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 – 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…

Panton Fellowship Application: Proposal of Work 2012-13

Just in case any of you are interested, here’s my proposal for the Panton Fellowship for 2012-13 – you can also view the corresponding video here. Much of the work will focus on establishing an open science training scheme for pre-doctoral graduates, as you’ll see from the following…

The open science movement is rapidly gaining momentum, as is evident from the level of interest in the recent ‘Evolution of Science’ debate in Oxford in February 2012, the well-publicised boycott of the publisher Elsevier, and the variety of blogs and discussion groups currently being established. Our data-rich scientific world requires an appropriate infrastructure to disseminate data, code and associated writing, as well as a means of training people in the access and use of this information. Adoption of open data practices throughout the research community therefore demands changes in the working habits of existing academics and appropriate training of upcoming new researchers.

My proposal for the Panton Fellowship focuses primarily on the latter aspect. I intend to establish an Open Science Training Initiative (OSTI) for graduate students, prior to the onset of their doctoral research. Participants in the scheme will learn about the constraints and legal frameworks governing open data and discuss the ethics of scientific research. The programme will educate in the use of open data, will provide first-hand experience of implementing this approach and will equip students with the skills and knowledge to sustain this outlook when they finally enter the research environment. Successful conclusion of the pilot scheme will provide the foundations for expansion of the training programme across other universities and educational centres.

The Doctoral Training Centre (DTC) at the University of Oxford has an intake of around 40 graduate students per annum, all of whom are required to complete a pre-doctoral taught year. Many exercises in the existing DTC programme involve trying to reproduce results from published work. Often (> 50%) of the time it is not possible to fully achieve this, most commonly due to omission of detail (parameter values, etc.) or, occasionally, errors in the paper of interest. The DTC therefore provides a natural opening for our OSTI pilot scheme. The further particulars of the scheme, as detailed below, have already secured the support of Prof. David Gavaghan (DTC Director) and Ms. Sam Miles (Centre Administrator). Our OSTI approach is motivated by the need to include everything in the publication needed to reproduce results and links directly to development of standards such as MIASE, SED-ML, CELL-ML and SBML.

The OSTI pilot will take the form of group-based research over several days and will be incorporated into a two week course in computational/mathematical biology. The participants will be split into two groups, and each group presented with a different research problem. The chosen problems will provide a broad starting point (e.g. a general model in mathematical biology, or an existing paper in the field), rather than an explicit list of tasks to complete. Each group will devise their own research question to work on, supported throughout by experienced academic demonstrators. Members of each group will work collaboratively, but discussion between the separate groups will be prohibited, for reasons which we now outline.

After a specified period (which could range from 1-2 days up to a full week, according to the scope and difficulty of the exercise), the problems will rotate; successors will be expected to develop their new research question solely on the basis of the data, code and documentation supplied by their predecessors. Verbal queries are not permitted between the groups, and successors will need to verify the existing findings they are presented with before developing the research further. This heightens the need for teams to provide coherent documentation of their work and adequate means of verifying the data they release. Academic demonstrators will provide particular support during the group
rotation phase to ensure a smooth transition, especially where a group has to deal with omissions in the research documentation. Successors will also be expected to complete a brief questionnaire critiquing the success of their predecessors in providing a coherent, accessible research story.

Ultimately the aim is for the entire cohort to maximise their collective research progress throughout the rotation phase, thus inducing groups to aid one another through good written communication, rather than compete to produce results. The rotation phase will culminate in oral presentation and discussion of the work (potentially streamed online), along with release of the documentation, code and findings.

2.1 – Phase 1: Planning (April 2012 – October 2012)
Success of the pilot programme will require rigorous planning and preparation. Ongoing work throughout this phase will include:

  • Course Preparation: The course will be developed in discussion with the DTC; in particular, this phase will require preparation of appropriate seminars and selection of the computational research problems involved. I will also need to establish and test the online infrastructure for the sharing of data and code during the project. Care must also be taken to ensure adequate division of subject expertise when assigning students to groups.
  • Legal Frameworks: Liaise with the legal department of the University of Oxford in advance to obtain an appropriate licence for the data.
  • Long-Term Sustainability: We are already in regular contact with Neil Chue Hong of the Software Sustainability Institute and intend to maintain this dialogue throughout Phase 1 to lay the foundations for the report and promotion tasks of Stage 3. This phase would benefit from coordination with the Open Knowledge Foundation, as regards the development of data-sharing approaches and open science seminar content.

2.2 – Phase 2: Delivery (November 2012)
The two main aims of the scheme are to educate in open science definitions and to provide first-hand experience of open science practice. The OSTI pilot will require students to question the suitability of their own working practices in relation to the implementation of open science and will encourage them to improve their research methods over the course of the problem rotations.

  • Open Data Aspects: A computational teaching module will be used for the pilot scheme, providing data-intense problems to work on and requiring students to produce open-source code. Students will be required to develop good coding skills (e.g. sensible structuring, appropriate commenting) that facilitate code reuse by others, as well as providing accessible documentation. For example, coding could be performed using the open-source Chaste framework, which is already covered by an OSI-conformant licence.
  • Public Process: There is added potential to advertise the pilot amongst the open science community and to establish a public webpage for the project, helping to generate advance interest in OSTI which could aid its adoption and extension afterwards.
  • External Involvement: It may also be possible to admit a small number of talented undergraduates if space allows; at the very least, the potential for undergraduate involvement in future will be explored in the Report (see Section 3).

The finer details of the OSTI pilot (e.g. group numbers, number of research problems) are
contingent on the capacity of the DTC in 2012-13 and will become clearer in the coming months. Dates of the Delivery phase will be known upon confirmation of the module schedule for the next academic year.

2.3 – Phase 3: Evaluation and Promotion (December 2012 – April 2013)
Successful completion of the Delivery phase will be followed by an evaluation period. I will solicit feedback from all participants and compile a detailed report on the outcomes of the OSTI pilot. This report will form the basis of my submission to the Software Sustainability Institute, although the SSI submission will also include details of proposed target locations and suitable OSTI leaders, along with the necessary support and documentation to expand the initiative further afield. We have already established a dialogue with Neil Chue Hong of the SSI to discuss the potential for extending the OSTI scheme and the SSI believe there will be a good market for our initiative. Indeed the OSTI format could be realised in many other forms and could lend itself to internship-style undergraduate training just as easily, or even to a two-week workshop for established academics. Its content and duration can be tailored accordingly, providing a flexible training approach that can be adapted to the needs of the institution or department wishing to adopt it. Furthermore, I have already generated interest in setting up a postdoctoral OSTI for the academics involved in the 2020 Science project and a young researchers’ OSTI for new students joining the Oxford Computational Biology Group. These additional implementations would also provide useful comparative studies for my report to the SSI and would help to showcase the adaptability of the OSTI format.

Planning, delivery and promotion of the OSTI scheme(s) would be expected to form the most significant component of my open science activities over the course of the coming year. Nonetheless, I would also be engaged in the following endeavours, as discussed in my covering letter:

  • Research Tasks: Dissemination of my own research online as regards combined release of data and code, involving bolt-on projects in the Chaste framework, and promotion of these approaches when speaking at conferences and other events.
  • Communication and Access: My involvement with the Ashlawn Pathways Conference as Director of Science would enable me to introduce data ethics to young scientists at the top end of pre-18 education while also promoting scientific careers to the brightest students.
  • Additional involvement: Potential to institute a series of Open Science seminars across Oxford, possibly through furthering my existing involvement with the recently established Oxford Open Science working group.