|

How I got into Open Science

1 Leave a comment on paragraph 1 0 Michael Nielsen, one morning at breakfast at Scifoo in 2008 asked one of those questions which never has a short answer; ‘So how did you get into this open science thing?’ and I realised that although I have told the story to many people I haven’t ever written it down. Perhaps this is a meme worth exploring more generally but I thought others might be interested in my story, partly because it illustrates how funding drives scientists, and partly because it shows how the combination of opportunism and serendipity can make for successful bedfellows.

2 Leave a comment on paragraph 2 0 In late 2004 I was spending a lot of my time on the management of a large collaborative research project and had also had a run of my own grant proposals rejected. I had a student interested in doing a PhD but no direct access to funds to support the consumables cost of the proposed project. Jeremy Frey had been on at me for a while to look at implementing the electronic lab notebook system that he had lead the development of and at the critical moment he pointed out to me a special call from the BBSRC for small projects to prototype, develop, or implement e-science technologies in the biological sciences. It was a light touch review process and a relatively short application. More to the point it was a way of funding some consumables.

3 Leave a comment on paragraph 3 0 So the grant was written. I wrote the majority of it, which makes somewhat interesting reading in retrospect. I didn’t really know what I was talking about at the time (this seems to be a theme with my successful grants). The original plan was to use the existing, fully semantic, rdf backed electronic lab notebook1 and develop models for use in a standard biochemistry lab. We would then develop systems to enable a relational database to be extracted from the rdf representation and present this on the web.

4 Leave a comment on paragraph 4 0 The grant was successful but the start was delayed due to shenanigans over the studentship that was going to support the grant and the movement of some of the large project to another institution with one of the investigators. Partly due to the resulting mess I applied for a job that I ultimately accepted at the Rutherford Appleton Laboratory and after some negotiation organised an 80:20 split between RAL and Southampton.

5 Leave a comment on paragraph 5 0 By the time we had a student in place and had got the grant started it was clear that the existing semantic ELN was not in a state that would enable us to implement new models for our experiments. However at this stage there was a blog system that had been developed in Jeremy’s group and it was thought it would be an interesting experiment to use this as a notebook. This would be almost the precise opposite of the rdf backed ELN. Looking back at it now I would describe it as taking the opportunity to look at a Web 2.0 approach to the notebook as compared to a semantic web approach but bear in mind that at the time I had little or no idea of what these terms meant, let alone the care with which they need to be used.

6 Leave a comment on paragraph 6 0 The blog based system was great for me as it meant I could follow the student’s work online and doing this I gradually became aware of blogs in general and the use of feed readers. The RSS feed of the LaBLog was a great help as it made following the details of experiments remotely straightforward. This was important as by now I was spending three or four days a week at RAL while the student was based in Southampton. As we started to use the blog, at first in a very naïve way we found problems and issues which ultimately led to us thinking about and designing the organisational approach I have written about elsewhere 2. By this stage I had started to look at other services online and was playing around with OpenWetWare and a few other services, becoming vaguely aware of Creative Commons licenses and getting a grip on the Web 2.0 versus semantic web debate.

7 Leave a comment on paragraph 7 0 To implement our newly designed approach to organising the lab notebook we decided the student would start afresh with a clean slate in a new blog. By this stage I was playing with using the blog for other things and had started to discover that there were issues that meant the ID authentication we were using didn’t always work through the RAL firewall. I ended up having complicated VPN setups, particularly working from home, where I couldn’t log on to the blog and I have my email online at the same time. This, obviously, was a pain and as we were moving to a new blog which could have new security settings I said, ‘stuff it, let’s just make it completely visible and be done with it’.

8 Leave a comment on paragraph 8 0 So there you go. The critical decision to move to an Open Notebook status was taken as the result of a firewall. So serendipity, or at least the effect of outside pressures, was what made it happen.  I would like to say it was a carefully thought out philosophical. I was somewhat aware of open access and open science and this no doubt prepared the background that led me to think down that route, but it was essentially the result of frustration.

9 Leave a comment on paragraph 9 0 So, so far, opportunism and serendipity, which brings us back to opportunism again, or at least seizing an opportunity. Having made the decision to ‘go open’ two things clicked in my mind. Firstly the fact that this was rather radical. Secondly, the fact that all of these Web 2.0 tools combined with an open approach could lead to a marked improvement in the efficiency of collaborative science, a kind of ‘Science 2.0’.  Yes, I know, don’t laugh too hard, this would have been around March 2007. Here was an opportunity to get my name on a really novel and revolutionary concept! Literally my first thought was “I bet you could get a Nature paper out of this”. A quick Google search revealed that, funnily enough, I wasn’t the first person to think of this (yes! I’d been scooped!), but more importantly it led to what I think ought to be three of the Standard Works of Open Science, Bill Hooker’s three part series on Open Science at 3 Quarks Daily 3, Jean-Claude Bradley’s presentation on Open Notebook Science at Nature Precedings4 (and the associated original blog post coining the term5), and Deepak Singh’s talk on Open Science at Ignite Seattle6. From there I was inspired to seize the opportunity, get a blog of my own, and get involved. The rest of the story story, so far, is more or less available online.

10 Leave a comment on paragraph 10 0 Which leads me to ask. What got you involved in the ‘open’ movement? What, for you, were the ‘primary texts’ of open science and open research? There is a value in recording this, or at least our memories of it, for ourselves, to learn from our mistakes and perhaps discern the direction going forward. Perhaps it isn’t even too self serving to think of it as history in the making. Or perhaps, more in line with our own aims as ‘open scientists’, that we would be doing a poor job if we didn’t record what brought us to where we are and what is influencing our thinking going forward. I think the blogosphere does a pretty good job of the latter, but perhaps a little more recording of the former would be helpful.

11 Leave a comment on paragraph 11 0 Notes

12 Leave a comment on paragraph 12 0 This was originally posted under the same title at Science in the Open on 22 August 2008.

  1. 13 Leave a comment on paragraph 13 0
  2.  Hughes, G., Mills, H., de Roure, D., Frey, J., Moreau, L., schraefel, m. c., Smith, G. and Zaluska, E. (2004)
    The semantic smart laboratory: a system for supporting the chemical eScientist, Organic and Biomolecular Chemistry 2:3284-3293 http://dx.doi.org/10.1039/B410075A
  3. In a series of blog posts initially written for the blog I had on OpenWetWare http://cameronneylon.net/blog/the-southampton-e-lab-blog-notebook-part-1-aims/ http://cameronneylon.net/blog/the-southampton-e-lab-blog-notebook-part-2-eln-strategy/ http://cameronneylon.net/blog/the-southampton-e-lab-blog-notebook-part-3-implementation/ A better description of out ultimate design is found in the paper we eventually published in PLOS ONE Milsted AJ, Hale JR, Frey JG, Neylon C (2013), LabTrove: A Lightweight, Web Based, Laboratory “Blog” as a Route towards a Marked Up Record of Work in a Bioscience Research Laboratory. PLoS ONE 8(7): e67460, http://dx.doi.org/10.1371/journal.pone.0067460
  4. Bill Hooker had published three of the earliest pieces I know of online setting out the stall for Open Science on a very early online new site called 3 Quarks Daily http://3quarksdaily.blogs.com/3quarksdaily/2006/10/the_future_of_s_1.html http://3quarksdaily.blogs.com/3quarksdaily/2006/11/the_future_of_s.html http://3quarksdaily.blogs.com/3quarksdaily/2007/01/the_future_of_s.html The site still publishes regularly making it one of a pretty small number of surviving news and opinion sites from the time
  5. Bradley, J-C (2007), Open Notebook Science Using Blogs and Wikis, Nature Precedings, http://dx.doi.org/10.1038/npre.2007.39.1
  6.  Bradley, J-C (2006), Open Notebook Science, Drexel CoAS E-Learning (blog), available online at http://drexel-coas-elearning.blogspot.co.uk/2006/09/open-notebook-science.html
  7. The video for this talk seems to have disappeared from the internet which is probably tells us something about the importance of preservation standards
Page 16

Source: http://book-shaped-object.cameronneylon.net/wp/a-personal-digression/how-i-got-into-open-science/