 18 March - you can find details at the website.
@combine_au Thanks for helping out with our next @swcarpentry bootcamp - should be a great event! pic.twitter.com/v4THmhOUC1 #HackerWin #ResBaz
— Damien Irving (@DrClimate)
February 27, 2014
We’re also in the initial stages of planning a Python bootcamp for the medical imaging community, and in the second half of the year we’re looking to offer some R and Matlab-based bootcamps.
If you think your research community could benefit from a bootcamp, come down to Hacky Hour and chat with us (every Thursday, 3-4pm, Tsubu Bar). We’re happy to have prospective organisers sit in on our bootcamps, so the bioinformatics event represents a great opportunity to come and see what bootcamps are all about.
The Hacker Within gets a mention on the Software Carpentry blog!
By Paul Mignone
Unless you’ve been living, working or conducting research under a rock in recent years, chances are that cloud computing has affected your life in some way. From consumer mobile phone apps, to the massive roll out of corporate (e.g., Telstra) and research (e.g., NeCTAR) services, more and more consumers and organisations are looking to the cloud for cost and time efficiencies. It is therefore no surprise, that the cloud technology has not only been disruptive to organisational processes, but also to traditional software and hardware business models.
A recent conversation article by Associate Professor David Glance (University of Western Australia) discussed how cloud computing platforms like Amazon Web Services are challenging companies such as IBM, HP and Dell, who have made their money traditionally from selling physical computing hardware to customers. Companies such as VMWare provide virtualisation technologies that have facilitated the rise of cloud computing. However this also represents a ‘double-edged sword’ for such companies as they also profit from having their software installed on physical machines.
It’s therefore no surprise that these challenges would eventually trickle down to software re-sellers and their distributors. Software as a service (known as Saas) is a software delivery method in which software and associated data are centrally hosted on the cloud. Using Saas, companies can pay a subscription fee to use the software, while its associated data can also be stored by the Saas provider. The Saas business model is also viewed as a way to potentially eliminate software piracy.
A global study conducted by the Business Software Alliance (BSA) in 2011 placed the commercial value of software theft to $63.4 billion, with over half of the world’s computer users (57%) admitting they used pirated software. It could be that the best solution to software piracy is for the software companies to never release (or sell) their software to client, but rather lease it to their clients and host it on their own cloud infrastructure. Methods such as Saas may still be open to piracy in the form of shared login credentials or ‘Dark clouds’ (i.e. cloud servers that deploy pirated SaaS), however Saas is still regarded as method to greatly reduce it.
The Saas model will also present challenges at the reseller level, since many of these subscription-based programs severely undercut the cost and difficulty of server-based programs. With Saas, businesses can use an array of software solutions in the cloud for hundreds of dollars a month instead tens (or even hundreds) of thousands of dollars when buying from resellers. Software distribution is also immediate, and there are fewer complexities involved with software trails (e.g., most software come with at least 30-days) giving greater potential for direct sales.
However, there are some legitimate concerns with cloud software that resellers are quick to exploit. Cloud security is a persistent one, yet every day, more and more solutions at both the hardware (e.g., Cisco) and software (e.g., VMWare) levels are seeing these concerns slowly abate. Graphics rendering in the cloud is traditionally seen as a limitation for cloud adoption of Computer Aided Engineering (CAE) programs, as real-time graphics rendering in the cloud can suffer due to performance and latency issues. These issues are also being resolved at the hardware level with Nvidia releasing their GRID graphics card. The technology can offload the processing of graphics-intensive CAE programs from the CPU to the GPU in virtualized cloud environments.
What is clear is that times are changing. As more individuals and organisation adopt the Saas model, software resellers will need to focus less selling software, and more on providing value-added services to cloud products (e.g., training and implementation of cloud products into businesses). Otherwise software vendors and pirates may become the strangest of bedfellows, struggling to survive against the increasingly unfavourable odds that the cloud brings.
By David Flanders
Here at UniMelb we’ve been working on a project focused on migrating research apps into the national .EU.AU cloud (funded by NeCTAR). NeCTAR have asked to share why we have selected the following apps for researchers. We hope that this post will help encourage our fellow NeCTAR cloud projects to talk about the cool stuff they are doing with the cloud so that we can leverage the full collaborative researcher potential.
How are we picking the best research apps? - Early on, we came up with the following key selection criteria: a.) demonstrable researcher lead demand for the tool, b.) sustainability via research community participation, c.) breadth of use across our campus, d.) technical feasibility and e.) economic feasibility and/or business case.
Based on this list we started approaching our various ‘research precincts’ as per this color-coded campus map:
[University of Melbourne Precinct Campus Map]
From a sample of our ten-thousand researchers, we quickly discovered that the research tools our researchers want are primarily discipline based; even where tools such as Matlab or #Rstat are used in multiple schools, the use of the tool is very different per research usage (e.g. customising R with CRAN plugin tools effectively makes R a different tool for each subject area). In support of our qualitative approach, we were pleased to see our fellow cloud node [1] in South Australia, eResearch SA, discover similar findings through their quantitative survey:
[eResearch SA 2013, The eResearch Landscape 2013: A Snapshot, By Sarah Nisbet and Jarrad Greenham, Adelaide, South Australia]
Which brings us to the first lesson we feel we can share with our fellow research cloud #appsmigration projects: To engage researchers in the use of the cloud we must provide discipline specific tools which groups of co-located researchers can use (with a shared sample of discipline specific data if possible).
Accordingly, the following is our current list of research groups whom we are going to engage in the communal use of cloud apps (priority list subject to change):
“Low hanging fruit apps” aka priority research apps list for migrating to the cloud:
1. Neuroscience with iPython (SciPy) and/or Matlab through ‘Software Carpentry’ methods.
- Usability Engineer: Damien Irving and Katie Ewing
- Developer: Russell Sim, (scoping potential work with Aptira)
2. Biosciences with the use of iPython/RStat through ‘Software Carpentry’ methods.
- Usability Engineer: Damien Irving
- Developer: Tim Dettrick
3. Engineering with the use of an HTML5 CAD browser (like 3DTin?) through 3D Printing “Digital Blacksmith” methodologies.
- Usability Engineer: Paul Mignone
- Developer: TBC
NB: As you can see by the above, we are focusing on what we are calling ‘data intensive tools’, which we define as tools for data larger or more complex than what a spreadsheet can handle.
“Back-burner” apps list (we hope to get around to these during the course of the project, no promises, but any collaborative partners out there welcome!):
4. Government (Social Science) with Rstat via the use of Rstudio through Software Carpentry methodologies
- Usability Engineer: Dejan Jotanovic
- Developer: Steve Bennett or Tim Dettrick
5. Genomics/Bioinformatics with use of Galaxy training via VLSCI.
- Usability Engineer: Guillermo Lopez (HABIC) & Claire Sloggett (VLSCI)
- Developer: Nuwan Goonasekera (VLSCI)
6. Arts (Cultural Communications) using a tool like ?Tableau? for doing visualisations and infographics:
- Usability Engineer: Fiona Tweedie
- Developer: Steve Bennett
7. Social Sciences using a tool like ?NVivo/TSense? for doing word analysis?
- Usability Engineer: Fiona Tweedie
- Developer: Steve Bennett
TileMill, a cloud app successfully run as part of our ‘Mapping for Academics’ training bootcamp, demonstrates the value of the above approach. In fact, we are pleased to say that Cathy Miller, at the University of Adelaide, has already repeated the TileMill course. Just recently we’ve also been made aware of two research papers published utilising TileMill to create their own custom maps.
We are thus actively looking at expanding this ‘Mapping for Academics’ platform with additional tools like CartoDB and other mapping tools, as well as welcoming any partner institutions looking to use our open source apps and creative commons training material. Please get in touch!
#!= Yay! we’ve just been made aware of two research papers published utilising TileMill to create maps for the research paper. #win
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Research can be ‘bazaar’… so we’re here to help!Flick us a tweet (here, or here), watch a video, check out our page and follow our blog-posts - both formal and fun. Even better than the virtual, meet like minded researchers at one of our events. Come engage with the Melbourne research community.
Get started by contacting your discipline’s ‘Research Community Coordinator’ who can help you learn new tools and have fun collaborating with fellow researchers! Here’s the full list.
The Research Bazaar is a campaign by the University of Melbourne’s central IT Services Researcher department to engage researchers in the digital apps they need to produce world-class research. Read our #ResBaz mission statement here.
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[1]= The National Research Cloud is made up of eight higher education institutions who are on course to create the largest federated research cloud in the world.
By Paul Mignone
Regardless of your political persuasion, Australian tertiary education is going through some challenging times with regards to government funding. With Labour and Greens recently blocking the Coalition’s $2.3 billion worth of funding cuts (a policy which Labor originally proposed), the chances for increased government funding to the sector in the near future appear slim at best. While this tragic comedy plays out, it will be up to Universities, research institutes and researchers to find alternative forms of funding and/or cost efficiencies.
Enter 3D printing…
The net is saturated with examples of how the technology can speed up and reduce costs in manufacturing processes. Yet despite the recent boom in open source 3D printing technologies, its use in speeding up and reducing costs in academic research processes hasn’t been as extensive. One of the first off the mark to demonstrate this appears to be Associate Professor Joshua M. Pearce, from Michigan Technological University.
I posted about this group earlier on their fantastic efforts in developing the first open-source metal printer. Joshua’s research group has become well-known for cutting the costs of scientific research by designing open-source hardware using 3D printers and micro-controllers. He’s also recently published a book on the subject, which may well be the first ‘bible’ for low-cost research.
Image Source: http://tinyurl.com/n973fd6
On a personal level, this cost saving potential was realised through my own research. In July 2013, I went over to the ISIS facility to conduct an experiment on the Engin-X beamline. This device has the ability to use neutrons to investigate the internal stresses of components while under mechanical load. The experiment required the design of a specialised sample holder made of metal to hold the samples in the beamline.
The part was to be made of machined aluminium to conduct high temperature test runs. 3D printing was used to prototype the design of the holder. Using an Objet 3D printer, it produced a resin part with a resolution of 26 microns. In English, the quality of the print was so good, that if my experiments were conducted at room temperature, I wouldn’t have needed the aluminium version!
While the 3D printed holder was not used in the Engin-X experiments, the prototype exercise made me and my group aware of the time and cost saving potential of 3D printed apparatus in research. The picture below shows the time and cost difference of the two different sample holders. The final aluminium part costed approximately $600.00 (inc. material and labour), and had a lead time of approximately two months. The 3D printing service at ITS research was able to produce the resin part for approximately $13.30 (i.e. approximately 2% of the aluminium holder price), which was ready the next day (i.e., approximately 2% of the aluminium holder lead-time)!
The comparison of sample holder costs and lead-times.
While not every experiment is going to benefit from the benefits of 3D printed equipment, getting the research community aware and skilled in the technology will go a long way in helping them determine its suitability for their research. If suitable, it can only be a win/win outcome as it can potentially:
The 3D Printing Summer School will be the first attempt by #resbaz to educate Melbourne University researchers in this technology.
Stay tuned…
By Paul Mignone
With just over a week to go before the University of Melbourne’s inaugural 3D Printing Summer School, it can’t get any more exciting. The five-day intensive course by ITS Research is the first of its kind in Australia, and the mere whisper of it produced enough demand to re-run the course many times over.
From February 17th – 21st, twenty four students from various backgrounds will learn what it takes to become ‘Digital Blacksmiths’. David Flanders and Bernard Meade give a great explanation of the digital blacksmith concept at Melbourne University’s 3D Printing showcase in November last year. The traditional blacksmiths conceptualise an object and create it from wrought iron or steel by forging the metal. They then use tools to hammer, bend and cut the object to its desired shape and function.
Same profession, different tools…
The digital blacksmith replaces the hammer with a 3D printer to create objects, but new skills are required for the conceptualisation and design stages. The summer school aims to deliver those new skills to students, by teaching them how to use Computer-Aided Design (CAD) and 3D printing software. This will help Melbourne University researchers and the 3D printing community in developing ideas and producing better research outcomes.
Watch this space…