About Sophie Kershaw

Sophie is a final-year doctoral student at the University of Oxford. Interested in interdisciplinary collaboration, open science and discussing the experiences of women in science, she is also a keen participant in science communication projects and university outreach. You can find her on Twitter as @StilettoFiend.

#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 Academia.edu 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.

Open Science Training in Practice

I know some of you have been waiting for a while to hear in full about the outcomes of January’s pilot scheme for the Open Science Training Initiative (OSTI). Well – the moment is finally here. Those of you who’ve been keeping a close watch on the Open Science Training Initiative website may have noticed that the post-pilot report went live last Saturday. In case you haven’t happened upon it yet, you can download a copy here:

Click here to reach the download page for the Open Science Training Initiative post-pilot report.

I should also clarify that the link above isn’t for my year summary, Panton Fellowship report (which provides a more general overview of the Panton year and the open science work that’s entailed beyond the OSTI project). For that, you’ll need to look at blog postings for April…

Just so you know what to expect, the report:

  • provides an outline of the general OSTI pattern,
  • explains how this template was modified to suit the needs of the Doctoral Training Centres in Systems Biology and Life Sciences at the University of Oxford;
  • delivers an in-depth analysis of the feedback from the auxiliary demonstrators and the students themselves, alongside my own perspectives as course leader.

You’ll also notice that it’s been a busy time for the OSTI website: videos from the pilot initiative have been appearing on the site over the last week, for those of you who’d like to see how the pilot went. Unfortunately we weren’t able to take any videos from the main work area, or from the daily supervisions, which is where the bulk of the teaching and discussion took place – as you can see from the photos below.

group-discussion-3group-discussion-1

The videos you can see on the OSTI website only represent a small fraction of the pilot scheme: much of the teaching relies on discussion with individuals or small groups and the students’ hands-on application of licensing and other Open approaches is a core part of the learning process within the initiative.

Hopefully this heralds the start of an exciting new era for open science training, in which our graduates enter the research world fully equipped with experience in open science techniques and the confidence to implement these practices under their own judgment in their day-to-day working life!

Feel free to add your comments below if you have any thoughts on the post-pilot report, or feel that OSTI’s rotation-based learning techniques could benefit students in your institution.

Panton Fellowship: End of Year Report

PLEASE NOTE: This article is just the advert for my Panton report, NOT the report itself! You can download a PDF of my 12-page end of year report here, all in glorious technicolour…

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Twelve months on from the start of mine and Ross Mounce‘s Panton Fellowships with the Open Knowledge Foundation, it’s time to take stock of where we’ve got to in that time. And how quickly the time has gone!

The Contents of a Year

Yes, the time might have flown by, but it’s time for the concluding Panton report. At the request of the OKFN, I’ve produced a full report on my work in Open Science and Open Education over the past year – you can download a copy here. I’ve tried to provide a fairly all-round picture of the major meetings, trips and of course an overview of the Open Science Training Initiative. Alas though, there wasn’t space to fit every last bit of news in, so feel free to leave me a comment/message on this blog or on my Twitter account if you’d like to know more about my Panton experiences!

Just to clear up any confusion though: I know some of you are also awaiting my post-pilot report on the inaugural OSTI scheme. It should be released in the next fortnight , and is a completely separate report to the one I’ve listed above. So don’t worry – those details, and indeed all the OSTI course materials, will be appearing very soon. I’ll be publicising it on Twitter and here on my blog once that happens, although I can add you to the direct mailing list for OSTI releases if you send an email to enquiries(at)opensciencetraining.com :)

Much of my focus has been on furthering the integration of open practices within academia, through development and delivery of graduate-level open science education. Meanwhile, my Bath-based counterpart, Ross Mounce, has done a phenomenal amount of work for policy development in open access and open data, including trips to Brussels and appearances on the radio, alongside data mining work inspired by his background in phylogenetics. That’s only the tip of the iceberg though, so I’ll leave it to Ross to tell the story in his own words – I’ll be posting a link to his blog in the next 24 hours, as soon as his review appears online. [EDIT: Ross' review now up on the OKFN blog - read it here] So definitely take a look! And we’ve both enjoyed some great opportunities to promote the world of Open at conferences, workshops and meet-ups to a diverse range of audiences. We’ve met some fantastic people along the way.

And last but not least…

I also want to reiterate the final message from my end-of-year report: many thanks to the Panton Advisory Board, and indeed to all the folks at the OKFN who have provided sterling support throughout the last year. While I’m keen to avoid the excessive “Gwynnie” approach, there are nonetheless some particular names I’d like to mention. Thanks to Laura Newman, for seeing me through the hectic early days of the fellowship term and to Joris Pekel for stepping in to look after the Fellows since September; to Peter Murray-Rust, for inspirational, ebullient mentorship; to Greg Wilson, for being an absolute guru for educational practice and a bringer of calm; to Puneet Kishor, for his advice and faith in OSTI’s potential; and to Jenny Molloy, for advice, opinions and Oxford-based support!

I’m aiming to put together another blog post in early May, reflecting on what it’s been like to combine the Panton role with my DPhil/PhD commitments. If you’re a prospective Panton applicant for future Fellowship calls, hopefully it’ll prove useful.I should stress though that the end of the Fellowship certainly isn’t spelling the end of my work with OSTI – in fact, it’s more of a beginning. The fellowship year has provided the opportunity to create this wonderful initiative – now we move on to the process of growing it over time. But for today, it’s back to research with me (more specifically, to making my little in silico cells behave in C++). Bye for now!

Bringing Open Science Training to San Francisco

It’s been great visiting the States this week – and California, of all places. For starters, it made for a significant jump in the mercury on leaving the UK on Monday. What to Californians is a bit of an off week weatherwise is way, way better than what I could expect from the British summer!

Funny what travelling abroad does to you though. My friends know I’m a coffee drinker. I’ll take coffee over tea almost any day. Yet, set me down in a coffee house in SF and I find myself saying, “could I have an English Breakfast tea, please?” in what must sound like the most stereotypically English accent. Whether or not this is some subconscious response on my part to those wonderfully relaxed Californian requests for “caw-fee“, I’m not entirely certain. Seen objectively though, it feels a bit fraudulent on my part. Perhaps it’s indicative of some ingrained loyalty to the motherland.

From coffee to (scientific) culture…

National cultural differences and beverage selection aside, it’s time I mentioned what I’m actually doing in California. I’m talking now about scientific culture. Or, more to the point, how we can go about changing the prevailing culture for the better. Following on from the OSTI pilot, we’re now trying to establish the scheme at other institutions in the UK and beyond. Hence my visit to San Francisco this week – I’ve been visiting Puneet Kishor at Creative Commons, and together we’ve been on a promotional drive involving several institutions in the area. And as you know, SF isn’t short of world-class universities. One look at the parking lot in Berkeley campus tells you that much:

20130308-143937.jpg

Proof of concept for the OSTI approach to training may be complete, but adapting the initiative to diverse course structures in particular institutions is the next challenge. Discussions this week have really helped shape plans for how we can achieve this…Monday to Friday has seen a fair few open science conversations. Jet lag well and truly kicking in, I made it to dinner on the night of my arrival, meeting with Greg Wilson and several others involved with either Software Carpentry, Wikimedia Foundation or open data projects. A great start to my US visit – I can only hope that I wasn’t too incoherent from the 19 hours of travel that preceded it! :S

Tuesday was spent at Creative Commons HQ in Mountain View (plus a trip to a Big Data event at LinkedIn in the evening). The guys and gals at CC are a fantastic group of people and I enjoyed some great discussions with various members of the team over the course of the day. I had the opportunity to present their “Lunch & Learn” seminar to promote my OSTI and gain some feedback from them on how it might be applied elsewhere. If you’d like to read more about that, you might want to take a look at the Creative Commons blog post covering the event. And their generosity even extended to gifting me a Creative Commons T-shirt, which should be making some appearances at Open events in the future :)

20130308-144142.jpg

Since Wednesday, I have become vastly more acquainted with the SF public transport system, as Puneet and I made our way around various institutions, talking to a number of academics who may be able to suggest potential openings for my open science training regime. These have included: Jonathan Eisen of UC-Davis; Roberta Katz, VP for Strategic Planning at Stanford; Sameer Verma of SF State U; Rich Schneider of UCSF; and Michael Eisen at Berkeley. Hopefully this will pave the way for a variety of OSTI applications in the US and indeed other countries too! There’s now massive incentive for me to get to work on curating the slide decks and other course materials into a ready-for-release version.

This week has felt really productive and incredibly exciting. I think we’re on the verge of a whole new era of science education (and in a way, professional development training for academics). The coming months and years will hopefully see this realised across the disciplines, delivering to its full potential the multitude of benefits it can provide. It only remains for me to thank the OKFN and Panton Fellowship funders, without whose financial support this trip would not have come about; and of course a huge debt of gratitude to Puneet for hosting me this week and arranging such a fantastic schedule. Thanks all :)

Making the Case for Open Science Training: Panton in Jan/Feb 2013

Without a doubt, I’ve never blogged from a nicer location. This month’s update comes to you from the Creative Commons offices at Mt. View, just outside San Francisco. The California sunshine has put me in a good mood to write about the happenings of the past 2 months of my Panton Fellowship…and a LOT has happened since my last update. Setting aside my wonderment at how the year went by so quickly, it’s time I updated you on the Open Science Training Initiative (OSTI) pilot, the follow-up meetings in the immediate aftermath, and developments at Oxford with potential for further instances of the OSTI.

Culmination of the Panton work: Running the OSTI Pilot

I realise now that I was being seriously optimistic in hoping to blog progress with the OSTI pilot day-by-day. Perhaps inevitably, the demands of running a course for 43 graduates, involving in-person supervisory meetings with all the groups and delivery of the accompanying lecture series, left little time for me to get near a computer. Apologies to those who had anticipated watching the course unfold through my blogging!

The pilot scheme ran from January 10th through to January 18th, at the Doctoral Training Centre at the University of Oxford. Themed on computational biology, the course developed knowledge of programming and mathematical modelling, while mandating students to license their research outputs and deliver a coherent research story. This required them to draw on all elements of the research process (code, data, writing) as an integrated whole, rather than focusing on the written report alone. Lecturing in Open is all very well and good, but it’s first-hand experience of the techniques, approaches and culture that is most effective in breaking down misapprehensions and which provides researchers with the confidence to implement Open approaches in the future.

The first lecture of the course provided one of the biggest wake-up calls to the Open community I’ve yet encountered. Informally, I asked the students to raise their hands if they’d heard of open science, or knew something about it. Of those 43 students, only ONE raised their hand. Now this might be a fairly approximate metric, but it says a great deal about how much work we need to do in educating people about the ways of Open – let’s not forget, these are pretty switched on, well informed students in general. There’s plenty of fantastic work going on in the development of policy and infrastructure to support the transition to an open working culture, but we have a lot of work to do if the transition to openness is to happen effectively and smoothly. Now is the time to ask how we can engage with those who aren’t part of the Open community.

So here’s a challenge for you. If each of us could find even one way to engage with academics at our respective institutions – BEYOND the open community – at some time over the next 2 months, to educate in Open, raise awareness, and dispel the myths and misinformation, then that will represent some small progress in what we’re all trying to achieve.

Students filled in a questionnaire on completion of the course, and I’ve also been able to draw on the opinions and experiences of our course demonstrators and centre directors. Based on this, and on my own impressions of how things went (it was hard work, but I was there full-time for the whole thing, supervising each research team on a daily basis), I’m compiling a post-pilot report on the outcomes. Watch out for that over the coming weeks – as soon as it’s ready, it’ll be made available for download online.

OSTI Online

Yep, I mentioned the post-pilot report being released online just now, didn’t I? More to the point, it’s going to be released via the OSTI website, which is now live at www.opensciencetraining.com and whose content will grow over the coming months as I have the opportunity to extend the copy. There’s a lot more to be done of course, but for now there’s a brief intro to the motivation behind OSTI and an outline of its structure. There are also listings for the Lightning Lecture component of the programme, to provide you with some idea of the topics addressed. I’m in the process of curating and refining the slide decks for the course, based on exit feedback from the pilot participants; these will be released online over the next month once final versions are available. So watch this space!

Open Training at Oxford

I’ve also spent some of the past month engaging with the administrative arm of the University of Oxford, regarding provision for open science training. Basically, MPLS Division (maths, physical & life sciences) have indicated an interest in taking my OSTI and putting it out for use in other departments. Really excited about this! If we can get the training initiative installed in other settings in a variety of forms, it should provide us with a template for adaptable open training across an institution. The OSTI pilot demonstrated proof of concept: now it’s time to diversify its applications and see which forms work for people, and in what form the course can be most beneficial.

And given my current location in SF, California, it’s apparent I’ve spent recent weeks preparing for a trip Stateside, to carry out a promo drive for the OSTI. But more on that another time…there’s going to be lots more to tell in my next posting. See you then!

Open Science Training Initiative – Pilot Scheme Complete!

You could be forgiven for thinking I’d gone very quiet this week. As many of you may remember, the pilot scheme for my Open Science Training Initiative kicked off on January 10th. It’s been a pretty hectic time since then, but we’ve finally reached the closing day – the students are pushing final versions of all their work onto GitHub in the next hour, before presenting their findings from 10:30am onwards.

I’d had this insanely optimistic idea at the outset of blogging progress with the course every other day, or at least at the end of each of the rotation phases. Yep, that turned out to be WAY too optimistic. Once all the lecturing and project supervision meetings were factored in, I barely made it anywhere near my computer each day. Those of you who emailed me may have noticed the, ahem, somewhat tardy replies. All for good reason though – the students have done a fantastic job, produced some really creative work, and I’m looking forward to seeing all the results today – even if it’ll leave me stuck under a stack of marking for a fortnight!

I released a short feedback questionnaire to the students just now, so by the end of today we should have some idea of what they’ve enjoyed in the course, and importantly, how they think we could improve it in the future. I don’t think I’ve ever been subjected to this much judgment in one go before, so let’s hope it all goes ok… Ultimately I’ll be releasing all the findings and analysis in an evaluation report (most probably sometime in February), which will also take account of comments from the course demonstrators, some of whom were with the projects right from the beginning of the course. So keep an eye out for that.

I have to say I was seriously impressed by how they’ve taken to licensing as well. From the general show of hands I asked for in lectures, this area was completely new to all of them. This really shows how much work we need to do in educating our academics in Open practice if we’re going to aid the uptake of these approaches – at the moment, the awareness isn’t there in vast sections of the community. By the end of Phase 1 on the Monday, they’d got the hang of data, code and content licensing to the point where I was fielding some fairly subtle questions in specific cases. Some of you may have noticed me tendering one of these out to the OKFN discussion lists… GitHub for Windows proved really problematic though – more on that in the report and any other blog posts I get around to writing. We’d definitely need to do things differently in that department next time.

Anyway, proper update on the details of both rotation phases will follow, once I get through today and actually get some sleep. For now though, it’s probably time to get ready for the onslaught of the talks. It’s already snowing pretty heavily outside – something tells me I may end up walking home tonight, once the day is done! :S

Promotion, Preparation and Productivity: Open Science Sabbatical, December 2012

This month’s posting comes to you from a train somewhere between Manchester and Oxford – I’m making my most of the work time as I journey home from the seventh wedding I’ve been to in the past eight months. At time of writing, the start of the OSTI pilot is only 5 days away, so as you can imagine it’s been a bit of a nonstop month! The run-up to Christmas brought a combination of a website launch, promotional work, design and brand development for the OSTI, masses of lecture planning and preparation of course materials.

Perhaps the most significant development of December was the supervisors giving the thumbs-up to a “mini-sabbatical” of sorts, allowing me to focus solely on my open science fellowship. It’s really helped shape the course materials into an almost-finished state. I’ll save the finer details for the OSTI blogging phase later in the week, but the rough schedule of lightning lectures looks something like this:

  • Thursday 10th – (2 lectures) Reproducibility and Open Science; Open Source Coding & Version Control Using GitHub
  • Friday 11th – Licensing Your Data
  • Monday 14th – Data Management Plans & Scientific Workflows (incl. guest speaker Jun Zhao)
  • Tuesday 15th – The Changing Face of Publication
  • Thursday 17th – OKFN Session
  • Friday 18th – Presentation Day (assessment requirement for all participants)

Bear in mind that by the start of the course, the students will have already received 2 weeks’ training in Matlab and its applications, including GUI development and parallel implementation. The OSTI phase will span the assessment period for the course, themed around mathematical modelling of cancer and infectious disease.

The NERC Town Meeting (as I mentioned in my post from August 2012) provided considerable motivation for development of a website and other promotional materials for the OSTI, and took place in London on December 11th. Trialling the OSTI in an EPSRC DTC provides an excellent basis for transferring the course to similar DTP teaching models in other disciplines, and so I joined the preliminary meeting to promote the OSTI to prospective contract bidders. Drawing academics from across the UK, the meeting proved to be a reasonably productive day for open science discussion and I enjoyed some really good conversations with representatives and educationalists from, amongst others, Warwick, Oxford, Royal Holloway and the Natural History Museum.

So, what of the new aesthetic for the OSTI brand? In the interests of developing a cohesive identity for the initiative, the design needed to be consistent across all physical handouts and the website. I opted for a green, black and gold colour scheme in the end, and you can see the results in the images below (front and reverse sides of the leaflet are shown). And in keeping with the spirit of OSTI, the striking images in the design are all Creative Commons licensed content – it’s a pleasure to see such high-quality images available for use under CC license and certainly made the design process much easier for me. A CMYK version for printing will be made available via the OSTI website once the content is expanded.

OSTI Promotional Leaflet (Reverse)So, what of that website? I should warn you now that the site is live in its basic form, but hasn’t had its official public launch yet (announcement on that will follow when the time comes). You can find it at http://www.opensciencetraining.com – at present there’s just a mission statement on the opening page and a couple of other tabs with contact details. I’ll be adding content over the next month, starting with a description of the course structure and lectures, and extending to downloadable slides and materials once the course is underway. Feel free to drop me a message if you’d like to be emailed once full content and materials downloads start to appear…

Another exciting development in December was a meeting with Will Hutton, author of the bestselling work “The State We’re In” and current Principal of Hertford College, Oxford. Organised by Jenny Molloy, the gathering included a variety of faces from the Open community in Oxford, including Chas Bountra of the Structural Genomics Consortium, Simon Benjamin of Quantalk and Sally Rumsey of the Bodleian Library. Will discussed his plans to establish a series of studentships in Open Science at Hertford College, potentially in association with the Big Innovation Centre, and provided us all with a fantastic opportunity to debate the state of open science too. If this project gains the necessary funding and support to come to fruition then it could lead to a considerable hub of open research activity being established in Oxford, with the power to unify the diverse threads of open activity already taking place within the University’s departments, and to inspire novel working practices in young academics. I should stress that it’s early days yet, so keep an eye out for further news as the project develops.

So, what for January 2013? This year involves something of a running start, given the imminent beginning of the OSTI pilot on the 10th. I’m aiming to blog my progress with the course as it happens, or at least every other day if things end up being pretty hectic. Once we hit the 18th (and, moreover, once marking of the assessed work is out of the way) it’ll be onto the evaluation phase and the post-pilot report. I’ll also be following up with a few people from the NERC Town Meeting and meeting with MPLS (the physical and life sciences division) in Oxford to discuss how the OSTI might be applied to other departments outside the DTC. And there may even be a trip to the States in the pipeline…but more on that in a few weeks’ time…

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!