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!

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A World of Digital Openness: Panton in September

With October now well underway, I’m actually halfway through my Panton Fellowship year: how on earth did the time pass by so quickly? Time does indeed fly by when you’re having lots of (open science) fun. Much of September centred around data release and licensing and digital management, thanks to two big conference events. It was always clear that September was going to be a busy month! Juggling two conferences a week apart with DPhil research/chapter writing/papering up felt like an adrenaline sport at the time (offering the same combination of excitement, fear and tiredness) but was a really valuable and enjoyable experience. So, here’s what went on in September…

First up was the Digital Research 2012 conference, hosted by the Oxford e-Research Centre and held in the striking surroundings of St. Catherine’s College at the University of Oxford. Peter Murray-Rust, Jenny Molloy and I organised and led the OKFN session on the Tuesday morning, starting with Peter’s plenary lecture (read his blog on the subject here, followed by Jenny showcasing several different OKFN projects, including CKAN, DataHub and PubCrawler, through an on-screen software demo. I rounded out the session by chairing a 45 minute panel debate entitled, “Surfing the Wave of Open Data: Why, When and How?“, which aimed to generate discussion on how we release and publish our data and to consider how our approaches to this need to evolve in the years to come. We were joined by a fantastic line-up of panel speakers: Mark Hahnel of Figshare, Juan Bicarregui of STFC, Mark Elliot of CCSR and Brian Hole of Ubiquity Press. As far as I’m aware, the entire conference programme was filmed: the footage is being processed at the moment and should be up on the ‘Digital Research 2012‘ YouTube channel as soon as it’s ready. Will update you as soon as I hear anything! Hopefully the OKFN session will be online for viewing very soon, so you can all catch up on the presentations, demos and debate you may have missed.

The intervening period between the two conferences was mostly given over to completing the Panton Principles video I mentioned in my previous two posts. I started scripting and filming this at the end of August: it’s only the second video I’ve ever made, so I’m still getting used to the medium really, but it’s great fun. The first ‘film short’ I made was actually my application video for the Panton Fellowship (back in February of this year). Location spotters amongst you may be interested to know that we filmed this one in the library of Keble College, Oxford – it seemed appropriate that I should be surrounded by lots of scientific information while promoting principles which support the release of scientific data! Thankfully I overcame most of my filming nerves earlier this year, so it was easier to stand in front of the camera second time around. It wasn’t without its problems though: natural lighting conditions on the first morning of filming were far too bright and I ended up looking practically corpse-like on screen; not a healthy look for a promotional video! Thankfully the second morning of filming (assisted by the return of my now-familIar red dress) proved more successful. Huge thanks to Alastair Kay for endless patience behind the camera and for all his work editing the material into finished form, and to Ross Mounce for looking over the script and suggesting some additions…hopefully they’re as pleased with the end result as I.

The video is available on YouTube, released under a CC-BY-3.0 licence, so please feel free to use it to spread the open science gospel further afield 🙂 I’m also arranging for a downloadable version to be released in the very near future, so watch this space. Information in text form might be useful in some cases, but lots of legal-looking writing or formal guidelines can look rather intimidating and deter people sometimes. Alternative media such as film provide a great way of imparting the same information in an accessible, friendly and non-intimidating way. Let’s embrace this more in the future!

The subject of OKFest needs no introduction really…with the #okfest hashtag not just trending but skyrocketing on Twitter from the first day of the conference, it was always set to be a dynamic, exciting and much talked about event. I won’t repeat the multitude of bloggers who’ve already described so many aspects of the week: suffice to say it was utterly fantastic and I was sad that I could only join for two days (and you can read my previous blog post with all the relevant video links here). I arrived in Helsinki on the Tuesday and was on a plane flying back to Heathrow by the Thursday night, but it realy was a fantastic two days. Wednesday was the busiest day for me, with plenty of involvement in the Open Education stream, chairing the panel discussion on ‘Immediate Access to Raw Data from Experiments‘ before Ross Mounce and I showcased our Fellowship work. And so it was time for the much-awaited unveiling of my new Panton Principles video I mentioned earlier…and then into my presentation as part of the Panton Fellows’ session (available on Bambuser here, and you should also check out the other videos from the stream, including the panel discussions and Ross Mounce’s Panton presentation, as well). Much of my talk addressed the issues of reproducibility in scientific research, before introducing the audience to my OSTI ahead of its launch in December 2012. Following on from OKFest, I have a few articles in the pipeline on the reproducibility issue, so keep your eyes peeled for those.

Equally invaluable at OKFest were the many opportunities to make new contacts: amongst others, I was fortunate to be introduced to Puneet Kishor of Creative Commons and Philipp Schmidt of the Peer-to-Peer University. It was great to meet them and discuss my plans: my discussions with Puneet will hopefully help in expanding the OSTI approach into the US once I’ve run the pilot, which is a hugely exciting prospect. In fact, all my conversations with fellow scientists, data wranglers, educationalists and open science aficionados over the past month has made me really excited about the prospects for my OSTI when we launch later this term. My conversations with Puneet were in fact one of the things that cemented my resolve to establish a proper website for the scheme, which will be one of the major focuses in the coming months. It’ll provide you all with updates, progress, information and more as the project evolves and is being planned right now. Needless to say, I’ll keep you posted…

Well time is short this month, so  I’ll have to disappear for now – but it looks as though plenty of things are happening in October. I’ll be liaising further with several people at NERC to confirm the details of the town meetings for their prospective Doctoral Training Partnerships in Nov/Dec: getting our OSTI up and running across the UK would be really exciting! I’m also getting to work on planning course content and a further video on “Demystifying Data Licensing” as well as doing early-stage planning and development on the OSTI website. Lots to keep me busy – I’ll let you know how it all goes!

NERC, Young Researchers and the Buildup to OKFest: Panton in August

Firstly, how on earth did the end of August come around so quickly? With OKFest only a couple of weeks away, I think it’s fair to say that everyone within the open science community has had a busy month…and things are likely to continue this way as we head into September. My Panton counterpart in Bath, Ross Mounce, has also had a mightily busy month from the sound of things, so there’s also plenty of #pantonscience news available on his blog.

But before we get to talking about OKFest, I should really provide an update on what’s been going on in recent weeks. It certainly feels like a great deal has happened: news from me this month ranges from significant progress with my open science training initiative, to discussion with NERC regarding their provision for OS training in their forthcoming Doctoral Training Partnerships, to designing some promo literature for the Panton Principles. All exciting stuff!

The second week of August saw Jenny Molloy and me meet with Kirsty Grainger, who is Head of Skills and Careers for the Natural Environment Research Council (NERC). NERC are in the process of establishing Doctoral Training Partnerships nationally – for those of you unfamiliar with the DTP/DTC model, these centres typically offer four-year doctorates, in which the three year research phase is preceded by a year of interdisciplinary and skills training. After I had explained the aims and structure of my OSTI scheme, Kirsty suggested that we attend the DTP Town Meetings in November/December of this year, where we’ll be able to meet the leaders of each NERC DTP application and discuss the possibility of them incorporating some or all of my open science training initiative into their own programmes. A massive thumbs-up to NERC for taking the lead with this! I’m hoping to convince many of the Natural Environment bidders later this year, and from there we can try to persuade other research councils to follow suit. The demands on DTPs/DTCs to include specific aspects of training in their skills provision can be high, but often it is entirely possible to enhance the content without overloading the existing syllabus and teaching burden, if one changes how a subject is taught. Let’s hope that this will translate into Open Science becoming an integral part of doctoral training over the next couple of years! And let’s not forget the JISC/British Library Researchers Of Tomorrow report from June of this year, which highlighted the tendency of young research students to adopt the existing practices of their group as regards attitudes to open science and coherent release of data. If we want open science to propagate through the system, we can’t ignore the need to train our researchers before they reach the research environment.

August has also seen significant progress with my Open Science Training Initiative (OSTI), the central focus of my Panton work. As a result of meetings with the DTC directors, we’ve now finalised the dates for the three-week course. Some rearrangement of the schedule from previous years has occurred, so my course will now be running over the penultimate week of December and the first two weeks of January. What better way to see out 2012 and welcome in 2013 than with lots of open science? The early phase of the course will involve training the students in programming skills, before progressing to some interesting applications at the start of the second week. Thursday of Week 2 will see the start of the ‘rotation‘ phase, where the students work in teams on a mini research problem and have to thoroughly document their code, provide a coherent written appraisal of the methods and outcomes, and release their code and data online for a successive group to work on. We also discussed the specifics of this and of how we’ll be assessing the students, but I’ll hold back for now to avoid this post getting too long. Plenty more details of this to come in the near future…

One of the main events of the past month for me was of course the Oxford Open Science session on the 22nd. We welcomed a fantastic line-up of speakers for the evening to discuss the current state of graduate training in data management and open science and to debate how we can take this forward in the future, so many thanks to Juliet Ralph, Oliver Bridle, Jez Cope, Anna Collins and Laura Newman for joining us. The evening saw a good turnout and some interesting outcomes in the discussion. There was a great deal of support for peer-led learning, and there was also the suggestion of establishing graduate-led “open science” advocates within academic departments: these advocates would act as the universal point of contact for open science matters. I don’t know of any universities in the UK already operating such a system – if you know of somewhere that is, let me know! One of the other key points that arose was the issue of students’ confusion as to what constitutes Open Access-this mirrors some of the concerns raised in the Researchers Of Tomorrow report and will require attention over the coming years until all our grads are well-informed as to the publishing options open to them. Those of you who weren’t able to attend will be pleased to hear that the talks and discussion were filmed: I’m currently waiting to receive the transferred movie files back from our tech managers so, all being well, you can expect to view the videos online later on next week. Another favourable outcome was that one of our attendees expressed an interest in establishing similar data and open science initiatives at her university in Saudi Arabia. Hopefully I’ll be meeting with her later this week to see how we might be of assistance in making this happen…

Exciting month ahead: OKFest in Finland! This week I’m planning, filming and cutting together a promo video for the Panton Principles, which I’ll be using to open my Helsinki talk on the 19th September. Expect to see some mock-up story boards and content online in the next few days – I’d love to hear your comments on those ahead of filming. I’ve also been busy designing some promotional postcards for the Principles over the last week. The OKFN team have already seen the provisional designs and I’ll be posting some images very soon once they’re a little further along! This is all part of a wider effort by other members of OKFN to develop promotional materials for open science and the Principles ahead of OKFest. Judging by progress over the last week, we’ll soon have some nice promo pieces at the ready to spread the word about Open Science.

Next week will also get off to a busy start as the Digital Research 2012 conference gets underway at St. Catherine’s College, Oxford. Tuesday 11th in particular will see a programme of talks and debate on open access and data publication, featuring keynotes from Steven Harnad, Peter Murray-Rust and Neil Chue Hong, concluding with a panel discussion at the end of the morning. I’ll try to tweet updates as the morning progresses, although there’s still time to register for the conference if you haven’t yet had chance to do so.

Well, I think that’s enough from me this time: I daresay there’ll be plenty of news over the coming weeks before, during and after OKFest. Watch out for the OxOpenSci video and slides being released in the next fortnight, and as always, feel free to comment or get in touch with me if you have any questions, suggestions, thoughts or advice on the work I’m doing.

See you in Helsinki!

Adapting to the age of Big Data: Speaker Event 22/08/2012

With the next meeting of the Oxford Open Science group only 2 days away now, it’s time to ink 7:30pm into your diary for this Wednesday (22nd August). The venue (OeRC, 7 Keble Road) is booked, our speakers are confirmed and I’m looking forward to a thought-provoking evening of talks and discussion. And you can even see a PDF of the promo flyer by clicking on the link below – feel free to pass the flyer on to anyone who might be interested:

Click here to see the promotional flyer for this Wednesday’s event

For those of you who live in London, remember that the Oxford-London bus services of the X90 and the Oxford Tube run regularly until around 3am, so it’s reasonably easy to scoot up country to join us for the evening.

I originally posted the speaker list in my Panton blog post for July, but in case you missed it, here it is again:

  • Juliet Ralph and Oliver Bridle from Oxford’s Bodleian Library, discussing information seeking amongst students and the current provision of digital/data management tools (including a discussion of the recent JISC/British Library report on the working practices of Generation Y research students);
  • Anna Collins from DSpace Cambridge, talking about the “long tail in the shadow of big data”, whose responsibility data management is in these contexts and how this might develop in the future;
  • Laura Newman from the Open Knowledge Foundation (OKFN), talking about progress and plans for the newly-launched School of Data;
  • Jez Cope from the Doctoral Training Centre in Sustainable Chemical Technologies at the University of Bath, talking about his experiences in data management and social media training with DTC students.

Our speakers will be taking questions during from the audience during the evening and we’re hoping to close the session with a group discussion (complete with tea and coffee) before heading off to the pub for those who are interested.

Panic ye not if you can’t join us though: Jenny Molloy and I are hoping to film the event (by which I mean the bit pre-pub 😉 ) so that those who can’t attend can still benefit from the presentations and associated discussion. I’m happy to ask questions to the speakers on your behalf too, so get in touch with me (either here on the blog or by tweeting me at @stilettofiend) if you have a question to pose to a particular speaker, or a more general comment to throw into the discussion at the end. All being well, I’ll try to release the video on YouTube as soon as possible, and hopefully by the end of the week.

Looking forward to seeing many of you on Wednesday!