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Articles tagged with: open science

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[14 Oct 2008 | Comments Off on Where does Open Access stop and ‘just doing good science’ begin? | ]

I had been getting puzzled for a while as to why I was being characterised as an ‘Open Access’ advocate. I mean, I do adovcate Open Access publication and I have opinions on the Green versus Gold debate. I am trying to get more of my publications into Open Access journals. But I’m no expert, and I’ve certainly been around this community for a much shorter time and know a lot less about the detail than many other people. The giants of the Open Access movement have been fighting the …

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[1 Oct 2008 | Comments Off on A personal view of Open Science – Part II – Tools | ]

The second installment of the paper (first part here) where I discuss building tools for Open (or indeed any) Science.
Tools for open science – building around the needs of scientists
It is the rapid expansion and development of tools that are loosely categorised under the banner of ‘Web2.0′ or ‘Read-write web’ that makes the sharing of research material available. Many of the generic tools, particularly those that provide general document authoring capabilities, have been adopted and used by a wide range of researchers. Online office tools can enable collaborative development of …

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[1 Oct 2008 | 8 Comments | ]

On Monday 1 September we had a one day workshop in Southampton discussing the issues that surround ‘Open Science’. This was very free form and informal and I had the explicit aim of getting a range of people with different perspectives into the room to discuss a wide range of issues, including tool development, the social and career structure issues, as well as ideas about standards and finally, what concrete actions could actually be taken. You can find live blogging and other commentary in the associated Friendfeed room and information …

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[30 Sep 2008 | 7 Comments | ]

For the Open Science workshop at the Pacific Symposium on Biocomputing I wrote a very long essay as an introductory paper. It turned out that this was far too long for the space available so an extremely shortened version was submitted for the symposium proceedings. I thought I would post the full length essay in installments here as a prelude to cleaning it up and submitting to an appropriate journal.

Introduction
Openness is arguably the great strength of the scientific method. At its core is the principle that claims and the data that …

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[18 Sep 2008 | 6 Comments | ]

So a bit of a first for me. I can vaguely claim to have contributed to two things into the print version of Nature this week. Strictly speaking my involvement in the first, the ‘From the Blogosphere‘ piece on the Science Blogging Challenge, was really restricted to discussing the idea (originally from Richard Grant I believe) and now a bit of cheerleading and ultimately some judging. The second item though I can claim some credit for in as much as it is a Q&A with myself and Jean-Claude Bradley that …

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[31 Aug 2008 | 4 Comments | ]

I am currently sitting at the dining table of Peter Murray-Rust with Egon Willighagen opposite me talking to Jean-Claude Bradley. We pulling together sets of data from Jean-Claude’s UsefulChem project into CML to make it more semantically rich and do a bunch of cool stuff. Jean-Claude has a recently published preprint on Nature Precedings of a paper that has been submitted to JoVE. Egon was able to grab the InChiKeys from the relevant UsefulChem pages and passing those to CDK via a script that he wrote on the spot (which …

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[22 Aug 2008 | 6 Comments | ]

So Michael Nielsen, one morning at breakfast at Scifoo 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 …

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[17 Aug 2008 | 18 Comments | ]

One of the many great pleasures of SciFoo was to meet with people who had a different, and in many cases much more comprehensive, view of managing data and making it available. One of the long term champions of data availability is Professor Helen Berman, the head of the Protein Data Bank (the international repository for biomacromolecular structures), and I had the opportunity to speak with her for some time on the Friday afternoon before Scifoo kicked off in earnest (in fact this was one of many somewhat embarrasing situations …

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[15 Aug 2008 | Comments Off on Southampton Open Science Workshop 31 August and 1 September | ]

An update on the Workshop that I announced previously. We have a number of people confirmed to come down and I need to start firming up numbers. I will be emailing a few people over the weekend so sorry if you get this via more than one route. The plan of attack remains as follows:
Meet on evening of Sunday 31 August in Southampton, most likely at a bar/restaurant near the University to coordinate/organise the details of sessions.
Commence on Monday at ~9:30 and finish around 4:30pm (with the option of discussion …

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[11 Aug 2008 | 4 Comments | ]

I am too tired to write anything even vaguely coherent. As will have been obvious there was little opportunity for microblogging, I managed to take no video at all, and not even any pictures. It was non-stop, at a level of intensity that I have very rarely encountered anywhere before. The combination of breadth and sharpness that many of the participants brought was, to be frank, pretty intimidating but their willingness to engage and discuss and my realisation that, at least in very specific areas, I can hold my own …