Archive for category Social Media

Is a knol a scientific publishing platform?

Image representing Knol as depicted in CrunchBaseImage via CrunchBase, source unknown

Google has recently released knol, which most people are calling Google’s version of Wikipedia. The main difference between a knol and a wikipedia article is that a knol has associated authorship or ownership against an article. This factor has caused some issues an outcries focusing on the merits of the wisdom of crowds verses the merits of single individuals and the whole ethos if information dissemination on the Web. (There are too many to cite but some discussion can be found on FriendFeed+knol)

However, on looking at knol and having a snoop around I was not drawn into thinking about competing with Wikipedia or advertising revenue, rather what struck me is that a knol, with owner authorship looks incredibly like a scientific journal publication platform…

According to the Introduction to knol (or instructions for authors)  you to can write about anything you like, so disseminiation of science must fall under that. You can collaborate on a unit of knowledge (or manuscript) with other authors and they are listed – I assume the contribution to the text will also be stored in the revision history, makes the authors contribution section a little easier to write. It is not limited to one article per subject, so this allows all manner of opinions or scientific findings to be reported contrasted and compared with each other. You can select your copyright and license for your article (rather than handing it over). You can request a (peer-) review of the article, However more important the article is available for continuous peer-review in the form of comments on the article.

So is a knol a Google Wikipedia or is it a scientific publishing platform? What would prevent publishiing a knol and getting credit (hyperlinks), citations (analytics) impact factors (page ranks) in the same way you do for the traditional scientific publishers? You would of course not have to pay for the privilage of trying to diseminate your findings, loosing copyright and then asking your institution to pay for a subscription so you and your lab members can read your own articles. In fact you, as an author (lab, institution) can even share revenue for your article via adsense.

Some traditional publishers are trying to embrace new mechanisms of disseminating scientific knowledge. Only today Nature Reviews Genetics (as described by Nacsent) published the paper Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges by Lincoln Stein and published the supplementary material as a community editable wiki.

With knol as a scientific publishing platform, what can the traditional scientific publishing houses now offer for the publishing fees? Faster turn around? revenue sharing? Are they really still the gatekeepers of scientific knowledge? Or in the Web 2.0 era has that mantle passed to Google? Certainly, in the first instance it would make a nice preceedings platform.

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Zotero library re-visioned

I have been wanting to use Zotero now for a while for my reference library but could never work out how back up my library using subversion. My life is contained within subversion, I do not know how I could have possibly survived before all my work; code, presentations, papers, images and not to mention my thesis, is all perfectly backed up and re-visioned and floating happily in the cloud available to me from any machine. Zotero installs itself inside the firefox profile which makes it difficult to revision within the C:\\my-subversion” folder. What I decided to do was to create a new firefox profile (instructions here) within my-subversion folder then install zotero creating:

C:\\my-subversion\firefoxprofile\zotero

I then only added the zotero folder to my subversion repository. You could always revision your firefox profile but I decided not to. Now every time I add a new item to zotero the my-subversion folder indicates there has been a change and requires a commit. Obviously every time you add a pdf file to the library you will actually have to “SVN add” the file itself. This is not a problem for me as I try to keep my library light and not store to many pdfs.

I am also going to try and use zotero as an interface to my subversion repository, describing and tagging documents and code that I write, but more specifically presentations, so no more trying to work out what is contained in “Presentation1.ppt” or what file name I gave to that talk on data standards which I have to give tomorrow!

I am tagging my hard drive via Zotero, its just one big cloud.

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goPubmed

In catching up with my reading lists of 2007 I was alerted to gopubmed via Deepak’s post. Gopubmed described itself as an ontology based literature search making use of both the Gene ontology and Mesh terms. There is also the ability to provide feedback or rather act as a curator for the search results. I have already noticed  some mis-match in author details.  In general though the interface  is a vast improvement on pubmed’s tiered interface and the ability to refine the searches looks interesting. I have added gopubmed to  my search engines within firefox and will have a play to see if it is any good. RSS feeds on search terms would be top of the wish list. Anybody used it in anger?

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I see science

It is interesting to see new developments in the dissemination of scientific discourse, such as scientific blogging and paradigms such as open science, come on-line with developments in web-based social media. The latest medium to receive the Science 2.0 treatment (poor pun on applying Web 2.0 technologies for science) is the video.

YouTube is probably the granddaddy, or at least the most prominent of the video upload and broadcast services. Although YouTube doesn’t not have a defined science category, it is easy to find science related videos and lectures, mixed in with the general population. However, several specialist sites have appeared dealing specifically with science research, all have been labeled as “YouTube for science”. The most recent site is SciVee, which is a collaboration of the Public Library of Science (PLoS), the National Science Foundation (NSF) and the San Diego Supercomputer Center (SDSC). The fact the a publishing house (PLoS) has got involved in this effort is encouraging, and maybe an admittance that a paper, in isolation of public commentary, the data used to produce the paper, and a sensible presentation mechanism, is no longer sufficient in the web-based publishing era (or maybe I have got over excited and read to much into it). The most interesting feature on SciVee, and probably the most powerful compared to some of the other broadcasters, is the ability to link to an Open Access publication, setting the context and relevance of the video. The flip side could also be true, where a video provides evidence of the experiment, such as the methods or the displays the result.

Another scientific video broadcaster is the Journal of Visualized Experiments (JOVE). As the name suggests, JOVE focuses on capturing the experiment performed within the laboratory, rather than a presentation, or general scientific discourse. As a result JOVE can be though of as a visual protocol or methods journal and is stylaised as a traditional journal, already on Issue 6; a focus on Neuroscience.

If JOVE is a visual journal for life-science experiments then Bioscreencast could be thought of as a visual journal of Bioinformatics. Bioscreencast focusses on screencasts of software, providing a visual “How-to” on scientific software, presentations and demonstrations.

No doubt these three may not be the last scientific video publishers, but they have an opportunity to become well established ahead of the others. Now, where is my webcam, I need to video myself writing code and submit it to JOVE, produce a demo and submit it to Bioscreencast. Then I have to write a paper on it, submit the pre-prints to Nature Preccedings get it published in an Open Access Journal, then video myself giving a presentation on the paper, submit it to SciVee and link them all together.

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RSS readers

I have outlined my growing tendency at the minute to handing over applications to the “Internet cloud” in an earlier post.

I prefer using web-based applications because I tend to jump from several machines throughout the day at work and then use a different machine at home. Having applications, floating in the ether cloud, means moving around is considerably easier. I have been using bloglines for quite a while now for my RSS feeds. I did have a early look at Google reader when it first launched, but I felt then it was not quite what I wanted and definitely not as good as bloglines at the time. However a re-visiting of Google reader over the last week or so has dramatically changed my perception. Re-vamped with a new interface (similar to bloglines) has made reading posts alot easier. All the post from your subscribed feeds are actually saved, by default and don’t disappear once read, unlike in bloglines (unless you check the “keep new” box). I think the biggest feature for me is the ability to tag posts, combined with the saved posts facility, this should prove to be a very handy source of reference rather that just an “recent-post viewer”.

A new feature that has just been added to Google reader is the offline mode. Working in conjunction with Google Gears this provides the ability to read the last 2000 recent items, a feature I am looking forward to testing during the flight to ISMB in a few weeks.

If you use another RSS reader or have an opinion on Google reader then let me know.

With using gmail, and calendar, with trying out Google reader (and probably switching from bloglines), using google docs and spreadsheets more everyday, there is every danger that my cloud is going to be raining google. With the added prospect of Google presentations round the corner will it be long before I am floating off to the Google OS cloud?

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Do scientists really believe in open science?

I am writing this post as a collection of the current status and opinions of “Open Science”. The main reason being I have a new audience; I am working for the CARMEN e-Neuroscience project. This has exposed me, first hand, to a domain of the life-sciences to which data sharing and publicly exposing methodologies has not been readily adopted, largely it is claimed due to the size of the data in question and sensitive privacy issues.

Ascoli, 2006 also endorses this view of the neuroscience and offers some further reasons why this is the case . He also includes the example of exposing neuronal morphological data and argues the benefits and counters the reticence to sharing this type of data.

Hopefully, as the motivation for the CARMEN project is to store and share and facilitate the analysis of neuronal activity data, some of these issues can be overcome.

With this in mind I want to create this post to provide a collection of specific blogs, journal articles, relevant links and opinions which hopefully will be a jumping-off point to understanding the concept of Open Science and embracing the future methodologies in pushing the boundaries of scientific knowledge.

What is Open Science?

There is no hard and fast definition, although according to the Wikipedia entry:

“Open Science is a general term representing the application of various Open approaches (Open Source, Open Access, Open Data) to scientific endeavour. It can be partially represented by the Mertonian view of Science but more recently there are nuances of the Gift economy as in Open source culture applied to science. The term is in intermittent and somewhat variable use.”

“Open Science” encompasses the ideals of transparent working practices across all of the life-science domains, to share and further scientific knowledge. It can also be thought of to include the complete and persistent access to the original data from which knowledge and conclusions have been extracted. From the initial observations recorded in a lab-book to the peer-reviewed conclusions of a journal article.

The most comprehensive overview is presented by Bill Hooker over at 3quarks daily. He has written three sections under the title “The Future of Science is open”

  1. Open Access.
  2. Open Science
  3. An Open Science World

In part 1, as the title suggests, Bill presents an overview on open access publishing and how this can lead to open-science (part 2). He suggests that

“For what I am calling Open Science to work, there are (I think) at least two further requirements: open standards, and open licensing.”

I don’t want to repeat the content already contained in these reviews, although I agree with Bill’s statement here. There is no point in having an open science philosophy if the data in question is not described or structured in a form that facilitates exchange, dissemination and evaluation of the data, hence the requirement of standards.

I am unaware of community endorsed standard reporting formats within Neuroscience. However, the proliferation of standards in Biology and Bioinformatics, is such, that it is fast becoming a niche domain in its own right. So much so, that there now exists a registry for Minimum Information reporting guidelines, following in the formats of MIAME and MIAPE. This registry is called MIBBI (Minimum Information for Biological and Biomedical Investigations) and aims to act as a “one-stop-shop” of existing standards life-science standards. MIBBI also provides a foundry where best practice for standards design can be fostered and disparate domains can integrate and agree on common representations of reporting guidelines for common technologies.

Complementary to standard data structures and minimum reporting requirements, is the terminology used to described the data; the metadata. Efforts are under way to standardise terminology which describes experiments, essential in an open environment, or simply in a collaboration. This is the goal of the Ontology of Biomedical Investigations (OBI) project which is developing “an integrated ontology for the description of biological and medical experiments and investigations. This includes a set of ‘universal’ terms, that are applicable across various biological and technological domains, and domain-specific terms relevant only to a given domain“. Already OBI is gaining momentum and currently supports diverse communities from Crop science to Neuroscience.

Open licensing of data may address the common arguments I hear for not releasing data, that “somebody might use it”, or the point blank refusal of “not until I publish my paper”. This is an unfortunate side effect of the “publish or perish” system as commented on bbgm and Seringhaus and Gerstein, 2007, and really comes down to due credit. In most cases this prevents real time assessment of research, complementary analysis or cross comparisons with other data sets to occur alongside the generation of the data, which would in no doubt enforce the validity of the research. Assigning computational amenable licenses to data, such as those proposed by Science Commons, maybe one way of ensuring that re-use of the data is always credited to the laboratory that generated the data. It is possible paradigm that “Data accreditation impact factors” could exist analogous to the impact factors of traditional peer-reviewed journals.

Open science may not just be be about releasing data associated with a peer-review journal, rather it starts from exposing the daily recordings and observations of an investigation, contained in the lab-book. One aspect of the “Open data” movement is that of “Open Notebook Science” a movement pioneered by Jean-Claude Bradley and the Useful Chemistry group, where their lab-book is is open and access-able on-line. This open notebook method was further discussed by a recent Nature editorial outlining the benefits of this approach. Exposing you lab-book could allow you to link the material and methods section of your publication, proving you actually did the work and facilitating the prospect of other researchers actually being able to repeat your ground breaking experiments.

Already many funders are considering data management or data sharing policies, to be applied to future research proposals. The BBSRC have recently released their data sharing policy which states that, “all research proposals submitted to BBSRC from 26th April 2007 must now include a statement on data sharing. This should include concise plans for data management and sharing or provide explicit reasons why data sharing is not possible or appropriate“. With these types of policies a requirement to research funding the “future of science is open“.

The “Open Science” philosophy appears to be gaining some momentum as is actively being discussed within the scientific blogosphere. This should not really come as a great surprise as science blogging can be seen as part of the “Open science” movement, openly sharing opinions and discourse. Some of the more prominent science blogs focusing on the open science ideal are Open access News, Michael Eisen’s Open Science Blog, Research Remix, Science Commons, Peter Murray-Rust.

There are of course alot more blogs discussing the issue. Performing an “open science search” on Postgenomic (rss feed on search terms please, Postgenomic) produces an up to the minute list of the open science discourse. Although early days, maybe even the “open science” group on Scintilla (still undecided on Scintilla) will be the place in the future for fostering the open science community.

According to Bowker’s description of the traditional model of scientific publishing, the journal article “forms the archive of scientific knowledge” and therefore there has been no need to hold on to the data after it has been “transformed” into a paper. This, incorporated with in-grained social fears, as a result of “publish or perish”, of not letting somebody see the experimental data before they get their peer-reviewed publication, will cripple the open science movement and slow down knowledge discovery. Computational amenable licences may go some way to solve this. But raising the awareness and a clear memorandum from the major journal publishers that, exposing real-time science and publishing data will not prevent publication as a peer-reviewed journal, can only help.

In synopsis I will quote Bill again as I think he presents a summary better than I could;

My working hypothesis is that open, collaborative models should out-produce the current standard model of research, which involves a great deal of inefficiency in the form of secrecy and mistrust. Open science barely exists at the moment — infancy would be an overly optimistic term for its developmental state. Right now, one of the most important things open science advocates can do is find and support each other (and remember, openness is inclusive of a range of practices — there’s no purity test; we share a hypothesis not an ideology).

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Digg the journals

I have been using the “user powered content” site Digg (any excuse at the moment to distract me from thesis writing) and I am enjoying the fact that the stories are coming to me with little effort, in other words I don’t have to find the blog or site first and then subscribe. One of the “stories” that I found on Digg was an interview with Matthew Sparkes, Web Executive at New Scientist, about the effects of social media on online publications (i.e Digg). It highlights the increase in social media sites such as blogging and user driven content, on the traditional media and even the traditional content providers. It stops short of saying how New Scientist are going to deal with this phenomenon but they obviously recognise the importance and impact.

Digg do have a section on science, but deals mostly with buzz stories, or media driven science reports. If this type of social media site existed specifically for the scientific domain then maybe it could go some way as to re-invent/add to, the traditional journal peer-review system, or make “community contributions” like Nature comments actually more prominent in the community? Maybe it could act as community citation system not dependant on traditional journal submissions? Or maybe a scientific community driven portal, similar to arXiv, will dispense with traditional journals altogether?

Lots of maybe’s and no answers…. An article in Wired Magazine also covers this very topic commenting on traditional peer-review and the notion of community driven content and review.

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