Curtin University

Cameron Neylon

Consider this yet another commitment to trying to write here a little more regularly. Lots of thinking has been going on but not much writing! At least not writing as I’m going…

Three things colliding over the past few weeks have led me to want to try and get some ideas down.

Epistemic diversity and knowledge production

This post was prompted by Donna Lanclos tweeting a link to a talk by Eamon Tewell:  https://twitter.com/DonnaLanclos/status/992843570238377984  His talk, on the problems of deficit models chimed with me on issues of tacit knowledge. I’m still noodling around an underpinning theory of knowledge for my work (blog post currently has spent nearly 12 months in the draft folder). The core to the model is that (general?

Thinking out loud: Tacit knowledge and deficit models

Three things come together to make this post. The first is the paper

 The 2.5% Commitment

by David Lewis, which argues essentially for top slicing a percentage off library budgets to pay for shared infrastructures.

Against the 2.5% Commitment

Open Access week is a fitting time to be finalising a project on Open Data. About two years ago I started working with the Canadian development funder, the International Development Research Center, to look at the implementation of Open Data policy. This week the final report for that project is being published.

Everyone, it seems agrees that opening up research data is a good thing, at least in the abstract.

Policy for Culture Change: Making data sharing the default

I had a dream, which was not all a dream. The bright sun was extinguish’d, and the stars Did wander darkling in the eternal space, Rayless, and pathless, and the icy earth Swung blind and blackening in the moonless air;

Darkness/Dream

Amongst all the hot takes, the disbelief and the angst the question many of us are asking is what to actually do. I don’t have answers to that question, or rather I have lots of answers and no clarity as to which to choose. An inventory of resources reveals this blog, a substantial, if not massive, social media following on Twitter and some degree of influence associated with that.

First steps&#8230;

Eight publishers will move to require ORCIDs for corresponding authors as part of the submission requirements for submitting articles.

It seems like a very long time ago that I got involved in the efforts to develop an ID system for contributors to research outputs.

Adopting ORCIDs

This is the approximate text of my talk at City University London on 21 October for Open Access Week 2015. If you prefer the “as live” video version then that its available at YouTube. Warning: Nearly 6000 words and I haven’t yet referenced it properly, put the pictures in or done a good edit…

Eight years of Open Access Week, massive progress towards greater access to research, not to mention data and educational resources.

The Limits on &#8220;Open&#8221;: Why knowledge is not a public good and what to do about it

Public Library of Science

For my holiday project I’m reading through my old blog posts and trying to track the conversations that they were part of. What is shocking, but not surprising with a little thought, is how many of my current ideas seem to spring into being almost whole in single posts. And just how old some of those posts are. At the some time there is plenty of misunderstanding and rank naivety in there as well.

Loss, time and money

It takes me a while to process things. It often then takes me longer to feel able to write about them. Two weeks ago we lost one of the true giants of Open Science. Others have written about Jean-Claude’s work and his contributions – and I don’t feel able to add much to those reflections at the moment.

Remembering Jean-Claude Bradley

Everything we have gained by opening content and data will be under threat if we allow the enclosure of scholarly infrastructures. We propose a set of principles by which Open Infrastructures to support the research community could be run and sustained.

Geoffrey Bilder

Cite as “
 
 Bilder G, Lin J, Neylon C (2015) Principles for Open Scholarly Infrastructure-v1, retrieved [date], http://dx.doi.org/10.6084/m9.figshare.1314859
 
 “


 UPDATE: This is the original blogpost from 2015 that introduced the Principles.

Principles for Open Scholarly Infrastructures

Science and Technology Facilities Council

I’ve avoided writing about the Climate Research Unit emails leak for a number of reasons. Firstly it is clearly a sensitive issue with personal ramifications for some and for many others just a very highly charged issue. Probably more importantly I simply haven’t had the time or energy to look into the documents myself. I haven’t, as it were, examined the raw data for myself, only other people’s interpretations.

It wasn&#8217;t supposed to be this way&#8230;

Neutrons in Biology – Santa Fe – 24-29 October 2009 First Biology on SANS2d View more presentations from Cameron Neylon.

First biology on SANS2d &#8211; Will accelerator source time-of-flight SANS deliver for structural biology

On Friday night we went down to London to see the final night of the English National Opera’s run of Doctor Atomic, the new opera from John Adams with a libretto by Peter Sellars. The opera focuses on the days and hours leading up to first test firing of an atomic bomb at the Trinity site on 15 July 1945.

Do high art and science mix?

I should be putting something together for the actual sessions I am notionally involved in helping running but this being a very interactive meeting perhaps it is better to leave things to very last minute. Currently I am at a hotel at LAX awaiting an early flight tomorrow morning.

Very final countdown to Science Online 09

There has been a lot of commentary around the blogosphere about Sergey Brinâ€™s blog post in which he announced that his SNP profile includes one variant which significantly increases his risk of developing Parkinsonâ€™s disease.

Why a 25% risk of developing Parkinsonâ€™s really does matter

This post is an opinion piece and not a rigorous objective analysis. It is fair to say that I am on the record as and advocate of the principles behind PLoS ONE and am also in favour of post publication peer review and this should be read in that light. [

 ed I’ve also modified this slightly from the original version because I got myself mixed up in an Excel spreadsheet]

To me, anonymous peer review is, and always has been, broken.

Can post publication peer review work? The PLoS ONE report card

As part of the BioSysBio meeting being held in London 20-22 of April, Mattias Rantalainen kindly asked me to contribute to a workshop on Open Science being held on the Wednesday. A number of OpenWetWare people including Julius Lucks and John Cumbers have agreed to come on board to help. You can see the draft abstract which is up at OpenWetWare.

Open Science at BioSysBio &#8211; London 20-22 April

The mainstream media has a lot of negative things to say about blogs and user based content on the web. Most of them can be discounted but there is one that I think does need to be taken seriously. The ability of communities to form and to some extent to close around themselves and to simply reinforce their own predjudices is a serious problem and one that we need to work against.

We still have a way to go folks&#8230;

I received the rejection letter late last week but hadn’t got as far as posting about this yet. Given the referee’s comments this was not surprising. We were ranked 20 out of 21 proposals that were considered by the panel. This is not nearly so bad as it sounds. The story as that there were over a hundred proposals so to actually get to the panel wasn’t a bad thing in its own right.

Network grant proposal unsuccessful

DUE TO SEVERE COMMENT SPAM ON THIS POST I HAVE CLOSED IT TO COMMENTS  On February 28/29 we held a workshop on our Blog Based notebook system at the Cosener’s House in Abingdon, Oxfordshire.

Workshop on Blog Based Notebooks

So we have received the referees comments on the network proposal and after a bit of a delay I have received permission to make them public. You can find a pdf of the referee’s comments here. I have started to draft a reply which is published on google docs. I have given a number of people access but if you are feeling left out and would like to contribute just drop me a line.

OPEN Network proposal &#8211; referees comments are in

Michael Barton has a very nice little video on web tools for science and sharing up at Bioinformatics Zen.

Gotta love the tinfoil

I wanted to followup on the post I wrote a few days ago where I quoted a post from Black Knight on the concept of making methodology open. The point I wanted to make was the scientists in general might be even more protective of their methodology than they are of their data. However I realised afterwards that I may have given the impression that I thought BK was being  less open than he ‘should’, which was not my intention.

Followup on &#8216;open methods&#8217;

This is the starting point for a description of the development work being done in the School of Chemistry at the University of Southampton on a blog-based electronic laboratory notebook for biochemistry/molecular biology. Ultimately the aim is for this document to form the first draft of a paper describing the system.

The Southampton E-lab blog notebook &#8211; Part 1 Aims

This a set of notes for my talk at Duke University this week. It draws on the Political Economy of Publishing series as well as other work I’ve beenÂ involved with by Jason Potts at RMIT amongst others. The title of the talk is “

Sustainable Futures for Research Communication

 ” and you can find the abstract at the Duke event page.


 The video is now available along with the slides.

The Goods in the Scholarly Marketplace

This is an approximation of my talk at OpenCon Cambridge on Thursday 26 November 2015. Any inaccuracies entirely mine. There is also a video recording of the actual talk.

The idea of OpenCon was borne out of the idea that the future belonged to young scholars and that helping them to be effective advocates for the world they want to work in was the best way to make progress.

Not what, not who, or how, but Why is Open?

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?

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

Ernesto Priego has invited me to speak at City University in London on Thursday the 22nd October as part of Open Access Week. I wanted to pull together a bunch of the thinking I’ve been doing recently around Open Knowledge in general and how we can get there from here. This is deliberately a bit on the provocative side so do come along to argue!

Speaking at City University London for OA Week

For a long time it was difficult for evolutionary biology to make sense of a (male) peacock’s tail. Clearly it is involved in courtship but the investment in growing it, and the disdvantage of carrying it around, would seem to be a disadvantage over all.

Costly signalling in scholarly communications

Response to Request for Information – FR Doc. 2011-28621 Dr Cameron Neylon â€“ U.K. based research scientist writing in a personal capacity

 Introduction

Thankyou for the opportunity to respond to this request for information and to the parallel RFI on access to scientific publications.

Response to the OSTP Request for Information on Public Access to Research Data

Image via Wikipedia  David Crotty, over atÂ Scholarly Kitchen has an interesting piece on metrics, arguing that many of these have not been thought through because they donâ€™t provide concrete motivation to researchers to care about them.

Metrics and Money

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?

Some months ago now I gave a talk atÂ very exciting symposiumÂ organized byÂ Greg WilsonÂ as a closer for theÂ Software CarpentryÂ course he was running at Toronto University.

Reflections on Science 2.0 from a distance &#8211; Part I

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

Euan Adie has asked for some help to do further analysis on the comments made on PLoS ONE articles. He is doing this via crowd sourcing through a specially written app at appspot to get people to characterize all the comments in PLoS ONE. Euan is very good at putting these kind of things together and again this shows the power of Friendfeed as a way of getting the message out.

Euan Adie asks for help characterising PLoS comments

This is a case of a comment that got so long (and so late) that it probably merited it’s own post. David Crotty and Paul (Ling-Fung Tang) note some important caveats in comments on my last post about the idea of the “web native” lab notebook. I probably went a bit strong in that post with the idea of pushing content onto outside specialist services in my effort to try to explain the logic of the lab notebook as a feed.

Third party data repositories &#8211; can we/should we trust them?

The following is the text from which I spoke today at the .Astronomy conference. I think there is some video available on the .Astronomy UStream account and I also have audio which I will put up somewhere soon.

Thereâ€™s a funny thing about the science and coding communities. Each seems to think that the other has all the answers.

Best practice in Science and Coding. Holding up a mirror.

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

Something that has been bothering me for quite some time fell into place for me in the last few weeks. I had always been slightly confused by my reaction to the fact that on UsefulChem Jean-Claude actively works to improve and polish the description of the experiments on the wiki.

The distinction between recording and presenting &#8211; and what it means for an online lab notebook

Greg Wilson and others are running a survey on how scientists’ perception of and use of software is changing.

Survey on scientists&#8217; use of software

Image via Wikipedia  Nature Publishing Group yesterday announced a new venture, very closely modelled on the success of PLoS ONE, titled Scientific Reports. Others have started to cover the details and some implications so I won’t do that here. I think there are three big issues here. What does this tell us about the state of Open Access? What are the risks and possibilities for NPG?

PLoS (and NPG) redefine the scholarly publishing landscape

As has been noted in a few places, Neil Withers, one of the editors of soon to be newest Nature journal, Nature Chemistry put out a request last week for input on a range of issues to do with how people use journals, formats, and technical widgets. Egon Willighagen, Rich Apodaca, and Oscar the Journal Munching Robot (masquerading as Peter Murray-Rust, or is that the other way around?) have already posted responses.

A new type of chemistry journal: Nature Chemistry requests input

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

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

Sometimes you read things that just make you angry. I’m not sure I can add much to this eloquent article written by Andrew Vickers in the New York Times (via Neil Saunders and the 23andme blog).  Shirley Wu has recently written on the fears and issues of being scooped and whether this is field dependent or not.

Sharing is caring&#8230;and not sharing can be reprehensible

The text of the proposal is now in a near complete form. I need to add references and a few others things but it is mostly in reasonable shape. If you would like to have your name included as a founder member of the network please drop me a comment on this post, email, or if I have given you editing rights then feel free to add yourself.

Research network proposal &#8211; Update III

I am constantly intrigued by the way that some sort of collective web-based intelligence seems to cause specific issues to pop up in multiple places at the same time.

There are crowds, and then there are crowds&#8230;

Some themes seem to emerge to me from the talks I have been to. One is that the many people are talking about the need to expand the reach of e-science tools out to the ‘general scientific community’.Â  As I noted in other posts part of this is a problem with language.

Themes at the All Hands Meeting

Interesting morning negotiating the problems of getting permission to re-produce figures in a review I am currently writing. I wanted to reproduce figures from four papers, two from J Mol Biol (Elsevier), one from Structure (Cell Press), one from J Biol Chem (ASBMB). I could request permission for all three journals from copyright.com and as I’m in a rush I did this.

Variations in reproduction charges for figures in a review article

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

Testing&#8230;testing&#8230;

Last week I was lucky enough to attend both SciBarCamp Palo Alto and SciFoo; both for the second time. In the next few posts I will give a brief survey of the highlights of both, kicking off with SciBarCamp.

Sci &#8211; Bar &#8211; Foo etc. Part I &#8211; SciBarCamp Palo Alto

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

As has been flagged up by Jean-Claude Bradley there are a couple of places now where people can sign up to say that they have Open Notebook Science in their laboratory, practise Open Notebook Science,or even would like to find a place where they canÂ keep anÂ Open Notebook.Â  Jean-Claude has put a list on the Nodalpoint Wiki and I have set up a database at DabbleDB.

Growing a community &#8211; Open Notebook Science directories

In a previous post I said I would try to replicate an experiment from the UsefulChem open Wiki notebook within our blog system to see how it might look. This post is to record what I am doing as I do it. Thus this is the lab book I am using to record the process and decisions I have taken in using a lab book.

Replication of UsefulChem Exp098 in the Southampton blog notebook

I don’t really want to add anything more to what has been said in many places (and has been rounded up well by Bora Zivkovic on Blog Around the Clock, see also Peter Suber for the definitive critique, also updates here and here). However there is a public relations issue here for the open science movement in general that I think hasn’t come up yet.

Through a PRISM darkly

I attended the session held on Nature Island as part of the Scifoo Lives On series being organised by Jean-Claude Bradley and Bertalan Mesko and wanted to record some of my impressions. The mechanics of the meeting itself were interesting. My initial reaction to the idea of meetings in Second Life was pretty sceptical. My natural inclination would have been to setup some sort of video cast or conference call.

How to get critical mass? Scifoo Lives on Session on Medicine and Web 2.0

Yesterday afternoon the Open Notebook Science case studies session was held as part of the Scifoo lives on sessions at Nature Island, Second Life. Jean-Claude Bradley organised, moderated and spoke first followed by me and Jeremiah Faith. We all spoke about experiences and implementation of different approaches to open notebook science. Jean-Claude has put the transcript up here.

Scifoo Lives On session: Open notebook science case studies

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

Pedro has written a thoughtful post detailing arguments he has received against Open Practice in science. He makes a good point that as the ideas around Open Science spread there will inevitably be a backlash. Part of the response to this is to keep saying – as Pedro does and as Jean-Claude, Bill Hooker and others have said repeatedly that we are not forcing anyone to take this approach.

Pedro Beltrao writes on the backlash against open science

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

So while on the train yesterday in somewhat pre-caffeinated state I stuck my foot in it somewhat. Several others have written (Nils Reinton, Bill Hooker, Jon Eisen, Hsien-Hsien Lei, Shirley Wu) on the unattributed use of an image that was put together by Ricardo Vidal for the DNA Network of blogs. The company that did this are selling hokum. No question of that.

My Bad&#8230;or how far should the open mindset go?

…but being straightforward is always the best approach. Since we published our paper in PLoS ONE a few months back I haven’t been as happy as I was about the activity of our Sortase. What this means is that we are now using a higher concentration of the enzyme to do our ligation reactions. They seem to be working well and with high yields, but we need to put in more enzyme.

It&#8217;s a little embarrassing&#8230;

I attended the first Sage Bionetworks Congress in 2010 and it left a powerful impression on my thinking. I have just attended the third congress in San Francisco and again the challenging nature of views, the real desire to make a difference, and the standard of thinking in the room will take me some time to process.

Some brief responses to the Sage Bionetworks Congress

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

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 &#8211; eScience Institute &#8211; 20 April

As I mentioned a couple of weeks or so ago I’ve been playing around with Friendfeed. This is a ‘lifestreaming’ web service which allows you to aggregate ‘all’ of the content you are generating on the web into one place (see here for mine). This is interesting from my perspective because it maps well onto our ideas about generating multiple data streams from a research lab.

Friendfeed, lifestreaming, and workstreaming

Given that most people reading this probably also read the UsefulChem Blog I would guess that they have already figured out I am visiting the States. However as I am now here and due to jet lag have a few hours to kill before breakfast I thougt I might detail the intinerary for anyone interested. Currently I am in Gaithersburg at the CanSAS V meeting.

The Soton Lab Blog Book US Tour

More on the discussion of structured vs unstructured experiment descriptions. Frank has put up a description of the Minimal Information about a Neuroscience Investigation standard at Nature Precedings which comes out of the CARMEN project. Neil Saunder’s has also made some comments on the resistance amongst the lab monkeys to think about structure. Lots of good points here. I wanted to pick out a couple in particular; From Neil;

The structured experiment

I’ve spent a long time talking about two things that our LaBLog enables, or rather that it should enable. One is that by changing the way we view the record we can look at our results and materials in a new way. The second is that we want to enable a machine to read the lab book. Andrew Milsted, the main developer of the LaBLog and a PhD student in Jeremy Frey’s group, has just enabled a significant step in that direction.

A new way of looking at science?

The Mars Phoenix landing has got a lot of coverage around the web, particularly from some misty eyed old blokes who remember watching landings via the Mosaic browser in an earlier, simpler age. The landing is cool, but one thing I thought was particularly clever was the use of Twitter by JPL to publicise the landing and what is happening on a minute to minute basis.

Twittering labs? That is just so last year&#8230;

I’m in Barcelona at a satellite meeting of the EuroScience Open Forum organised by Science Commons and a number of their partners.Â

Policy and technology for e-science &#8211; A forum on on open science policy

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

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’ve been conflicted about posting this. I had planned to write something along these lines for several weeks but the murder of Jo Cox threw that sideways. The way I write tends to involve pushing words around in my head for a week or so, and then writing it all out. Thus most of this existed in some form prior to her murder but it was not written down.

NotAllBrexiters

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 &#8220;soundness&#8221;. Is this the connection across disciplines?

Towards the end of last year I wrote up some initial reactions to the announcement of Nature Communications and the communications team at NPG were kind enough to do a Q&amp;A to look at some of the issues and concerns I raised. Specifically I was concerned about two things.

Why I am disappointed with Nature Communications

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?

I’m afraid I went to bed. It was getting on for midnight and it looked like another four hours or so before the petition would reach the magic mark of 25,000 signatures. As it turns out a final rush put us across the line at around 2am my time, but never mind, I woke up wondering whether we had got there, headed for the computer and had a pleasant surprise waiting for me.  What does this mean?

25,000 signatures and still rolling: Implications of the White House petition

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

Iâ€™ve been interested for some time in capturing information and the context in which that information is created in the lab. The question of how to build an efficient and useable laboratory recording system is fundamentally one of how much information is necessary to record and how much of that can be recorded while bothering the researcher themselves as little as possible.

Tweeting the lab

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

Our laboratory blog system has been doing a reasonable job of handling protocols and simple pieces of analysis thus far. While more automation in the posting would be a big benefit, this is more a mechanical issue than a fundamental problem. To re-cap our system is that every “item” has its own post. Until now these items have been samples, or materials. The items are linked by posts that describe procedures.

The problem with data&#8230;

Cultural change won’t happen overnight and may never happen at all. Policy mandates are a blunt instrument and may lead to a backlash. So how do we align incentives for researchers with the aim of making their research outputs more widely and effectively useable? Get the metrics right and the competitive market could manage the rest of the optimisation problem for us.

Image via Wikipedia  It has become reflexive in the Open Communities to talk about a need for “cultural change”. The obvious next step becomes to find strong and widely respected advocates of change, to evangelise to young researchers, and to hope for change to follow. Inevitably this process is slow, perhaps so slow as to be ineffective.

Metrics of use: How to align researcher incentives with outcomes

Well when it’s not open obviously.  There are many ways to provide all the information imagineable while still keeping things hidden. Or at least difficult to figure out or to find. The slogan ‘No insider information’ is useful because it provides a good benchmark to work towards. It is perhaps an ideal to attain rather than a practical target but thinking about what we know but is not clear from the blog notebook has a number of useful results.

When is open notebook science not?

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€

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

Late last year the Research Information Network held a workshop in London to launch a report, and in many ways more importantly, a detailed economic model of the scholarly publishing industry.

What is the cost of peer review? Can we afford (not to have) high impact journals?

It’s been an interesting week or so in the Chemistry online world. Following on from my musings about data services and the preparation I was doing for a talk the week before last I asked Tony Williams whether it was possible to embed spectra from ChemSpider on a generic web page in the same way that you would embed a YouTube video, Flickr picture, or Slideshare presentation.

The growth of linked up data in chemistry &#8211; and good community projects

On Friday (yes, that’s this Friday) a series of Unconferences that has been pulled together in response to the Digital Britain Report and Forum will kick of with one being held at the Rutherford Appleton Laboratory, near Didcot. The object of the meeting is to contribute to a coherent and succinct response to the current interim report and to try and get across to Government what a

 truly

Digital Britain would look like.

Digital Britain Unconference Oxfordshire &#8211; Friday 1 May &#8211; RAL

This quote is grabbed from a comment by Jean-Claude Bradley at bbgm in reply to my comment on Deepak’s post on my post on…. anyway my original comment was that our Wiki review would not be indexed on Google Scholar which is where people might go for literature searches  Now this is an interesting point and it mirrors what I do. Jean-Claude has established that a lot of the ‘new’ traffic coming to UsefulChem comes from Google searches for

Why and where we search&#8230;

I’ve been fiddling with this post for a while and I’m not sure where its going but I think other people’s views might make the whole thing clearer. This is after all why we believe in being open. So here it is in its unfinished and certainly unclarified form. All comments gratefully received.

Limits to openness &#8211; where is the boundary?

Brief notes on this parallel session from E-science all hands meeting on Tuesday morning. First talk in this session discussed the CARMEN project which aims to provide repositories and tools for neuroscience electrophyisology data. There was a short discussion on the challenges of persuading scientists to put the data in. The speaker’s (Paul Watson) view was that this would probably need to be driven by funders and journals.

AHM2007 Medical E-science session

Image via Wikipedia  Just a very brief note, which really follows on from the vigorous discussion in Jennifer Rohn’s blog at Nature Networks this week, to say that the guys at OpenWetWare appear to have gone live with some of the new functionality for laboratory notebooks on the wiki. Check it out from the OWW main page. I will have a closer look and make some comments as and when I have a bit of time but it looks like a good start.

Another lab notebook framework

More followup on feeds. I’ve set up a friendfeed which is available here. Amongst other things I’ve been trying to aggregate my comments on other people’s blogs. The way I am doing this is creating a tag in Google Reader which I have made public. When I leave a comment I try to subscribe to a comment feed for that Blog, I then tag it as ‘Comments feed’ which aggregates and makes it public as an RSS feed.

Science in the Open

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