Cameron Neylon

As I noted in the last post we are rapidly counting down towards the final few days before the Open Science Workshop at the Pacific Symposium on Biocomputing. I am flying out from Sydney to Hawaii this afternoon and may or may not have network connectivity in the days leading up the meeting. So just some quick notes here on where you can find any final information if you are coming or if you want to follow online.

Final countdown to Open Science@PSB

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.

Where does Open Access stop and &#8216;just doing good science&#8217; begin?

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 &#8211; a brief report

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 &#8211; My talk tomorrow at IWMW in Aberdeen

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&#8230;

A very interesting paper from Caroline Savage and Andrew Vickers was published in PLoS ONE last week detailing an empirical study of data sharing of PLoS journal authors. The results themselves, that one out ten corresponding authors provided data, are not particularly surprising, mirroring as they do previous studies, both formal [pdf] and informal (also from Vickers, I assume this is a different data set), of data sharing.

Show us the data now damnit! Excuses are running out.

Greg Wilson has put together an amazing set of speakers for a symposium entitled – “Science 2.0: What every scientist needs to know about how the web is changing the way they work“. It is very exciting for me to be sharing a platform with Michael Nielsen, Victoria Stodden, Titus Brown, David Rich and Jon Udell. The full details are available at the link. The event is free but you need to register in advance.

Science 2.0 in Toronto &#8211; MaRS Centre 29 July

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

Edit and update – I’ve been told that the Macmillan supporting SOPA is the Macmillan US and not the holding company of Nature Publishing Group. NPG are however explicitly listed as members of the Association of American Publishers who are listed as supporters. The AAP list includes American Chemical Society, American Institute of Physics along with a lot of smaller society publishers.

Image via Wikipedia

 Edit and update – I’ve been told that the Macmillan supporting SOPA is the Macmillan US and not the holding company of Nature Publishing Group. NPG are however explicitly listed as members of the Association of American Publishers who are listed as supporters. The AAP list includes American Chemical Society, American Institute of Physics along with a lot of smaller society publishers.

The stupidity of SOPA in Scholarly Publishing

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

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

One of the strong messages that came back from the workshop we held at the BioSysBio meeting was that protocols and standards of behaviour were something that people would appreciate having available. There are many potential issues that are raised by the idea of a ‘charter’ or ‘protocol’ for open science but these are definitely things that are worth talking about.

Protocols for Open Science

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&#8230;a nice specific example

A few days ago the UK Government report on the future of Britain’s digital infrastructure, co-ordinated by Lord Carter, was released. I haven’t had time to read the whole report, I haven’t even really had time to skim it completely. But two things really leapt out at me.  On page four:  And on page 18:  The first extract, is to me symptomatic of a serious, even catastrophic lack of ambition and understanding of how the web is changing.

Why the Digital Britain report is a missed opportunity

Image by davemc500hats via Flickr One thing that has been becoming clearer and clearer to me is the need to an agreed central authority for identify. This is one thing, possibly

 the

one thing, that needs to be absolutely secure and inviolable for Open Science to work. Trust relies on provenance. Attribution, which is at the heart of open practice, relies on provenance.

Provenance, identity, and Google App Engine

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 &#8211; Part II &#8211; Tools

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

Image via Wikipedia  I’m aware I’ve been trailing this idea around for sometime now but its been difficult to pin down due to issues with room bookings. However I’m just going to go ahead and if we end up meeting in a local bar then so be it! If Southampton becomes too difficult I might organise to have it at RAL instead but Southampton is more convenient in many ways.

Open Science Workshop at Southampton &#8211; 31 August and 1 September 2008

Image from Wikipedia via Zemanta  Following on from the discussion a few weeks back kicked off by Shirley at One Big Lab and continued here I’ve been thinking about how to actually turn what was a throwaway comment into reality:  There is a problem at the core of this. For someone to pay for access to the results, there has to be a monetary benefit to them.

More on the science exchance &#8211; or building and capitalising a data commons

Looking at the EPSRC website I came across the following call for proposals involving collaboration between a US and UK programme:  http://www.epsrc.ac.uk/CallsForProposals/NSF-EPSRCChemistryProposals07.htm  Now, being an academic I’m up for any method of trying to get money out the system, especially special programmes.

Joint NSF-EPSRC programme in Chemistry &#8211; an opportunity for ONS?

Image via Wikipedia  Once again a range of conversations in different places have collided in my feed reader. Over on Nature Networks, Martin Fenner posted on Researcher ID which lead to a discussion about attribution and in particular Martin’s comment that there was a need to be able to link to comments and the necessity of timestamps.

Attribution for all! Mechanisms for citation are the key to changing the academic credit culture

What Shirley said: The call for participation for the Open Science workshop at PSB 2009 is now up! We welcome anyone with an interest in open science to submit proposals for talks. Note that although space is limited for talks and demos, anyone who registers for the conference can present a poster, so we also encourage poster submissions! Please if you are interested in submitting a talk or poster get in touch.

What Shirley said:  Please if you are interested in submitting a talk or poster get in touch. We would like to have a good and robust discussion with a range of perspectives on a range of topics. We are limited with respect to the time available so there will be some tough decisions to make. Nonetheless, please do get in touch; we would very much like to have a good representation of posters as well as talks.

Open Science at PSB &#8211; Call for submissions

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 &#8211; update II

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

I blogged the other day about the way charges for reproducing figures in review articles appear to have gone ballistic. At that stage I only had the cost for J Biol Chem which was a whopping $USD73 to reproduce a figure. I had three other images I was using and was expecting around $20 for them, based on the website that Science Direct points you at for permissions. Well I was wrong, they have now come back at $USD3 each.

Variations in reproduction charges &#8211; the results are in!

I went along to a session on enabling uptake, which has evolved out of groups based in education and training. This mainly involved people focussed on education and training and support people. It was mainly focussed on Grid based systems. Two interesting things came out of this I thought.

BoF Session on enabling uptake of e-science

Having just posted that there didn’t seem to be too much of this we have a talk in the Social Sciences parallel session that covers exactly this.Pete Edwards talked (amongst other things) about ourSpaces, a tool providing a resource for sharing resources that can be tagged in all the expected Facebook style ways. He then went on to talk about how you record both data and how it is recorded i.e. methodology.

Web2.0 tools for Social Sciences at AHM2007

Following on from the post yesterday I actually went along to the workshop with the title I didn’t understand. There was much I didn’t understand and a lot of technical terminology that went straight over my head. Terminology is an issue here, particularly where there is a desire to bring in new people.

The &#8216;inpenetrable&#8217; OMII-UK workshop

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

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

It has been painful to watch the tensions at the Wikimedia Foundation explode over the last few months and with the stepping down of the Executive Director there seems a mood of conciliation and a desire for WMF to learn from the process. I know next to nothing of the details or the story, so while it is the spur for this post I don’t want to offer any opinions on WMF itself.

Boxing Gloves Â (Photo credit: Wikipedia)  It has been painful to watch the tensions at the Wikimedia Foundation explode over the last few months and with the stepping down of the Executive Director there seems a mood of conciliation and a desire for WMF to learn from the process. I know next to nothing of the details or the story, so while it is the spur for this post I don’t want to offer any opinions on WMF itself.

Beyond the culture clash: Developing leadership for open organisations

A couple of ideas have been rumbling along in the background for me for a while. Reproducibility and what it actually means or should mean has been the issue du jour for a while.

Italiano: network sociality (Photo credit: Wikipedia)  A couple of ideas have been rumbling along in the background for me for a while. Reproducibility and what it actually means or should mean has been the issue du jour for a while.

Speculation: Sociality and “soundness”. Is this the connection across disciplines?

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

The following is my application to join the European Commission Open Science Policy Platform. The OSPP will provide expert advice to the European Commission on implementing the broader Open Science Agenda. As you will see some of us have a concern that the focus of the call is on organisations, rather than communities.

European flag outside the Commission (Photo credit: Wikipedia)

 The following is my application to join the European Commission Open Science Policy Platform. The OSPP will provide expert advice to the European Commission on implementing the broader Open Science Agenda. As you will see some of us have a concern that the focus of the call is on organisations, rather than communities.

European Commission Open Science Policy Platform

This post wasn’t on the original slate for the Political Economics of Publishing series but it seems apposite as the arguments and consequences of the Editorial Board of Lingua resigning en masse to form a new journal published by Ubiquity Press continue to rumble on. The resignation of the editorial board of Lingua from the (Elsevier owned) journal to form a new journal, that is intended to really be “the same journal” raises interesting issues

Victory Press of Type used by SFPP (Photo credit: Wikipedia)

 This post wasn’t on the original slate for the Political Economics of Publishing series but it seems apposite as the arguments and consequences of the Editorial Board of Lingua resigning en masse to form a new journal published by Ubiquity Press continue to rumble on.

The resignation of the editorial board of Lingua from the (Elsevier owned) journal to form a new journal,

PolEcon of OA Publishing: What are the assets of a journal?

In the first post in this series I identified a series of challenges in scholarly publishing while stepping through some of the processes that publishers undertake in the management of articles. A particular theme was the challenge of managing a heterogenous stream of articles and their associated heterogeneous formats and problems, in particular at a large scale.

Reproduction of a Charles Mills painting (Photo credit: Wikipedia)  In the first post in this series I identified a series of challenges in scholarly publishing while stepping through some of the processes that publishers undertake in the management of articles. A particular theme was the challenge of managing a heterogenous stream of articles and their associated heterogeneous formats and problems, in particular at a large scale.

PolEcon of OA Publishing II: What&#8217;s the technical problem with reforming scholarly publishing?

A note on changes: I’m going to vary my usual practice in this series and post things in a rawer form with the intention of incorporating feedback and comments over time. In the longer term I will aim to post the series in a “completed” form in one way or another as a resource. If there is interest then it might be possible to turn it into a book. There is no statement more calculated to make a publisher’s blood boil than “Publishers?

Peer review system…in Polish (Photo credit: Wikipedia)

 A note on changes: I’m going to vary my usual practice in this series and post things in a rawer form with the intention of incorporating feedback and comments over time. In the longer term I will aim to post the series in a “completed” form in one way or another as a resource. If there is interest then it might be possible to turn it into a book.

PolEcon of OA Publishing I: What is it publishers do anyway?

A question I have got quite frequently over the last few months is “…no but seriously, what are you actually doing…”. The answer has got more precise bit by bit but I truly didn’t leave PLOS with a specific plan for world domination. What I did want to do was find a way to combine a return to a hard core research focus with projects that really are very practical.

Workhouse memorial, Banbridge (Photo credit: Wikipedia) A question I have got quite frequently over the last few months is “…no but seriously, what are you actually

 doing

…”. The answer has got more precise bit by bit but I truly didn’t leave PLOS with a specific plan for world domination. What I did want to do was find a way to combine a return to a hard core research focus with projects that really are very practical.

Next Steps&#8230;Joining the Centre for Culture &#038; Technology at Curtin

On March 30 the BBC broadcast a 40 minute talk from Martha Lane Fox. The Richard Dimbleby Lecture is an odd beast, a peculiarly British, indeed a peculiarly BBC-ish institution. It is very much an establishment platform, celebrating a legendary broadcaster and ring marshaled by his sons, a family that as our speaker dryly noted are “an entrenched monopoly” in British broadcasting.

Martha Lane Fox (Photo: The Cabinet Office License: OGL v1.0)  On March 30 the BBC broadcast a 40 minute talk from Martha Lane Fox. The Richard Dimbleby Lecture is an odd beast, a peculiarly British, indeed a peculiarly BBC-ish institution. It is very much an establishment platform, celebrating a legendary broadcaster and ring marshaled by his sons, a family that as our speaker dryly noted are “an entrenched monopoly” in British broadcasting.

.everyone or .science? Or both? Reflections on Martha Lane Fox&#8217;s Dimbleby Lecture

Thereâ€™s an argument I often hear that brings me up short. Not so much short because I donâ€™t have an answer but because I havenâ€™t managed to wrap my head around where it comes from.

Mathematics in a PhD thesis. (Photo credit: Wikipedia) Thereâ€™s an argument I often hear that brings me up short. Not so much short because I donâ€™t have an answer but because I havenâ€™t managed to wrap my head around where it comes from.

Who do you get to say I am?

“Open source” is not a verb Nathan YerglerÂ viaÂ John Wilbanks I often return to the question of what “Open” means and why it matters. Indeed the very first blog post I wrote focussed on questions of definition. Sometimes I return to it because people disagree with my perspective. Sometimes because someone approaches similar questions in a new or interesting way.

English: William Henry Fox Talbot’s ‘The Open Door’ (Photo credit: Wikipedia)  I often return to the question of what “Open” means and why it matters. Indeed the very first blog post I wrote focussed on questions of definition. Sometimes I return to it because people disagree with my perspective. Sometimes because someone approaches similar questions in a new or interesting way.

Open is a state of mind

The Finch Report was commissioned by the UK Minister for Universities and Science to investigate possible routes for the UK to adopt Open Access for publicly funded research. The report was released last night and I have had just the chance to skim it over breakfast. These are just some first observations. Overall my impression is that the overall direction of travel is very positive but the detail shows some important missed opportunities.

First thoughts on the Finch Report: Good steps but missed opportunities

Changing the world is hard. Who knew? Advocating for change can be lonely. It can also be hard. As a scholar, particularly one at the start of a career it is still hard to commit fully to ensuring that research outputs are accessible and re-useable.

The Whitehouse - from Flickr User nancy_t3i  Changing the world is hard. Who knew? Advocating for change can be lonely. It can also be hard. As a scholar, particularly one at the start of a career it is still hard to commit fully to ensuring that research outputs are accessible and re-useable.

Send a message to the Whitehouse: Show the strength of support for OA

Ten years ago today, the Budapest Declaration was published. The declaration was the output of a meeting held some months earlier, largely through the efforts of Melissa Hagemann, that brought together key players from the, then nascent, Open Access movement. BioMedCentral had been publishing for a year or so, PLoS existed as an open letter, Creative Commons was still focussed on building a commons and hadn’t yet released its first licences.

Budapest: Image from Wikipedia, by Christian MehlfÃ¼hrer  Ten years ago today, the Budapest Declaration was published. The declaration was the output of a meeting held some months earlier, largely through the efforts of Melissa Hagemann, that brought together key players from the, then nascent, Open Access movement.

On the 10th Anniversary of the Budapest Declaration

Response to Request for Information – FR Doc. 2011-28623 Dr Cameron Neylon â€“ U.K. based research scientist writing in a personal capacity

 Introduction

Thank you for the opportunity to respond to this request for information. As a researcher based in the United Kingdom and Europe, it might be argued that I have a conflict of interest. In some ways it is in my interest for U.S. federally funded research to be uncompetitive.

Response to the OSTP Request for Information on Public Access to Scientific Publications

Have you written your response to the OSTP RFIs yet? If not why not? This is amongst the best opportunities in years to directly tell the U.S. government how important Open Access to scientific publications is and how to start moving to a much more data centric research process. You’d better believe that the forces of stasis, inertia, and vested interests are getting their responses in. They need to be answered.

Response to the RFI on Public Access to Research Communications

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

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%

The software code that is written to support and manage research sits at a critical intersection of our developing practice of shared, reproducible, and re-useble research in the 21st century.

Image by olliepalmer.com via Flickr  The software code that is written to support and manage research sits at a critical intersection of our developing practice of shared, reproducible, and re-useble research in the 21st century.

Good practice in research coding: What are the targets and how do we get there&#8230;?

The Research Data Management movement is moving on apace. Tools are working and adoption is growing. Policy development is starting to back up the use of those tools and there are some big ambitious goals set out for the next few years. But has the RDM movement taken the vision of data intensive research to its heart? Does the collection, sharing, and analysis of data about research data management meet our own standards?

Image by Idaho National Laboratory via Flickr I wrote this post for the Digital Curation Centre blog following the Research Data Management Forum meetingÂ run in Warwick a few weeks back. If you feel moved to comment I’d ask you to do it over there.

 The Research Data Management movement is moving on apace. Tools are working and adoption is growing.

Reflections on research data management: RDM is on the up and up but data driven policy development seems a long way off.

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

This is an edited version of the text that I spoke from at the Altmetrics Workshop in Koblenz in June. Impact as re-use and the way it enables us to reframe the argument around the impact and dissemination of curiosity driven research.

Image by tribalicious via Flickr

 This is an edited version of the text that I spoke from at the Altmetrics Workshop in Koblenz in June. There is also an audio recording of the talk I gave available as well as the submitted abstract for the workshop.

I developed an interest in research evaluation as an advocate of open research process.

(S)low impact research and the importance of open in maximising re-use

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&#8230;

Image via Wikipedia  Peter Murray-Rust has sparked off another round in the discussion of the value that publishers bring to the scholarly communication game and told a particular story of woe and pain inflicted by the incumbent publishers. On the day he posted that I had my own experience of just how inefficient and ineffective our communication systems are by wasting the better part of the day trying to find some information.

How to waste public money in one easy step&#8230;

One of the things we want the Open Research Computation journal to do is bring more of the transparency and open critique that characterises the best Open Source Software development processes into the scholarly peer review process. But you can talk about changing the way peer review works and you can actively do something about. Michael Barton and Hazel Barton have taken matters into their own hands and thrown the doors completely open.

Image via Wikipedia The submissions for Open Research Computation (which I blogged about a month or so back) are starting to come in and we hope to be moving towards getting those initial papers out soon. One of the things we want the journal to do is bring more of the transparency and

 openÂ critique

that characterises the best Open Source Software development processes into the scholarly peer review process.

Open Source, Open Research and Open Review

I spend a lot of my time arguing that many of the problems in the research community are caused by journals. We have too many, they are an ineffective means of communicating the important bits of research, and as a filter they are inefficient and misleading. Today I am very happy to be publicly launching the call for papers for a new journal. How do I reconcile these two statements? Computation lies at the heart of all modern research.

Open Research Computation: An ordinary journal with extraordinary aims.

Image via Wikipedia  Last Friday I spoke at the STM Innovation Seminar in London, taking in general terms the theme I’ve been developing recently of focussing on enabling user discovery rather than providing central filtering, of enabling people to act as their own gatekeeper rather than publishers taking that role on for themselves.

Forward linking and keeping context in the scholarly literature

Image via Wikipedia  I know Iâ€™ve been a bit quiet for a few weeks. Mainly Iâ€™ve been away for work and having a brief holiday so it is good to be plunging back into things with some good news. I am very happy to report that the Open Society Institute has agreed to fund the proposal that was built up in response to my initial suggestion a month or so ago.

Beyond the Impact Factor: Building a community for more diverse measurement of research

I recently made the most difficult decision Iâ€™ve had to take thus far as a journal editor. That decision was ultimately to accept the paper; that probably doesnâ€™t sound like a difficult decision until I explain that I made this decision despite a referee saying I should reject the paper with no opportunity for resubmission not once, but twice.

Image by Gideon Burton via Flickr  I recently made the most difficult decision Iâ€™ve had to take thus far as a journal editor. That decision was ultimately to accept the paper; that probably doesnâ€™t sound like a difficult decision until I explain that I made this decision despite a referee saying I should reject the paper with no opportunity for resubmission not once, but twice.

Binary decisions are a real problem in a grey-scale world

Image via Wikipedia  Richard Stallman and Richard Grant, two people who I wouldnâ€™t ever have expected to group together except based on their first name, have recently published articles that have made me think about what we mean when we talk about â€œOpenâ€ stuff. In many ways this is a return right to the beginning of this blog, which started with a post in which I tried to define my terms as I understood them at the time.

Free&#8230;as in the British Museum

Image via Wikipedia  I had a bit of a rant at a Science Online London panel session on Saturday with Theo Bloom, Brian Derby, and Phil Lord which people seemed to like so it seemed worth repeating here. As usual when discussing scientific publishing the dreaded issue of the Journal Impact Factor came up. While everyone complains about metrics I’ve found that people in general seem remarkably passive when it comes to challenging their use.

Warning: Misusing the journal impact factor can damage your science!

If we imagine what the specification for building a scholarly communications system would look like there are some fairly obvious things we would want it to enable. Registration of priority, archival, re-use and replication, and filtering.

Image by cameronneylon via Flickr  I’ve largely stolen the title of this post from Daniel Mietchen because I it helped me to frame the issues. I’m giving an informal talk this afternoon and will, as I frequently do, use this to think through what I want to say. Needless to say this whole post is built to a very large extent on the contributions and ideas of others that are not adequately credited in the text here.

What would scholarly communications look like if we invented it today?

So Google has abandoned Wave. Not really that surprising but obviously dissappointing to those of us who were excited about its potential. Here I argue that part of the problem is that most of us are still restricted in our thinking to static documents on the web. Wave was always about a next generation kind of document that was active and dynamic and that might have contributed to some of the confusion around what it was good for.

Image via Wikipedia  I am frequently overly enamoured of the idea of where we might get to, forgetting that there are a lot of people still getting used to where weâ€™ve been. I was forcibly reminded of this by Carole Goble on the weekend when I expressed a dislike of the Utopia PDF viewer that enables active figures and semantic markup of the PDFs of scientific papers.

The triumph of document layout and the demise of Google Wave

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

The following is my contribution to a collection prepared by the British Library and released today at the Wellcome Trust, called â€œDriving UK Research. Is copyright a help or a hindrance?â€ which is being released under a CC-BY-NC license. The British Library kindly allowed authors to retain copyright on their contributions so I am here releasing the text into the public domain via a CCZero waiver.

Image via Wikipedia

 The following is my contribution to a collection prepared by the British Library and released today at the Wellcome Trust, called â€œDriving UK Research. Is copyright a help or a hindrance?â€Â  -Â Press Release â€“ Document[pdf] – which is being released under a CC-BY-NC license.

Driving UK Research &#8211; Is copyright a help or a hindrance?

The idea that “it’s not information overload, it’s filter failure” combined with the traditional process of filtering scholarly communication by peer review prior to publication seems to be leading towards the idea that we need to build better filters by beefing up the curation of research output before it is published.

Image via Wikipedia Clay Shirkyâ€™s famous soundbite has helped to focus on minds on the way information on the web needs to be tackled and a move towards managing the process of selecting and prioritising information. But in the research space Iâ€™m getting a sense that it is fuelling a focus on

 preventing

publication in a way that is analogous to the conventional filtering process involved in peer reviewed publication.

Itâ€™s not information overload, nor is it filter failure: Itâ€™s a discovery deficit

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

Last Thursday night I was privileged to be invited to the 10th anniversary celebrations for BioMedCentral and to help announce and give the first BMC Open Data Prize. Peter Murray-Rust has written about the night and the contribution of Vitek Tracz to the Open Access movement. Here I want to focus on the prize we gave, the rationale behind it, and the (difficult!) process we went through to select a winner.

Image via Wikipedia  Last Thursday night I wasÂ privilegedÂ to be invited to the 10th anniversary celebrations for BioMedCentral and to help announce and give the first BMC Open Data Prize. Peter Murray-Rust has written about the night and the contribution of Vitek Tracz to the Open Access movement. Here I want to focus on the prize we gave, the rationale behind it, and the (difficult!) process we went through to select a winner.

The BMC 10th Anniversary Celebrations and Open Data Prize

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 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€

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 &#8211; Researcher identifiers

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 &#8211; Some thoughts on good practice for Research Robots

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

A number of things recently have lead me to reflect on the nature of interactions between social media, research organisations and the wider community. What the first decade of the social web has taught us is that organisations that effectively harness the goodwill of their staff or members using social media tools do well. This approach is antithetical to traditional command and control management structures.

Image by cameronneylon via Flickr  A number of things recently have lead me to reflect on the nature of interactions between social media, research organisations and the wider community. There has been an awful lot written about the effective use of social media by organisations, the risks involved in trusting staff and members of an organisation to engage productively and positively with a wider audience.

The personal and the institutional

Image by cameronneylon via Flickr

 This post, while only 48 hours old is somewhat outdated by these two Friendfeed discussions. This was written independently of those discussions so it seemed worth putting out in its original form rather than spending too much time rewriting.

I wrote recently about Sciencefeed, a Friendfeed like system aimed at scientists and was fairly critical.

&#8220;Friendfeeds for Science&#8221; pt II &#8211; Design ideas for a research focussed aggregator

Image via Wikipedia  Which is not to say that I am any good at software engineering, good practice, or writing decent code. And you shouldn’t take Greg to task for some of the dodgy demos I’ve done over the past few months either.

Everything I know about software design I learned from Greg Wilson &#8211; and so should your students

A talk given at the Edinburgh University IT Futures meeting late in 2009. The talk discusses the strengths and weaknesses of Wave as a tool for research and provides some pointers on how to think about using it in an academic setting. The talk was recorded in a Wave with members of the audience taking notes around images of the slides which I had previously uploaded.

Image by thelastminute via Flickr  A talk given at the Edinburgh University IT Futures meeting late in 2009. The talk discusses the strengths and weaknesses of Wave as a tool for research and provides some pointers on how to think about using it in an academic setting. The talk was recorded in a Wave with members of the audience taking notes around images of the slides which I had previously uploaded.

Google Wave: Ripple or Tsunami?

Regular readers will know I am a great believer in the potential of Web2.0 tools to enable rapid aggregation of loose networks of collaborators to solve a particular problem and the possibilities of using this approach to do science better, faster, and more efficiently.

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

I am speaking at the Eduserv Symposium on London in late May on the subject of the importance of identity systems for advancing the open research agenda. From the announcement:  The Eduserv Symposium 2009 will be held on Thursday 21st May 2009 at the Royal College of Physicians, London.

Eduserv Symposium 2009 &#8211; Evolution or revolution: The future of identity and access management for research

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 &#8211; Part I

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?

I realised the other day that I havenâ€™t written an exciteable blog post about getting an invitation to SciFoo! The reason for this is that I got overexcited over on FriendFeed instead and havenâ€™t really had time to get my head together to write something here.

Science in the Open

Open drug discovery in the undergraduate lab