Cameron Neylon

Tap…tap…is this thing still on…..SKKRRREEEEEEEEEEEEEE

Testing&#8230;testing&#8230;

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.

Linking up open science online

I and a few others have been working for some time on converting a review I wrote some time ago for publication on OpenWetWare. Jason Kelly put the initial work in in developing an area for reviews and it was from him that I had the idea of taking this forward. The traditional review is a cornerstone of the research literature. The first port of call for virtually any researcher on moving into an unfamiliar area is to find a good review.

The Directed evolution library construction Wiki Review

*This post is aiming to get down some thoughts around how the superset of evolutionary models can be framed. It’s almost certainly work that has been done somewhere before but I’m struggling to find it so it seemed useful to lay out what I’m looking for.Â *  Evolutionary models are extraordinarily powerful, in part because they are extremely flexible.

Speculations: Abstracting Evolution

There’s an article doing the rounds today about public understanding and rejection of experts and expertise. It was discussedÂ in an article in the THES late last yearÂ (which ironically I haven’t read). I recommend reading the original articleÂ by Scharrer and co-workers, not least because the article itself is about how reading lay summaries can lead to a discounting of expertise.

Dr Brewer’s Guide to Science. (Photo credit: Wikipedia)  There’s an article doing the rounds today about public understanding and rejection of experts and expertise.

Transmission and mediation of knowledge

The following will come across as a rant. Which it is. But it’s a well intentioned rant. Please bear in mind that I care about good practice in data sharing, documentation, and preservation. I know there are many people working to support it, generally under-funded, often having to justify their existence to higher-ups who care more about the next Glam Mag article than whether there’s any evidence to support the findings.

As a researcher…I’m a bit bloody fed up with Data Management

It has become rather fashionable in some circles to decry the complain about the lackÂ of progress on Open Access. Particularly to decry the apparent failure of UK policies to move things forward. I’ve been guilty of frustration at various stages in the past and one thing I’ve always found useful isÂ thinking back to where things were.

Solution extinction measurements of (A) faceted (B) and Au@MNPs and (C) photos of the particles. From Silva et al Chem. Commun., 2016 DOI:10.1039/C6CC03225G  It has become rather fashionable in some circles to decry the complain about the lackÂ of progress on Open Access. Particularly to decry the apparent failure of UK policies to move things forward.

Open Access Progress: Anecdotes from close to home

Over the past week this tweet was doing the rounds. I’m not sure where it comes from or precisely what its original context was, but it appeared in my feed from folks in various student analytics and big data crowds. The message I took was “measurement looks complicated until you pin it down”. But what I took from this was something a bit different. Once upon a time the idea of temperature was a complex thing.

A thermometer showing âˆ’17Â°C. (Photo credit: Wikipedia)  Over the past week this tweet was doing the rounds. I’m not sure where it comes from or precisely what its original context was, but it appeared in my feed from folks in various student analytics and big data crowds. The message I took was “measurement looks complicated until you pin it down”.  But what I took from this was something a bit different.

What measurement does to us…

Image via Wikipedia  A few weeks ago I attended a workshop run by the ESRC Genomics Forum in Edinburgh which brought together humanists, social scientists, and science focused folks with an interest in how open approaches can and should be applied to genomic science. This was interesting on a number of levels but I was especially interested in the comments of Marina Levina on citizenship.

A citizen of the network

The development of the acronym “FAIR” to describe open data was a stroke of genius. Standing for “Findable, Accessible, Interoperable and Reusable” it describes four attributes of datasets that are aspirations to achieve machine readability and re-use for an open data world.

Brussels Accessible Art Fair Logo (Wikipedia)  The development of the acronym “FAIR” to describe open data was a stroke of genius. Standing for “Findable, Accessible, Interoperable and Reusable” it describes four attributes of datasets that are aspirations to achieve machine readability and re-use for an open data world.

FAIR enough? FAIR for one? FAIR for all!

On the 8th December David Willetts, the Minister of State for Universities and Science, and announced new UK government strategies to develop innovation and research to support growth.

Image via Wikipedia

 On the 8th December David Willetts, the Minister of State for Universities and Science, and announced new UK government strategies to develop innovation and research to support growth.

An Open Letter to David Willetts: A bold step towards opening British research

Just to declare various conflicts of interest: I regard Gregg Gordon, CEO of SSRN as a friend and have always been impressed at what he has achieved at SSRN. From the perspective of what is best for the services SSRN can offer to researchers, selling to Elsevier was a smart opportunity and probably the best of the options available given the need for investment. My concerns areÂ at the ecosystem level.

English: Yellow canary (Photo credit: Wikipedia)  *Just to declare various conflicts of interest: I regard Gregg Gordon, CEO of SSRN as a friend and have always been impressed at what he has achieved at SSRN. From the perspective of what is best for the services SSRN can offer to researchers, selling to Elsevier was a smart opportunity and probably the best of the options available given the need for investment.

Canaries in the Elsevier Mine: What to watch for at SSRN

Open Access Week kicks off for the fourth time tomorrow with events across the globe. I was honoured to be asked to contribute to the SPARC video that will be released tomorrow. The following are a transcription of my notes – not quite what I said but similar.

Image via Wikipedia

 Open Access Week kicks off for the fourth time tomorrow with events across the globe. I was honoured to be asked to contribute to the SPARC video that will be released tomorrow. The following are a transcription of my notes – not quite what I said but similar. The video


 was released at 9:00am US Eastern Time on Monday 18 October.

It has been a great year for Open Access.

Some notes on Open Access Week

I talk a lot about building tools that make it easy capture all the objects that we create as part of the research process and then connect all of these up together. Thus far there have been small and limited demonstrators. This is a proposal to build something that demonstrates the general principle at this coming weekend’s Science Hack Day in London.

Image by cameronneylon via Flickr  Jon Eisen asked a question on Friendfeed last week that sparked a really interesting discussion of what an electronic research record should look like. The conversation is worth a look as it illustrates different perspectives and views on what is important. In particular I thought Jonâ€™s statement of what he wanted was very interesting:  This is interesting to me because it maps onto my own desires.

Capturing and connecting research objects: A pitch for @sciencehackday

I wrote a few weeks back about the idea of re-imagining the formally published scientific paper as an aggregation of objects. I asserted that the tools for achieving this are more or less in place. Actually that is only half true. The tools for storing, displaying, and even to some extent archiving communications in this form do exist, at least in the form of examples.

Image by cameronneylon via Flickr  I wrote a few weeks back about the idea of re-imagining the formally published scientific paper as an aggregation of objects.

Implementing the â€œPublication as Aggregationâ€

There has been an awful lot recently written and said about author-pays business models for scholarly publishing and a lot of it has focussed on PLoS ONE.  Most recently Kent Andersen has written a piece on Scholarly Kitchen that contains a number of fairly serious misconceptions about the processes of PLoS ONE. This is a shame because I feel this has muddled the much more interesting question that was intended to be the focus of his piece.

Image by cameronneylon via Flickr  There has been an awful lot recently written and said about author-pays business models for scholarly publishing and a lot of it has focussed on PLoS ONE.Â  Most recently Kent Anderson has written a piece on Scholarly Kitchen that contains a number of fairly serious misconceptions about the processes of PLoS ONE.

In defence of author-pays business models

On April 26 I am attending a joint meeting of the NSF and EuroHORCS (European Heads of Research Councils) on “Changing the Conduct of Science in the Information Age”. I have been asked to submit a one page white paper in advance of the meeting and have been struggling a little with this. This is stage one, a draft document relating to researcher identifiers.

Image via Wikipedia

 On April 26 I am attending a joint meeting of the NSF and EuroHORCS (European Heads of Research Councils) on “Changing the Conduct of Science in the Information Age”. I have been asked to submit a one page white paper in advance of the meeting and have been struggling a bit with this. This is stage one, a draft document relating to researcher identifiers.

Draft White Paper – Researcher identifiers

I have long been an advocate of Friendfeed as a great tool for researchers. Here I discuss the new Friendfeed clone built for researchers, ScienceFeed, suggest what it is good for and what its weaknesses are.

Image via CrunchBase  I have been saying for quite some time that I think Friendfeed offers a unique combination of functionality that seems to work well for scientists, researchers, and the people they want to (or should want to) have conversations with. For me the core of this functionality lies in two places: first that the system explicitly supports conversations that centre around objects.

Friendfeed for Research? First impressions of ScienceFeed

The issue of licensing arrangements and best practice for making data available has been brewing for some time but has just recently come to a head. John Wilbanks and Science Commons have a reasonably well established line that they have been developing for some time. Michael Nielsen has a recent blog post and Rufus Pollock, of the Open Knowledge Foundation, has also just synthesised his thoughts in response into a blog essay.

Best practice for data availability â€“ the debate starts…well over there really

I had the great pleasure andÂ privilegeÂ of announcing the launch of the Panton Principles at the Science Commons Symposium – Pacific Northwest on Saturday. The launch of the Panton Principles, many months after they were first suggested is really largely down to the work of Jonathan Gray.

The Panton Principles: Finding agreement on the public domain for published scientific data

ChemSpidey lives! Even in the face of Karen James’ heavy irony I am still amazed that someone like me with very little programming experience was able to pull together something that actually worked effectively in a live demo. As long as you’re not actively scared of trying to put things together it is becoming relatively straightforward to build tools that do useful things.

Writing a Wave Robot – Some thoughts on good practice for Research Robots

Nat Torkington, picking up on myÂ post over the weekend about the CRU emailsÂ takes a slant which has helped me figure out how to write this post which I was struggling with.Â He says:  As IÂ responded over at Radar, yes I am absolutely calling for social software for scientists, but I didn’t mean to say that we could expect it to help us find the visionaries amongst the simply wrong. But this raises a very helpful question.

What should social software for science look like?

When it comes to getting data up on the web, I am actually a great optimist. I think things are moving in the right direction and with high profile people like Tim Berners-Lee making the case, the with meme of “Linked Data” spreading, and a steadily improving set of tools and interfaces that make all the complexities of RDF, OWL, OAI-ORE, and other standards disappear for the average user, there is a real sense that this might come together.

Capturing the record of research process – Part I

Tomorrow I am giving a talk at the UKOLN Institutional Web Managers workshop starting at 12:45 British Summer Time (GMT+1). In principle you will be able to see the talk video cast at the links on the video streaming page.

The full Web2.0 experience – My talk tomorrow at IWMW in Aberdeen

It’s not my joke but it still works. And given my pretty much complete failure to achieve even written resolutions it’s probably better to joke up front. But…here are a set of things I really need to write this year. Maybe more for my benefit than anyone else but it’s good to have a record.

2560 x 1440 (except while traveling)

This is a piece I wrote for Jisc, as part of a project looking at underpinning theories of citation. There are a few more to come, and you can read the main report for the project at the Jisc repository. This post cross-posted from the Open Metrics blog.

Citations, we are told, are the gold standard in assessing the outputs of research.

Leaving the Gold Standard

One thing that we have been thinking about a bit recently is how best to link elements of a peer reviewed paper back to an Open Notebook. There are a number of issues that this raises, both technical and philosophical about how and why we might do this.

Connecting Open Notebook data to a peer reviewed paper

Peter Murray-Rust is going to take an Open Notebook Science approach to a project on checking whether NMR spectra match up with the molecules they are asserted to represent. The question he poses is how best to organise this.

How best to do the open notebook thing…a nice specific example

I wanted to pull out some of the comments Jean-Claude Bradley has made on the e-notebook posts and think them through in more detail. Thinking about this and looking at some examples on the UsefulChem Wiki I wondered whether this is largely down to a different way of thinking about the notebook rather than differences in field. I will use the UsefulChem Exp098 as an example for this.

Blogs vs Wikis and third party timestamps

This is the first pass at an introductory chapter for a book I’ve had in my head to work on for a long time. The idea is that it relates some of personal history shifting from my grounding science towards the humanities, while interleaving this with a survey of the theoretical work that develops those different perspectives. This is just a first draft written on a Sunday afternoon.

Telling a story…

Like many people over the past week, and months, I’ve had some cause to reflect on what it is I do, and why. A lot of that circles around an issue that’s been troubling me for a while, how do you simultaneously acknowledge a personal and historical failure to act and credibly and coherently move to change that. How can I know when to challenge and when to shut up and listen – because its not always immediately obvious.

Some thoughts on safety pins

I am currently on holiday. You can tell this because I’m writing, reading and otherwise doing things that I regard as fun. In particular I’ve been catching up on some reading. I’ve been meaning to read Danah Boyd’sÂ

 It’s Complicated

Â for some time (and you can see some of my first impressions in the previous post) but I had held off because I wanted to buy a copy. That may seem a strange statement.

A Prison Dilemma

I have a distinct tendency to see everything through the lens of what it means for research communities. I have just finally read Danah Boydâ€™s *Itâ€™s Complicated*Â a book that focuses on how and why U.S. teenagers interact with and through social media.

Researcher as Teenager: Parsing Danah Boydâ€™s Itâ€™s Complicated

…one of the motivations I had to get writing again was a request from someone at a traditional publisher to write more because it “was so useful to have a moderate voice to point to”. Seems I didn’t do so well at that with that first post back. When you get a criticism about tone it is easy to get defensive.

It’s funny…

Image by Gideon Burton via Flickr  It hasn’t been a real good week for peer review.

Peer review: What is it good for?

I have long being sceptical of the costs and value delivered by our traditional methods of peer review. This is really on two fronts, firstly that the costs, where they have been estimated are extremely high, representing a multi-billion dollar subsidy by governments of the scholarly publishing industry.

A question of trust

Last Friday afternoon (was it really only a week ago?) about 200 people made their way to the Googleplex in Mountain View for the fourth SciFoo. There are many people who got their blog posts out well before me so I will focus on the sessions which don’t seem to have been heavily discussed and try to draw a few themes out. For me, the over riding theme that came through was Engagement.

Sci – Bar – Foo etc. Part II – SciFoo – Engaging with the world

I spent two days this week visiting Peter Murray-Rust and others at the Unilever Centre for Molecular Informatics at Cambridge. There was a lot of useful discussion and I learned an awful lot that requires more thinking and will no doubt result in further posts. In this one I want to relay a conversation we had over lunch with Peter, Jim Downing, Nico Adams, Nick Day and Rufus Pollock that seemed extremely productive.

A breakthrough on data licensing for public science?

So in the last post I got all abstract about what the record of process might require and what it might look like. In this post I want to describe a concrete implementation that could be built with existing tools. What I want to think about is the architecture that is required to capture all of this information and what it might look like. The example I am going to use is very simple.

Capturing the record of research process – Part II

Following on from my post last month about using OpenID as a way of identifying individual researchers,Â  Chris Rusbridge made the sensible request that when conversations go spreading themselves around the web it would be good if they could be summarised and aggregated back together. Here I am going to make an attempt to do that – but I won’t claim that this is a completely unbiased account.

Contributor IDs – an attempt to aggregate and integrate

There is an interesting meta-discussion going on in a variety of places at the moment which touch very strongly on my post and talk (slides, screencast) from last week about “web native” lab notebooks.

What are the services we really want for recording science online?

I love Stephen Sondheim musicals. In particular I love the way he can build an ensemble piece in which there can be 10-20 people onstage, apparently singing, shouting, and speaking complete disconnected lines, which nonetheless build into a coherent whole.

A funny thing happened on the (way to the) forum

Yesterday on the train I had a most remarkable experience of synchronicity. I had been at the RIN workshop on the costs of scholarly publishing (more on that later) in London and was heading of to Oxford for a group dinner. On the train I was looking for a seat with a desk and took one up opposite a guy with a slightly battered looking mac laptop.

The people you meet on the train…

A thought sparked off by a comment from Maxine Clarke at Nature Networks where she posted a link to a post by David Crotty. The thing that got me thinking was Maxine’ statement:  Alright, in isolation this doesn’t look like much, read through both David’s post and the comments, and then come back to Maxine’s,Â

Convergent evolution of scientist behaviour on Web 2.0 sites?

I wouldn’t normally try to pick a fight with Chad Orzel, and certainly not over a post which I mostly agree with, but I wanted to take some issue with the slant in his relatively recent post We are science (see also a good discussion in the comments).Â  Chad makes a cogent argument that there is a lot of whining about credit and rewards and that ‘Science’ or ‘The Powers That Be’ are blamed for a lot of these things.

Wonâ€™t someone please think of the policy wonks?

This is the second in a series of posts (first one here) in which I am trying to process and collect ideas that came out of Scifoo. This post arises out of a discussion I had with Michael Eisen (UC Berkely) and Sean Eddy (HHMI Janelia Farm) at lunch on the Saturday. We had drifted from a discussion of the problem of attribution stacking and citing datasets (and datasets made up of datasets) into the problem of academic credit.

The problem of academic credit and the value of diversity in the research community

Image via Wikipedia The Royal Society is running a public consultation exercise on Science as a Public Enterprise. Submissions are requested to answer a set of questions. Here are my answers.

 1. What ethical and legal principles should govern access to research results and data?

Submission to the Royal Society Enquiry

I am thinking about how to present the case for Open Science, Open Notebook Science, and Open Data at Science in the 21

 st

Century, the meeting being organised by Sabine Hossenfelder and Michael Nielsen at the Perimeter Institute for Theoretical Physics.

The economic case for Open Science

This is more a note to write something on this up in some more detail. In the original post What is it publishersÂ

 do

anyway? I gestured towards the idea that one of the main value-adds for the artist formerly known as the publisher is in managing a long tail of challenging, and in some cases quite dangerous issues.

What is it publishers DO? (Reprise)

I’m afraid I didn’t manage to record anything in the end. Video card on laptop wasn’t up to the job. Will try to write a report up over dinner tonight and post later.

Brief report on open science workshop at BioSysBio

Frank Gibson has posted again in our ongoing conversation about using FUGE as a data model for laboratory notebooks. We have also been discussing things by email and I think we are both agreed that we need to see what actually doing this would look like. Frank is looking at putting some of my experiments into a FUGE framework and we will see how that looks. I think that will be the point where we can really make some progress.

More on FuGE and data models for lab notebooks

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.

The Southampton Open Science Workshop – a brief report

The play Arcadia byÂ Tom Stoppard‘sÂ links entropy and chaos theory, the history of englishÂ landscape gardens, romantic literature and idiocies ofÂ academia.

Cover of first edition (Photo credit: Wikipedia) The play

 Arcadia

byÂ Tom Stoppard’sÂ links entropy and chaos theory, the history of englishÂ landscape gardens, romantic literature and idiocies ofÂ academia.

The problem of expertise: The Brighton/English Touring Theatre production of Stoppard’s Arcadia

Access to ResearchÂ is an initiative from a 20th Century industry attempting to stave off progress towards the 21st Century by applying a 19th Century infrastructure. Depending on how generous you are feeling it can either be described as a misguided waste of effort or as a cynical attempt to divert the community from tackling the real issues of implementing full Open Access.

Improving on “Access to Research”

Two things caught my attentions over the past few days. The first was the text of a Graduation Address from Dorothea Salo to the graduating students of the Library and Information Sciences Program at the University of Wisconsin-Madison. The second was a keynote from Chris Bourg, whose blog is entitled “Feral Librarian”, gave at The Acquisitions Institute.

The bravery of librarians

The holy grail of research assessment is a means of automatically tracking the way research changes the way practitioners act in the real world. How does new research influence policy? Where has research been applied by start-ups? And have new findings changed the way medical practitioners treat patients?

Tracking research into practice: Are nurses on twitter a good case study?

With major governments signalling a shift to Open Access it seems like a good time to be asking which organisations in the scholarly communications space will survive the transition. It is likely that the major current publishers will survive, although relative market share and focus is likely to change. But the biggest challenges are faced by small to medium scholarly societies that depend on journal income for their current viability.

Cemetery Society (Photo credit: Aunt Owwee)  With major governments signalling a shift to Open AccessÂ it seems like a good time to be asking which organisations in the scholarly communications space will survive the transition. It is likely that the major current publishers will survive, although relative market share and focus is likely to change.

The challenge for scholarly societies

In the previous postÂ  I discussed a workflow using Wave to author and publish a paper. In this post I want to look at the possibility of using it as a laboratory record, or more specifically as a human interface to the laboratory record. There has been much work in recent years on research portals and Virtual Research Environments.

Google Wave in Research – Part II – The Lab Record

Image via Wikipedia  One of the things you notice as a visitor from the UK in South Africa is how clean the toilets are. In restaurants, at the University, in public places. Sometimes a bit worn down but always clean. And then you start to notice how clear and clean the pavements are and your first response, well at least my first response, is that this is a sign of things going right. One element of the whole is working well.

Open Access for the other 85%

![A UV-vis readout of bis(triphenylphosphine) ni...]( “A UV-vis readout of bis(triphenylphosphine) ni…”)  Image via Wikipedia  While there has been a lot of talk about data repositories and data publication there remains a real lack of good tools that are truly attractive to research scientists and also provide a route to more general and effective data sharing.

Building the perfect data repository…or the one that might get used

Image via Wikipedia  Quite some months ago an article in Cancer Therapy and Biology by Scott Kern of Johns Hopkins kicked up an almighty online stink.

Wears the passion? Yes it does rather…

So there’s been a lot of antagonistic and cynical commentary about Web2.0 tools particularly focused on Twitter, but also encompassing Friendfeed and the whole range of tools that are of interest to me. Some of this is ill informed and some of it more thoughtful but the overall tenor of the comments is that “this is all about chattering up the back, not paying attention, and making a disruption” or at the very least that it is all trivial

Now that’s what I call social networking…

This is an important discussion that has been going on in disparate places, but primarily at the moment is on theÂ Open Science mailing listÂ maintained by the OKF (seeÂ hereÂ for an archive of the relevant thread). To try and keep things together and becauseÂ Yishay Mor asked, I thought I would try toÂ summarizeÂ the current state of the debate.

Licenses and protocols for Open Science – the debate continues

Issues surrounding the relationship of Open Research and replication seems to be the meme of the week. Abhishek Tiwari provided notes on a debate describing concerns about how open research could damage replication and Sabine Hossenfelder explored the same issue in a blog post.

Replication, reproduction, confirmation. What is the optimal mix?

Image via Wikipedia  Iâ€™ve been meaning for a while to write something about peer review, pre and post publication, and the attachment of the research community to traditional approaches. A news article in Nature though, in which I am quoted seems to have really struck a nerve for many people and has prompted me to actually write something.

What is it with researchers and peer review? or; Why misquoting Churchill does not an argument make

AtÂ Science Online 09Â and at the Smi Electronic Laboratory Notebook meeting in London later in January I talked about how laboratory notebooks might evolve. At Science Online 09Â the sessionÂ was aboutÂ Open Notebook ScienceÂ and here I wanted to take the idea of what a â€œweb nativeâ€? lab record could look like and show that if you go down this road you will get the most out if you are open.

The integrated lab record – or the web native lab notebook

I’ve been watching the reflection on the Science Blogs diaspora and the wider conversation on what next for the Science Blogosphere with some interest because I remain both hopeful and not very confident that someone somewhere is really going crack the problem of effectively using the social web for advancing science.

Image by cameronneylon via Flickr  I’ve been watching the reflection on the Science Blogs diaspora and the wider conversation on what next for the Science Blogosphere with some interest because I remain both hopeful and sceptical that someone somewhere is really going crack the problem of effectively using the social web for advancing science.

The Nature of Science Blog Networks

If youâ€™ve been around either myself or Deepak Singh you will almost certainly have heard the Jeff Jonas/Jon Udell soundbite: â€˜Data finds data. Then people find peopleâ€™. The naÃ¯ve analysis of the success of consumer social networks and the weaknesses of science communication has lead to efforts that almost precisely invert the Jonas/Udell concept.

Image by cameronneylon via Flickr  If youâ€™ve been around either myself or Deepak Singh you will almost certainly have heard the Jeff Jonas/Jon Udell soundbite: â€˜Data finds data. Then people find peopleâ€™. Jonas is referring to data management frameworks and knowledge discovery and Udell is referring to the power of integrated data to bring people together.

Why the web of data needs to be social

I’m a little shell shocked really. I’ve spent the last couple of weeks running around like a lunatic, being at meetings, organising meetings, flying out to other meetings.

The long slow catchup…

For those not in the UK this will probably be a little parochial.Â Don Foster is my local MP in Bath. The Digital Economy Bill, currently going through a “wash-up” process triggered by the announcement of a general election yesterday in the British Parliament has drawn extensive criticism from most of the British technology community. Last night an unprecedented number of people followed its second reading on BBC and via Twitter.

A letter to my MP

â€¦is knowing what you meanâ€¦  I posted last week about the spontaneous CMLReact hackfest held around Peter Murray-Rustâ€™s dining room table the day after Science Blogging in London.

The trouble with semantics…

This is the fourth and final part of the serialisation of a draft paper on Open Science. The other parts are here – Part I – Part II – Part III

A question that needs to be asked when contemplating any major change in practice is the balance and timing of ‘bottom up’ versus ‘top-down’ approaches for achieving that change.

A personal view of Open Science – Part IV – Policies and standards

So Michael Nielsen, one morning at breakfast at Scifoo asked one of those questions which never has a short answer; â€˜So how did you get into this open science thing?â€™ and I realised that although I have told the story to many people I havenâ€™t ever written it down.

How I got into open science â€“ a tale of opportunism and serendipity

So Ian Mulvaney asked, and as my solution did not fit into the margin I thought I would post here. Following on from the two rants of a few weeks back and many discussions at Scifoo I have been thinking about how scientists might be persuaded to make more use of social web based tools. What does it take to get enough people involved so that the network effects become apparent.

How to make Connotea a killer app for scientists

As I mentioned yesterday and Shirley Wu picked up on, the final session of Science Blogging 2008 offered a challenge to the audience (and to anyone else) to get more senior scientists blogging. The official announcement is now live – and a free trip to next year’s Science Foo Camp the ultimate prize.

Science blogging challenge goes live

So far weâ€™ve had a fun week. Jean-Claude arrived in the UK on Thursday last, followed up with a talk at Bath University to people at UKOLN on Friday. The talk kicked off an extended conversation which meant we were very late to lunch but it was great to follow up on issues from a different perspective to that. Jean-Claude will be making a screencast of the talk available on his Drexel-CoAs Podcast blog.

The Open Science Endurance Event  – Team JC-C

…is that someone needs to make money out of them. It was inevitable at some point that Friendfeed would take a route that lead it towards mass adoption and away from the needs of the (rather small) community of researchers that have found a niche that works well for them.

The trouble with business models (Facebook buys Friendfeed)

‘No data model survives contact with reality’ – Me, Cosener’s House Workshop 29 February 2008 This flippant comment was in response to (I think) Paolo Missier asking me ‘what the data model is’ for our experiments.

This flippant comment was in response to (I think) Paolo Missier asking me ‘what the data model is’ for our experiments. We were talking about how we might automate various parts of the blog system but the point I was making was that we can’t have a data model with any degree of specificity because we very quickly find the situation where they don’t fit.

Proposing a data model for Open Notebooks

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.

Re-inventing the wheel (again) – what the open science movement can learn from the history of the PDB

On Tuesday I was able to sit in on a conversation that is regularly held within the Computer Science department at University of Toronto that focuses broadly on what can computer science bring as a discipline and a skill set to the sciences more generally. The conversation is lead by Steve Easterbrook so there is a focus on climate science but we also roamed much more widely than that.

Telling stories…

The UKOLN Institutional Web Managers Workshop is running in Aberdeen from 22-24 July and I am giving a talk discussing the impact of Web2.0 tools on science. My main theme will be the that the main cultural reasons for lack of uptake relate to the fear of losing control over data and ideas. Web2.0 tools rely absolutely on the willingness of people to make useful material available.

Science in the YouTube Age – introductory screencast for a talk I’m giving at IWMW

On Monday I am speaking as part of a meeting on Use Cases for Provenance (Programme), which has a lot of interesting talks scheduled. I appear to be last. I am not sure whether that means I am the comedy closer or the pre-dinner entertainment.

Use Cases for Provenance – eScience Institute – 20 April

All good traditions require someone to make an arbitrary decision to do something again. Last year I threw up a few New Year’s resolutions in the hours before NYE in the UK. Last night I was out on the shore of Sydney Harbour. I had the laptop – I thought about writing something – and then I thought – nah I can just lie here and look at the pretty lights.

New Year’s Resolutions 2009

I am probably supposed to be writing up some weighty blog post on some issue of importance but this is much more fun. Last year’s International Conference on Intelligent Systems for Molecular Biology (ISMB) kicked off one of the first major live blogging exercises in a mainstream biology conference. It was so successful that the main instigators were invited to write up the exercise and the conference in a paper in PLoS Comp Biol.

Conferences as Spam? Liveblogging science hits the mainstream

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.

A personal view of Open Science – Part II – Tools

On Wednesday and Thursday this week I was lucky to be able to attend a conference on Electronic Laboratory Notebooks run by an organization called SMI. Lucky because the registration fee was Â£1500 and I got a free ticket. Clearly this was not a conference aimed at academics. This was a discussion of the capabilities and implications for Electronic Laboratory Notebooks used in industry, and primarily in big pharma.

Reflections from a parallel universe

I hold no particular candle for traditional peer review. I think it is inefficient, poorly selective, self reinforcing, often poorly done, and above all, far too slow. However I also agree that it is the least worst system we have available to us.Â  Thus far, no other approaches have worked terribly well, at least in the communication of science research.

Thinking about peer review of online material: The Peer Reviewed Journal of Open Science Online

So I have given three talks in ten days or so, one at the CanSAS meeting at NIST,Â  one at Drexel University and one at MIT last night. Jean-Claude Bradley was kind enough to help me record the talk at Drexel as a screencast and you can see this in various formats here. He has also made some comments on the talk on the UsefulChem Blog and Scientific Blogging site. The talks at Drexel and MIT were interesting.

Talks on Open Notebook Science – some initial thoughts

Thanks to all those who have sent letters of support, paragraphs of text, and made comments or modifications to the proposal. Just a quick update on where we are. The text of the proposal is up at GoogleDocs. I believe I have given anyone who has commented on the original post access to edit but if not give me a yell or just send me any comments by email or pop them in as comments here.

The research network proposal – update II

When I saw the anonymous piece â€œOpenness is Inclusivityâ€ it both struck a chord and made me uncomfortable. Striking a chord because Iâ€™m increasingly concerned about the institutionalization and centralization of Open Science activities. Uncomfortable because it comes across as an attack, and an anonymous one at that, on one organization.

Envy: 7 deadly sins (Photo credit: Wikipedia)  When I saw the anonymous piece â€œOpenness is Inclusivityâ€? it both struck a chord and made me uncomfortable. Striking a chord because Iâ€™m increasingly concerned about the institutionalization and centralization of Open Science activities. Uncomfortable because it comes across as an attack, and an anonymous one at that, on one organization.

Taking a principled approach to envy

Understanding how a process looks from outside our own echo chamber can be useful. It helps to calibrate and sanity check our own responses. It adds an external perspective and at its best can save us from our own overly fixed ideas. In the case of the ongoing Elsevier Boycott we even have a perspective that comes from two opposed directions.

Science in the Open

Defining error rates in the Illumina sequence: A useful and feasible open project?