Open Science Training: Lego, Languages & Lo-Fi, No-Fi

Well, it’s been quite a while since I last had a chance to blog about progress with the Open Science Training Initiative, so it’s about time I provided you with a bit of an update. Nor have things have been quiet on the open science front – admittedly I have been providing some soundbites over at the News feed of the main OSTI website – but juggling the final months of thesis writing with everything else is making things pretty busy!

So: this month’s update gives you a bit of Lego, a bit of Berlin, some opportunities to get involved with translation and/or education activities and a little glimpse at some upcoming changes to the OSTI website. Read on…

Calling All Linguists!

Currently, the bulk of OSTI teaching materials are only available in English, over at the Open Science Training GitHub repository. However, OSTI was designed for in-person teaching and for adapting local, subject-specific courses to deliver integrated open science training too. English-language versions alone cannot provide for this. Last year, some of the slides made it into Finnish as part of the Finland Open Knowledge Roadshow, care of Joona Lehtomaki and colleagues. I’d love to see a broader range of translations to take things further – some of you may already know about this from our recent discussion on the OKFN Open Science community call the other week.

Image by Tobias Mikkelsen (Flickr), CC-BY-NC-SA 2.0

Do you have language skills to offer? Image by Tobias Mikkelsen (Flickr), CC-BY-NC-SA 2.0

Realistically, I’m going to need YOUR help in translating OSTI materials into other languages. I’ve already heard from individuals from a variety of countries who would like to translate the resources we have into French, Spanish, Portuguese and Russian – I’d like to add Arabic and German to that list too. If you have language experience and an interest in open science, then I would love to hear from you – feel free to email me via the OSTI “Contact Us” details, or drop me a message in the reply box below. And if your language isn’t listed above but you’d like to be the person to add it to the list and recruit a communtiy of fellow translators, then let me know!

So, a few things you might want to know:

  • Before we can start the process of translating OSTI, I’m looking to revise the materials and get them into Markdown or similar;
  • Transifex has been suggested to me as one tool to assist with translations. If you know of any others which might be useful, or have any experience (good or bad) of working with Transifex, then leave a message below…
  • I’ll also be adding a Translations page to the OSTI website, as a central place for information, and establishing some mailing lists for our volunteer translator team to share their thoughts and ideas and to discuss any obstacles they meet during the translation process;
  • Obviously the above will take me a little time, so keep an eye on this blog and the OSTI site for further announcements – if I know you’re interested in being one of our translators, then I can email you once plans are taking shape.

So get in touch now and help to lead OSTI to pastures new!

Learning With Lego

Some of you may recall the  “Consequences of (Bad) Communication” workshop which I ran at last year’s SpotOn conference in London, which addressed the issue of science communication through the fabulous medium of Lego. I’ve been absolutely delighted with the response to this one – but then, who doesn’t love Lego (bare feet treading-on-bricks notwithstanding)? I have a suspicion that part of the appeal of Lego-based teaching sessions lies in the happy childhood memories it evokes in so many of us…

Happiness and Lego at SpotOn 2013 :) Photo by Sophie Kay

Happiness and Lego at SpotOn 2013 🙂 Photo by Sophie Kay (@StilettoFiend), licensed under a Creative Commons Attribution Licence, CC-BY-4.0

Microscope base in progress. Photo by Sophie Kay (@StilettoFiend), licensed under a Creative Commons Attribution Licence, CC-BY.

Microscope base in progress at SpotOn 2013. Photo by Sophie Kay (@StilettoFiend), licensed under a Creative Commons Attribution Licence, CC-BY 4.0.

Since I ran the session at SpotOn in November 2013, the session instructions have been downloaded from the OSTI website a fantastic 193 times. Although I can’t be sure which of these were read out of interest and which involved practical use, hopefully this means the ideas surrounding the session are spreading further. Furthermore, the mathematics department at Royal Holloway, University of London, will be adopting our Learning With Lego workshop as of this September. It’ll form a compulsory course for the first-year undergraduates and will take place on a weekly basis. It’s designed to get the students to identify what makes for good communication in a general (for which read, “Lego”) setting and, it is hoped, to pave the way for translating these experiences into improved communication of mathematical concepts during their day-to-day work.

Lego on Mozilla’s “Lo-Fi, No-Fi” Kit

And if you’ve been keeping an eye on that OSTI News page, you’ll also be aware that the Learning With Lego workshop is soon to appear as part of Mozilla’s “Lo-Fi, No-Fi” teaching kit. Established by Kat Braybrooke and colleagues at Mozilla and drawing on input from a variety of educators, the kit provides templates and ideas for teaching the web – and associated skills for using the web – in situations where connectivity might be low or even non-existent. I’m currently revising my original, informal instructions and packaging them for the kit, so I’ll be letting you know when our Lego lesson has officially appeared.

Homepage of Mozilla's Lo-Fi, No-Fi Teaching Kit
Homepage of Mozilla’s Lo-Fi, No-Fi Teaching Kit, offering educational sessions ranging from “Code Thief Cards to Teach Javascript Offline” to “Use Puzzles to Teach HTML”.

Open Knowledge Festival 2014: Berlin, July 15th-17th

Well, I did promise a little of Berlin at the start of this post, although it’s a visit to come rather than one that’s already taken place. Thanks to the generosity of the Wikimedia Foundation, I’ll be attending OKFest next month on a Wikimedia Scholarship. While I’m in Berlin, I’ll be looking to find ways of extending and adapting OSTI, as well as starting to build a strong community of educators willing to teach OSTI programmes in their home institutions – if that sounds like your kind of thing, then please come and talk to me at OKFest! I’ll be around for all three days of the festival and will also be hosting a session – I’m co-presenting Skills and Tools for Web Native Open Science with Karthik Ram on the final day of the programme, so I hope to see a mixture of new and familiar faces in the audience… And if you haven’t bought a ticket yet, then sign up here.

Well, it seems as though my “short” update is more than long enough for now. There’ll be more news later this week though, so watch out for a second post before we hit the weekend. You wait ages for a bus eh, and then… 🙂

#solo13lego: Research Roles Through Lego

Ah, it’s been a busy week. Already several days have passed since the end of SpotOn 2013, so it’s about time I blogged my session from the Saturday, #solo13lego. I’m not able to deliver the kind of prolific blogging which some of my fellow attendees at the #solo13blogs session are capable of.

My workshop did admittedly have its own title, “Making Research Useful: The Consequences of (Bad) Communication“, but that didn’t prove as catchy as referring to it as “The One With Lego“, which was perhaps a better indicator of the main aspect of its appeal. Peter Murray Rust has already blogged about his experience of the session, so you can also head over there to hear an attendee’s perspective.

We were also highly fortunate in that SpotOn keynote, Salvatore Mela, inadvertently kicked off the Lego vibe on Day One of the conference when he showed us pictures of a gloriously Lego-fied particle collider. Couldn’t have asked for a better theme-setting ahead of our workshop!

The Main Premise

Participants deep in thought and Lego at Solo13. Photo by Neil Chue Hong, CC-BY

Participants deep in thought and Lego at Solo13. Photo by Neil Chue Hong (@npch). Licensed under a Creative Commons Attribution Licence, CC-BY-3.0.

There’s been a lot said about reproducibility of late (indeed, the result of much work and discussion in the scientific community over many years – see discussion here), whether that’s to do with working culture, tools, infrastructure or incentives – all highly relevant factors and issues that need to be dealt with. Ultimately though, the reproducibility issue boils down to a failure on the part of the research producer to anticipate or account for the needs of the research user (that may sound an oversimplification, but it’ll do for now – I’ll go into details in a future blog post, otherwise I’ll ramble on for ages here).

A microscope from one of our Group B teams. Photo by Suzi Gage (@soozaphone).

A microscope from one of our Group B teams. Photo by Suzi Gage (@soozaphone).

#solo13lego aimed to redress the balance and get participants thinking about how to identify the needs of the end user. By dealing with the frustrations of poorly communicated instructions, could they pinpoint where the problems lay, how the original writer had failed in their communication, and how the situation might be improved?

Optical Microscopes in Lego

Split into groups of ten, the participants had to download a set of Lego instructions to build an optical microscope, complete with “mirror”, stage, objective lenses and eyepieces. We had three sets of instructions, each describing the same item in a slightly different way.

Photo by Sarah Cosgriff (@Sarah_Cosgriff).

The results of (I think) one of the Group B efforts. Here the faulty instructions for the middle section have caused problems in constructing the microscope stage. Photo by Sarah Cosgriff (@Sarah_Cosgriff).

And now for the catch: these were faulty instructions, deliberately written to confuse, confound and completely obstruct the user, and devoid of diagrams, schematics, images or any other visual aid. Although the participants were aware of this from the beginning, it didn’t prevent them from becoming highly frustrated with the situation!

In addition to dealing with the pecularities of the instructions, our Lego builders had to identify precisely what made these instructions bad instructions, how they had failed to address the user’s needs, and how they should be improved.

And the rules: no discussion between groups, no sneaky peeks at each other’s models, no looking at other group’s instructions. So, how far did they get in 35 minutes?

The End Result…

Given that they’d only had just over half an hour to interpret the instructions and build their microscopes, the groups made some good attempts. Notably though (and as one would expect) none of the groups managed to reproduce the original microscope model: hardly surprising, given the flaws in the instructions.

Finished micrscope by Group A. Photo by Jonathan Pritchard, @jr_pritchard.

Finished microscope by Group A – note how the alignment of the eyepieces differs from the other models shown above. Photo by Jonathan Pritchard, @jr_pritchard.

In fact, if you take a look at the photos in this blog, what may at first glance seem to be identical models clearly have quite obvious differences.

Some models completely missed out the band of dark green bricks in the middle of the microscope. Some didn’t manage to include the microscope stage. Others misplaced the focus dial or missed it out altogether; the alignment and position of the objective lenses and eyepieces varied wildly between models. And this really wasn’t the fault of our participants: they were doing their best with the instructions they had!

The discussion that followed identified various “improvements” required:

  • Use of a coordinate system to describe the position and orientation of blocks;
  • Corrections to the number and types of bricks listed for use;
  • Adequate description of where each level of bricks should be positioned in relation to the levels above and below;
  • Use of visual aids, such as photos, diagrams and schematics, to demonstrate how the sections of the model should fit together;
  • Inclusion of images for the end result…
  • …and lots more (full discussion can be viewed on the livestream footage).
Microscope base in progress. Photo by Sophie Kay (@StilettoFiend), licensed under a Creative Commons Attribution Licence, CC-BY.

Microscope base in progress. Photo by Sophie Kay (@StilettoFiend), licensed under a Creative Commons Attribution Licence, CC-BY-3.0.

Group work in full flight at #solo13lego. Photo by Sophie Kay (@StilettoFiend), licensed under a Creative Commons Attribution Licence, CC-BY-3.0.

Even this short exercise demonstrates how a supposedly simple set of instructions can produce wildly different results if ambiguities leave them open to misinterpretation. It really got us thinking about what the needs of the end user are – something which we’re not taught to think about (or indeed encouraged to do so) at any stage of our education. Could this kind of exercise, whether with Lego or with hands-on science, be used to promote better communication amongst our scientists?

The extended session at the upcoming hackday (see below) is going to take this idea further and train participants to produce instructions that account for this user perspective.

All five microscopes at the end of the session. Photo by Peter Murray Rust (@petermurrayrust).

All five microscopes at the end of the session, alongside Sophie’s slide of how the models should have looked. Photo by Peter Murray Rust (@petermurrayrust).

Upcoming Hackday

Now, dates are yet TBC, but I’ll be running an extended session of Lego-Based Learning at the upcoming SpotOn Hackday, which will probably happen sometime early 2014. I’m hoping this longer workshop will last around 3 hours. It’ll give us time to explore both the user and producer roles and I’ll be implementing the rotation-based learning approach of OSTI, so there’ll be an even stronger incentive for good communication skills. I’ll be posting the details on the OSTI News page once the time and place are confirmed, as well as tweeting the details, so keep an eye on all that and let me know if you’d like to join: I’m looking forward to seeing some returning faces as well as new ones! And there are worse ways to spend a Saturday than playing with Lego…

And What Next?

Although the instruction sheets are still available via my previous blogpost, I’ve posted the slide deck and the instructions up on the GitHub repository for the Open Science Training Initiative. If you’re interested in running a similar session, you can download those now – of course, you’ll need to buy your own stash of Lego (or get someone else to buy it for you) but at least that’s quite a fun task. Good Luck! 🙂

#solo13lego: The Instructions

If you’re reading this then chances are you want to participate in the #solo13lego session, “Making Research Useful: The Consequences of (Bad) Communication“. After all, who doesn’t like Lego and science? You can follow our session remotely via the livestream, which will appear on the SpotOn Media page here.

This post has been scheduled to appear a little ahead of the session, to help remote participants with their preparations (and to make sure it’s available and working by the time #solo13lego kicks off!). So if you’re planning on attending the session, behave yourself and don’t be tempted to nosy at the downloads below ahead of time!

Groups who are in the session right now: You should be in groups of ten people at most. You need to assign a group leader and then form three smaller teams within your group. Your leader should help to coordinate the three sub-teams and (informally) collate feedback/critiques on the instructions as you progress with your Lego model. Talk within your team, but don’t talk to other groups – or sneak a peek at their models!

A (first) little word of warning…Now, a little caveat: ONLY click on the downloads below once you’ve had your group assigned and you know your group’s letter. Remember that you’re not allowed to discuss your work with the other groups, so you shouldn’t look at their sets of instructions either!

Remote participants should choose their favourite letter (without peeking at the instructions first!) and download the relevant set of instructions. Feel free to shout any questions via the hashtag #solo13lego. You can also message me via @StilettoFiend, or alternatively David, @drg1985, if you’d prefer to hear his dulcet Irish tones.

A (second) little word of warning… Remember, this session is about the consequences of poor communication. We’re encouraging you to gain the perspective of an information user rather than an information producer, so that you can bring those insights to the debate at the end of our session. So don’t be deterred by errors or ambiguities in the instructions: it’s your job to work around these, critique them and identify how these Lego recipes need to be improved (and as we said, they’re designed to have a LOT of room for improvement).

So, it’s time to reach for the Lego. You have half an hour. You may turn over the page and start…

  • Instructions for Group A: PDF ODT
  • Instructions for Group B: PDF ODT
  • Instructions for Group C: PDF ODT

Lego, the Universe and Everything

With SpotOn London kicking off today, it’s time I revealed a few more details about our workshop scheduled for tomorrow afternoon, “Making Research Useful: The Consequences of (Bad) Communication“, perhaps better known by its hashtag, #solo13lego. The entire conference programme is being livestreamed, so feel free to follow, or even participate in, our session even if you can’t be there in person – keep an eye on the #solo13lego hashtag and join in the fun from afar. And if you are at SpotOn this year, then get thee to the British Library’s Eliot Room at 3:30pm on Saturday – we can accommodate up to fifty participants in the session itself (there’s only so much Lego to go around!), so you might want to be reasonably prompt arriving.

The workshop will look at some of the issues surrounding reproducibility in scientific research and in particular, the roles of the information user and information producer. And all through the wonderful medium of Lego: the perfect way to spend your Saturday afternoon 🙂 If you keep an eye on this blog, another post will be appearing at the start of the session tomorrow, explaining exactly what’s going on and providing the instructions you need for Lego building.

And yes, our workshop is one of the final items in the #solo13 programme. By this stage of the conference, you’ll have enjoyed lots of fantastic talks, seminars and workshops, but may also be flagging a little with all the activity. We want our #solo13lego workshop to combine thought-provoking discussion with the fun of playing with Lego. It should be a friendly session and hopefully a great way to close out your SpotOn 2013 experience – before the official Wrap Up, that is!

Just a few words of advice on the dress code: the wearing of shoes is strongly advised. To quote Michael Rosen, “you know what it’s like treading on Lego with your bare feet” 😉

And just in case you had any questions…

– Do I need to bring my own Lego to the session?

Don’t worry about that – we’ll be providing Lego kits for each team to use. If you can’t make it to the conference but would still like to take part in our session, then you’ll want to have a stash of Lego to hand. Each group in our session will be using a 32 x 32 backing board and a 650 piece Lego kit, which contains an assortment of basic bricks in several colours, including lots of those pesky 3×1, 2×1 and 1×1 pieces. So if you’re planning on remote participation, you don’t need to have any fancy Technic. Just a decent number of basic bricks will do.

Each group will have one of these...

Each group will have one of these…

– What’s going to happen at the session?

We’ll spend the first 5 minutes on a brief introduction to the reproducibility problem in modern science, before getting hands-on with Lego in groups, using some pre-prepared instructions designed to give you an awkward time. Each of our five groups will be given a different set of instructions to build the same item. Main rule is this: NO DISCUSSION is allowed between the groups. You can talk amongst your group all you like, but not to the other teams.

It’s not expected to be plain sailing all the way: our instructions are intentionally problematic and you may have to modify them as you go or fill in the blanks if you find any omissions. At the end of the Lego building phase, our groups will be critiquing the instructions and, if they get ahead of time, providing their own new-and-improved versions. We’ll have a quick-fire discussion of what aspects were difficult, where the various Lego recipes fell down, and identify what the fundamental problems were with the way the methods were communicated.

...and one of these.

…and one of these.

After the Lego building, we’ll take those newly-gained insights and open out the session into a debate on policy and approaches for how we train our scientists, researchers – in fact, any kind of knowledge workers – to deliver their outputs. Does modern culture focus too much on information production at the expense of information utility? If so, what can we do to change this: what incentives, penalties and support are needed?

– I want to participate remotely, how can I view the session?

Once you get to 3:30pm, check out the conference’s Livestream and follow our session that way. You may also want to visit Sophie’s profile – a slide deck will be appearing under Talks sometime on Saturday, so you should be able to access the talk materials there.

– I want to participate remotely, how will I get hold of the Lego instructions for the session?

Another post will appear here at “The Stilettoed Mathematician” just before 3:30pm on Saturday 9th November. It’ll link you to downloads for the Lego instructions so you can get building with everyone else. Remember, this session is all about the consequences of bad communication, so you should expect a bit of a tussle with the instructions as you go and you’ll need to use your ingenuity.

– Who’s running the session and how can I contact them?

There’s a team of two running the session, myself (Sophie Kay) and David Robert Grimes, science writer for the Guardian and Irish Times.  Fire any questions at us over Twitter via the #solo13lego hashtag, or shout them directly to us at @StilettoFiend and @drg1985.

Research Workflows, Sustainability and Software Education: Panton in October

Well, October has been a rollercoaster month: owing to an unfortunate spell of ill health, it’s been a much quieter time than I originally intended. Nonetheless, there have been plenty of new contacts, interactions, meetings and developments…

October brought interesting discussions with Jun Zhao about sustainability in research, drawing on her expertise in scientific workflows. Jun is currently a postdoctoral researcher in the Zoology department at the University of Oxford, focusing on a broad spectrum of projects that address linked data, the semantic web and aim to facilitate fuller integration of data into our published research. In particular we spoke about one of her main projects, Wf4Ever, which aims to foster “repeatable, reproducible and repurposable research” by uniting scientific workflows and digital libraries as well as facilitating systematic data processing. We spoke at length about my plans for open science graduate training in Oxford and I’m looking into the possibility of incorporating a live demo of her research tools into the OSTI in January, as part of the “lightning lectures”.

My ongoing contact with Kirsty Grainger and Amy Vitale at NERC (the Natural Environment Research Council) has continued during October, ahead of the Town Meeting taking place on 11th December. NERC has this week officially opened the competition to award Doctoral Training Partnerships across the UK. Jenny Molloy and I are now officially signed up for the meeting in order to promote my OSTI and to generally encourage the applicant groups to incorporate open science into their courses. It’s a great opportunity to increase the uptake of open science practices nationally and we’re really looking forward to it! This also represents great timing in relation to my OSTI, which is entering the late stages of planning at the moment. The OSTI’s aims in fostering reproducibility and equipping students for interdisciplinary research across the sciences has great potential to contribute to the “research and training excellence” demanded of the new DTPs. The landscape of research is changing rapidly: we need to teach our upcoming young researchers to deal with this evolution NOW, and graduate training represents a fantastic way to achieve this. If science as a whole is to transition to an open model, we need this change to come from the bottom up as well as from the top down. With an OSTI website, flyers and other promotional material in production at present, there should be rather a lot to talk about in next month’s blog post 🙂

Unfortunately though I was ill for Open Access Week, which was a real shame. Quite a few events were arranged in Oxford, including a seminar series throughout the week from the Bodleian Library and culminating in a Wikipedia edit-a-thon, which extended the Women in Science work started earlier in 2012 by the Ada Lovelace Day event at the British Library. Seminars ranged from Open Law to examining the ethics of OA in health research, to looking at how OA initiatives are shaping the research environment for Generation Y, our youngest generation of researchers. And if you missed the talks you can find the slides on the Bodleian’s OA Week page here. And while I’m on the subject, those of you who haven’t yet seen the fantastic PhD Comics video on Open Access should take a look now:


I was fortunate to join the much-anticipated Software Carpentry workshop at the end of the month, held over two days at the University of Oxford’s Department of Biochemistry. These workshops introduce scientists to basic computing and programming skills, enabling them to program with confidence and handle coding more effectively and efficiently in their research. I was really impressed at how the material engaged with the broad spectrum of experience amongst the attendees: some people I spoke to had minimal experience in programming, while others joined for the more challenging tasks and applications. The session was friendly and accessible and the people I spoke to also praised the online tutorials available on the course website. Massive thanks to the main organiser of the Oxford workshop, Philip Fowler, for letting me sit in on the session! If you think there’s an opening for an SWC boot camp at your institution, I’d really recommend getting in touch with the team to see what can be arranged – it’s a great initiative that has a great deal to offer the scientific community. And even better, all their content is available under a Creative Commons Attribution licence.

MozFest, Mozilla’s annual festival showcasing a variety of tech and web developments, hands-on peer learning sessions and educational initiatives, is a matter of hours away at time of writing. I’ll be arriving in London on the Friday and am really looking forward to it…if you’re going to be there and fancy some open science chat, then feel free to drop me a message! And keep an eye out for my OKFN colleagues running the Saturday workshop, “Data Expeditions: Scouting the Data Landscape with our Data Sherpas” which focuses on data wrangling skills and techniques and promises to be both fun and informative.

So, what for the next month? Planning and preparation for the OSTI will really start to gather pace over November: in my next Panton update, I’ll be reporting on the OSTI website and promo materials; hopefully releasing the provisional timetable; sharing my experiences of MozFest; and keeping you up to date on progress with the plans Jenny and I are forming for an Oxford-based hackday. And to finish on a lighthearted (and tasty) note: in lieu of full participation in OA Week, I am tempted to make some Open Access Cupcakes in the very near future…methinks an Open Knowledge Okapi can be realised in ready-to-roll icing. Bring on the Open Kitchen – photos to appear soon!

A month in the life of a Panton Fellow: June 2012

Well, June has been another productive month of fellowship work! To start on a positive note, Ross Mounce and I received the good news that our proposal for OKFest has been accepted, so we’ll be in Helsinki this September to tell you about the work we’re doing for our Panton Fellowships, as part of the “Open Research and Education” topic stream on Wednesday 19th September. Looking forward to it! June has also seen several different online meetings with various working groups, in addition to my first official quarterly report for the Fellowship, so there’s been plenty to keep me occupied.

Many of you reading this will already be aware of my focus on developing graduate training schemes for open science, data management and reproducible computation. I’m really conscious of how much our early research years are influenced by the ethos of the first group we join: this emphasises a pressing need to adequately train our graduates while they’re still at a pre-doctoral stage. So you can imagine how interested I was to read the newly released JISC-funded report, entitled,“Researchers of Tomorrow: the research behaviour of Generation Y doctoral students.” The report outlines the findings of a three-year study on our youngest research generation, the children of the so-called “baby boomers”. Amongst other things, the findings identify the need for enhanced training in digital technologies, data management and collaborative working – so encouraging to hear this while I’m in the process of developing my graduate training initiative. You can download a PDF of the report here – definitely worth a look!

June has also seen further discussion with Greg Wilson and the rest of the team involved in the development of the Software Carpentry initiative. I first mentioned SWC back in my April blog posting – they provide fantastic courses in coding and software development for scientists with a limited experience of programming, combining intense in-person workshops with online learning materials. I initially heard of them as a result of my contact with the Software Sustainability Insititute, and was keen to hear more about their work and how they’ve scaled the initiative up to work in many different countries and locations. After a great Skype call with Greg earlier this month, I remotely joined their conference on 20th June, which gave me the chance to meet (from across the Atlantic, at least!) many other people involved in the project (including OKFN’s own Cameron Neylon). I’m keen on the idea of integrating some of their courses – all available under a Creative Commons Attribution license – into my own training scheme later this year, so I really appreciated getting a chance to hear about how their work is progressing. One further note: the guys at SWC are really keen to get more female scientists into programming too (something which I completely support!), so if your department/organisation might be interested in holding a female-targeted session, then please do get in touch with them ASAP.

On 28th June, Jenny Molloy and I met up with various representatives from Oxford’s Bodleian Library. Alena Ptak-Danchak, Sally Rumsey, Juliet Ralph and Oliver Bridle all took time out of their busy schedules to talk to us, providing a picture of the existing state of data training provision across Oxford and discussing where my course might fit into that framework. Our librarians (and I mean this in a country-wide sense) represent a massive source of expertise in information management that we’re lucky to have. All the Bodleian representatives provided us with valuable insights into what kinds of training the students are most receptive to, and how I might adjust my own approach to course delivery in order to account for this. And I now have plenty of resources to explore and contacts to pursue. All in all, a successful meeting – and many thanks to Jenny for helping to bring this about!

I’ve also started to organise the Oxford Open Science meeting for August 22nd, provisionally entitled, “How best can we train graduates for research in the age of ‘Big Data’?” I’m hoping to:

  • generate debate on the evolution of training schemes for open science, data management and/or digital technologies;
  • discuss how we as a community can maximise the uptake of training initiatives in these areas;
  • think about how we might begin to use such training as a platform to engage those outside the open science community.

The group wiki can be found here and includes details of other upcoming meetings too: we’re a friendly bunch of people, so please do come and join, whether you want to listen to the discussion or to actively add to the debate. I’m in the process of recruiting speakers at the moment – if you, or someone you know, might be interested in speaking at our meeting, then I would love to hear from you. I’d better hold back on full details until names are fully confirmed, so watch this space…

July looks to be an exciting month, with several big meetings planned already. On 5th July I’m heading over to Cambridge for the day to meet with Anna Collins of DSpace, the digital repository for the University of Cambridge, to chat about our shared interests in data management and graduate training. The trip will also provide me with a chance to meet up with OKFN’s Laura Newman, Peter Murray-Rust and Tom Oinn over lunch – we should have plenty to talk about, and I’m really looking forward to hearing about the progress of the newly-launched School of Data. I’ll also be meeting with David Gavaghan and James Osborne of the Oxford DTC this Friday in order to develop plans for the open science training initiative I’ll be piloting this Michaelmas. Despite juggling work with a house move in a couple of days’ time, I’m hoping to join the OKFN hackday over Skype for a couple of hours this Saturday (unpacking chaos permitting!). Furthermore, I should also be meeting with David De Roure, Jenny Molloy and Peter Murray-Rust to discuss the potential for an open science workshop at Digital Research 2012, due to take place in Oxford this September. This month’s going to be a busy one…so if you wait a couple of weeks for my next Panton blog entry, I’ll let you know how it all turns out!

A month in the life of a Panton Fellow: May 2012

And so another month draws to a close, and it’s time for the Panton Fellows to update you on what they’ve been up to recently. Before I start talking about my work though, I should draw your attention to Ross Mounce‘s Panton summary for May, addressing topics ranging from Michael Nielsen’s excellent read “Reinventing Discovery” to Ross’ recent attendance at the Progressive Palaeontology conference in Cambridge. May has indeed been a busy month, but also an enjoyable one. Quite a few different things have happened: I’ll provide edited highlights only here to avoid things getting too long, but I’ll try and blog at greater length about a couple of items over the coming week.

My month started out with a trip to Tavistock Square, London, meeting with John Wood and Ben Prasadam-Halls of the Association of Commonwealth Universities. I was also joined by Peter Murray-Rust and Laura Newman, which made for plenty of interesting discussion. As well as hearing from Laura about the newly-launched OKFN School of Data, we talked about the implications of the open data movement for the development of distance learning initiatives worldwide, and what’s being done at present to help achieve this. John is a great proponent of graduate training in open science and recognises the need to develop appropriate initiatives to train data experts who can support the evolution of scientific practice in this age of “Big Data”. Those of you unfamiliar with his existing work with the European open science agenda may be interested in reading the excellent 2010 report, “Riding the Wave: How Europe can gain from the rising tide of scientific data” or watch a video of John’s keynote speech from APE 2011 in Berlin:

The following week saw me travel to Helsingør, Denmark, where I attended Integrative Network Biology 2012: Network Medicine, an interdisciplinary symposium attracting scientists from a plethora of disciplines including biologists, biochemists, statisticians and mathematicians. Although the conference’s primary focus was network science in relation to disease treatment, it also provided many welcome opportunities for me to discuss open science with fellow delegates and to informally promote both the Panton Principles and the work of the OKFN. For now I’ll highlight two main items of interest. Data mining aficionados amongst you may be intrigued by the advances being made by Søren Brunak of the DTU and the University of Copenhagen. Søren’s group performs text mining of Danish medical records, using this information to identify hitherto unexplored links between medical conditions, paving the way for novel studies on protein interaction networks – valuable work which promises to have a real impact on healthcare provision in the near future. It was most encouraging to see the progress his group has made through data mining, and I hope it will inspire other communities to adopt similar approaches. You can view a short video of the symposium here – the complexity of the problems discussed during INB2012, and the benefit some researchers have gained from having access to large reserves of data, really underlines how vital it is that we as a community work to foster a climate of data sharing, appropriate licensing, and open research.

While at INB I also had the opportunity to speak at length with Peter Fraser Curle of IBM Zurich, who was promoting “IMPROVER”, a new crowdsourcing initiative which aims to foster greater verification and reproducibility in systems biology research. It’s good to see that some scientists are attempting to address these issues, especially given Begley and Ellis’ commentary in Nature earlier this year, which critiqued the lack of reproducibility of many experimental findings in oncology research. The project involves collaboration between academia and industry, participants being supplied with training data to develop their methods, before receiving fresh challenge data for the competitive stage. By challenging many groups to work on the same problem, they’re hoping to provide a means of evaluating the performance of different methods on a common data set and to “[identify] complementary methods to solve a problem“. Peter and I discussed the data licensing issues of the project and I also introduced him to the Panton Principles. He provided me with some extra literature, including a 2011 paper discussing the potential of crowdsourcing for driving greater scrutiny of scientific results. Although I’m a computational rather than an experimental scientist, I like to keep tabs on reproducability studies like this – it would be great if I could adapt the approaches of my open science training scheme for use in experimental disciplines as well (experimentalists, feel free to share your thoughts on this!). The IMPROVER team are keen to encourage scientists of all backgrounds to register, follow the projects and contribute ideas and expertise. Significant cash prizes are available to fund further research – so take a look at their website if you’re interested. Bear in mind that they intend to present several new challenges over time, so even if you’re too late for the first one, fresh challenges will be announced later.

Last week I also met up with Bushra Connors, a Senior Lecturer at the University of Hertfordshire, who asked to interview me as part of her research into the changing nature of education in the 21st century. Already familiar with the work of the Open Knowledge Foundation, Bushra was very interested in the graduate training initiative I’m developing during my Panton Fellowship. We spoke at length about the open data movement and the reproducability issues that affect a vast proportion of scientific research. She also provided a few literature references as a starting point for the question I asked in my blog last month about research group influence on the evolving style of a young researcher. I’m looking forward to following her work in the coming months to see what findings emerge from her interviews and analysis.

While all these things have been happening, I’ve also been further developing plans for my graduate training pilot scheme. At the moment I’m finalising my next meeting date with David Gavaghan (Director of the Oxford Doctoral Training Centre) and James Osborne (Associate Director at the DTC) to discuss my plans for this Michaelmas and to work out how I integrate these into the existing DTC programme most effectively. Much of the last month has been spent exploring the wide variety of teaching and training exercises available out there, particularly focusing on those in data management, coding practice and collaborative working. These include various exercises from the Peer-to-Peer University, the 20 Questions from David Shotton I mentioned last month, and the MRC’s new online course in Research Data and Confidentiality. I’m hoping to present you with a more comprehensive discussion of all this, along with a provisional course outline, next month, so watch this space!

And finally, a little insight into some of the open science reading I’ll be doing over the coming month. I’m lucky to have friends who also work in networked science and promote the open science agenda: one such person is Lucy Power, who’s just completed her doctorate at the Oxford Internet Institute. Entitled, “e-Research in the Life Sciences: from Invisible to Virtual Colleges“, her thesis addresses the evolution of scientific working methods in the life sciences in relation to the rise of the internet age. Interviews with a variety of academics engaged with open science practices form an integral part of the study, including, amongst others, the OKFN’s own Peter Murray-Rust and Cameron Neylon. Lucy’s work addresses many issues I’m hoping to weave into my open science training programme, so I’m really looking forward to working my way through this over the course of June.

And on that note, I shall leave you to enjoy your respective weekends. Just a little sneak preview for June though: a provisional schedule for my open science training scheme should be available for your perusal and comments; I’ll be talking to DSpace’s Anna Collins about our shared interests in open science graduate training, and also meeting with Kevin Page and David Ratcliffe in Oxford to discuss data mining and machine learning. And those are just a few highlights! Looking forward to sharing the outcomes of these events and others in a few weeks’ time…see you then!