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Posts Tagged ‘publishing’

A Three Stage Program to Become an Open Access Fundamentalist

In Uncategorized on November 13, 2008 at 2:51 pm

post to news.thinkgene.com

I must admit that I am not a fundamentalist myself, nor am I sure I will ever become one. But I try to advocate open access, and as much as possible I follow the first two steps below. In addition, I have set up a free site for anyone to publish according to step 3 which is sciphu.com (but any site will do…..ideally one using widely accepted publication identifiers – sciphu.com isn’t…yet).

Following the recommendations in step 1 and 2 makes you a supporter and Open Access activist. Following recommendations in step 3 will make you a full-fledged Open Access Fundamentalist…….

1. Supporter stage. Openly support initiatives like PloS and contribute to activities like Open Access day.

2. Activist stage.

a) Publish in Open Access journals as much as possible.

b) Mail authors for reprints. Whenever you need an article published in a pay-for-access journal, write to the corresponding author asking for a reprint. Even if you have access through your institutional subscription (or get it through friends and colleagues), write the author to notify him/her that the paper is not open access. This increases awareness….

3. Fundamentalist stage. Send in your paper to be peer reviewed like you normally would (preferably to a pay-for-access journal). Receive your reviewer comments, edit according to those comments, but do not send your manuscript back to the journal. Rather, publish on freely accessible web page. Include the peer-reviews if you want, but clear this with the reviewers first.

Image by asher taken from Elephantitis of the mind

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Quote of the month November 08

In Uncategorized on November 4, 2008 at 9:58 pm

Deepak at business|bytes|genes|molecules, on open access publishing (my highlighting):

Everyone should have access to the same scientific information (what that information should be is the subject of another post). It’s not even about who pays for it. It is science, and as such belongs to everyone.

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The Likes of Blog Publishing (Open Access Day 08 entry)

In Uncategorized on October 14, 2008 at 5:03 am


post to news.thinkgene.com

This post is my entry for Open Access Day 2008. It is about blogging, peer-review publishing, open access, elitism, prejudice and exclusion.

I had this dream: publishing directly on the web mixed with interactive comments to individual publications was to replace traditional peer-reviewed publishing in scientific journals. I set up SciPhu.com to achieve this. The core idea was (and still is) that any publication would remain fluid in its format and content since communication with referees was continuous and interactive. By letting the publication evolve in this way it should asymptote towards perfect.

Inspiration of how a series of comments can serve to paint the whole picture, I took from posts (and their comment-threads) like Anna Koushnir’s post on female scientists (where the comments are sometimes borderline harassment, but the comments taken together as a whole, nails the relevant issues, I think) and Olivia Judson’s post “The monster is back” (I could have taken any post with more than say -10- comments)……

I realize now that I was a bit naive in believing this could completely replace a system that has worked so well for so long. The system has after all allowed the scientific community to retain an unsurpassed credibility, worldwide.

But……..I am not accepting defeat just yet, because traditional peer-review publishing has it’s problems.

Firstly, most articles published are not open access. That means that if you need a scientific article and you do not work in an institution that has paid a large amount of money for subscription to the given journal (or you have a private subscription) you will not be able to access it (you can pay for individual articles, but that will become very expensive over time). In contrast, blog publishing would be free and accessible to all. The cost of publishing on a blog is very low indeed. It does not need printing and it will not need conventional employees. Editors and peer-reviewers (those who comment) would all be doing work on a volunteer basis. Consequently, no need to charge the readers,…….- at least not for scientific use (commercial use could potentially have a different set of rules).

Secondly, traditional paper-publishing is painstakingly slow and, compared to web-publishing, extremely inefficient. Blogs and scientific news-sites can publish in a matter of minutes and provide continuous updates (and corrections) on almost any topic. Also, web-publishing allows you to track your readers in an unprecedented way, – and most importantly, it provides a feedback channel for them. This feedback I think is essential in the next era of publishing. It does however, need some structure. The commenting anarchy of today will not suffice.

Thirdly, – the complete lack of such anarchy, has been one the strengths of the traditional peer-review model. But, to such an extent has peer-review been controlled that it has become the opposite of anarchy, namely dictatorship. Reviewers are handpicked by the publishers, creating potential old boy networks, with the journal editors as presidents. To add to this, reviewers are usually anonymous, potentially masking any conflicts of interest, be it financial, work-related or personal. In addition editors and peer reviewers tend to have agenda’s different to those who submit their papers. Thus, the traditional system does not serve to get as much quality scientific information out as possible, – this is contrary to the intentions. Below, I’ll quote from a discussion I had with (editor) T Ryan Gregory, to illustrate elitism, prejudice and exclusion, as examples of editor-agendas (comments from this genomicron post):

1. Elitism

My concern is that publish first, comment second represents an easy way around the rigors of review by experts in which publication is dependent on positive reviews and revision. I am all for open discussion, but initiatives started by people who don’t publish much in the peer-reviewed literature or do not themselves review many manuscripts do not really appeal to me because it adds to my sense of concern that this is a backdoor. I am not trying to seem elitist, I am just saying that peer review, for all its problems, is there for a reason. Submitted by T Ryan Gregory on 22 May 2008 – 8:10am.

2. Prejudice

May I ask what your record is in terms of reviewing manuscripts and publishing peer reviewed articles?  Submitted by T Ryan Gregory on 22 May 2008 – 9:00am.

One might also be forgiven for thinking that someone with only a few publications might be looking to skip the hard (but necessary) stage of getting through reviewers. Isn’t it a bit odd to complain about the anonymous nature of peer review while moderating a “review” blog anonymously? Submitted by T Ryan Gregory on 22 May 2008 – 9:00am.

3. Exclusion

Peer review isn’t supposed to be democratic. It is supposed to be done by peers — a set of individuals with highly specific knowledge in a particular field. The democratic part comes only once the paper gets through that filter, when it is made accessible to the entire community. Peer review is a vetting process, not a rating process. Submitted by T Ryan Gregory on 22 May 2008 – 9:42am.

By now I have concluded that SciPhu or similar blog-publishing alternatives is not going to replace traditional publishing, and that other alternatives will have to. Blogs can/will however, still be a valuable addition to traditional publishing, perhaps serving to correct some of the flaws:

“….fact is, at least now, if you come up for review and your citations are all on SciPhu or PLoS, you are going to get clobbered.”

This is very true. What I am saying is that I hope that it will be different in the future. Sciphu is probably not the final solution, but it is a starting point. And hopefully one of many similar initiatives to come. A site like this can be developed into a wiki or it can have staffed (unpaid) experts in given fields as reviewers or it can develop in any other direction. But, and this is important, it should never require fees of any sort from either referees, authors or readers. There are no fees attached to the sciphu site (it doesn’t even have google adds), it’s all non-profit scientific idealism. Submitted by Sciphu (not verified) on 22 May 2008 – 10:21am.

Money and open access, – this is the imperative issue that needs to be sorted out. Development of new publishing methods will most certainly follow. Peer-review publishing is dead, long live peer-review publishing.

Hence I pledge my complete and unrestricted support to any open-access initiative.

Some other views on peer review: nature debate on peer review, Certifying Online Research

The Elsevier Grand Challenge: Entry # 2

In Uncategorized on August 13, 2008 at 1:03 pm
Please find below, my rejected submission to “The Elsevier Grand Challenge“. I humbly admit defeat to some terrific-looking projects, – best of luck to:
Sean O’Donoghue and Lars Jensen
Reflect: Automated Annotation of Scientific Terms
Timothy Baldwin, Lawrence Cavedon, Sarvnaz Karimi, David Martinez, David Newman, Falk Scholer and Justin Zobel
Effective Search, Classification, and Visualisation of Information from Large Collections of Biomedical Literature
Vit Novacek, Siegfried Handschuh and Tudor Groza
Teaching Machines to Teach Us: A Truly Knowledge-Based Publication Management
Amr Ahmed, Andrew Arnold, Luis Pedro Coelho, Saboor Sheikh, Eric Xing, William Cohen and Robert F. Murphy
Information Retrieval and Topic Discovery using both Figures and Captions in Biological Literature
Stephen Wan, Robert Dale and Cecile Paris
In-Context Summaries of Cited Documents: A Research Prototype for Academic and Scholarly Literature
Roderic Page
Towards realising Darwin’s dream: setting the trees free
Jose Gonzalez-Brenes, Aabid Shariff, Sourish Chaudhuri and Carolyn Rose
Automating the Generation of Life Science Protocols
Glenn Ford, Sameer Antani, Dina Demner Fushman and George Thoma
Tools to build and use Interactive Publications
Michael Greenacre and Trevor Hastie
Guided Tours in N-Dimensional Space:  Dynamic Visualization of Multivariate Data
Alexander Garcia and Alberto Labarga
A tale of two cities in the land of serendipity: The semantic web and the social web heading towards a living document in life sciences.
Whoever wins it is my hope that Elsevier publication turns open access, and to survive I think they will have to, in one way or another.

SciPhu Project Description:

SciPhu.com (http://sciphu.com/) is a blog where anyone is invited to publish scientific content, and anyone is likewise, invited to review (comment on) these publications (blog posts). All posts and all comments are freely and publicly available to everyone. SciPhu= Science + Phusis (Phusis – An Ancient Greek word often translated as birth or nature – Wikipedia).

  1. Project Goals, Purpose, and Outcomes.
    SciPhu.com is a blog based, open access and unrestricted publishing model. A hybrid in the spirit of Wikipedia and JustScience.The idea behind SciPhu-publishing is to be able to publish and peer-review scientific information more efficiently than standard peer-reviewing.The SciPhu vision of the future of science publishing:

    a) Improve the process/methods/results of creating, reviewing and editing scientific content: We wanted the reviewing process while retaining its scientific credibility, to be faster and less rigid. One answer, we found, was blogger-reviewing (which in this setting is just a fancy name for commenting on blog posts).

    b) Interpret, visualize or connect the knowledge more effectively:
    Blogging is a good starting point since there are so many knowledgeable scientific bloggers on the internet scene.

    c) Provide tools/ideas for measuring the impact of these improvements. SciPhu.com is already launched and statistics on visitors, rating of posts (scientific articles), and comments are and will be, continously available for evaluation.

  2. Detailed Project Description: Content and Functionalities
    The end goal of SciPhu is to be able to quality control scientific information from any source, so that the twisted scientific reality that sometimes ends up in the popular press (and ultimately in public opinion) can be promptly countered with proper scientific information. To achieve this goal, a solid referee-base with scientific authority and credibility needs to be affiliated with the site. Building such a referee community is a major milestone and challenge. As a starting point towards this goal, the SciPhu.com blog provides a novel/preliminary blog/internet-publishing channel for the scientific community. Sciphu.com is already a way of publishing that is completely free of (any kind of) charge, less rigid, more efficient and more interactive than many existing publishing models. SciPhu publishing is unlimited open-access and has the potential to reach a broad audience and aims be a pivotal tool to keep scientific authority intact, free and unpolitical.
  3. Project Background
    Sciphu.com is run by molecular biologists currently working in diagnostics. Our professional and educational backgrounds are university PhD degrees and small business life-sciences research activities within, biochemistry, genetics, cancer (and cell) biology and molecular biology. We are enthusiasts of web development and experienced users of many computer applications, but have little formal training in programming and web-design/develoment. Running a blog and possibly a future wiki however, requires only minimum skills to achieve adequate functionality.
  4. Methods
    While SciPhu today is a blog, future plans involve developing the site into a proper web-portal of some sort within the next 4-7 years. A wiki-based model is planned as the next developing step within the next 2 years. Such a wiki would have enhanced interaction with publishers and revieweres and the posssibilities for building a referee-community will improve over the blog-model. The blog model requires very little programming as most of the necessary tools are already provided gratis by hosting companies (Blogger/google, WordPress etc.) or by blogging community members. A wiki-based web-site requires more programming and web-design, but still at a level manageable by enthusisasts rather than requiring professionals. However, the goal is to involve web-developers to reach the maximum potential of this publishing model. A requirement will always be free of charge, open access, without restrictions, both for reading and publishing. A possible future business model is to offer peer-review expertise to commercial publishers or other commercial entities in need of scientific content quality control.

This publishing solution is not very high tech (but, it may evolve to be), it does not enjoy the recognition that many of the high ranked science journals do (but with active commenting, it can).

As with so many other things in professional life, the potential lies in the numbers. Only if many scientists are willing to use publishing channels like these, will it become a success.

Also at minimum two other issues need to be resolved to make the model into a proper publishing channel: 1) DOI numbers and 2) Proper backup and safe long term data storage. To solve the DOI-number issue, the use of the researchblogging (http://researchblogging.org/) icon and tracking is used, but this solution must be improved upon, presumably in cooperation with an exisiting publishing entity.

This is the age of the web and no-limit communication accessible to all. Our recommendation is: Say goodbye to the stale publishing standards of yesterday and come participate in the interactive self-justice of web-publishing.

More on the SciPhu model:

1. http://sciphu.com/

2. https://sciphu.wordpress.com/2008/04/07/launching-sciphucom/

3. https://sciphu.wordpress.com/2008/05/19/new-post-on-sciphucom-the-advantages-of-blog-publishing/

Publication phusis, Call for help

In Uncategorized on June 16, 2008 at 11:10 am

I have had many thoughts on how to present scientific data, and will have many more. SciPhu is, so far, the compilation of some of those, and blogging is the adverse event from trying to realize them. I have however come as far as I can on my own and need help to carry this project through.

This is what I have been planning: SciPhu is supposed to develop into a certification site for scientific thoughts, ideas and data. It is supposed to gather a large community of competent reviewers from virtually any scientific field. These reviewers are supposed to provide thorough peer-reviews of any scientific presentation as requested for evaluation on SciPhu.com. A successful review is supposed to give the author(s) a stamp to put on their presentation as a guarantee for scientific quality and credibility.

Through a FriendFeed discussion (original post by Bill Hooker) I came across this commentary on the problems of evaluating online publications. The author, Gary A. Olson, presents some solutions that are very similar to the principles I’ve worked out for Sciphu.

Clearly, the scholarly community needs to devise a way to introduce dependability into the world of electronic scholarship. We need a process to certify sites so that we all can distinguish between one that contains reliable material and one that may have been slapped together by a dilettante. We need to be able to ascertain if we can rely on a site for our own scholarship and whether we should give credit toward a colleague’s tenure and promotion for a given site.

And he proposes to establish certification bodies to achieve these goals.

The major professional and scholarly organizations in each discipline should (devise a certification process in which a site owner can apply to have a site reviewed and recognized, perhaps for a nominal processing fee. The site would be subjected to a formal and rigorous review by peers in the disciplinary area covered by the site.

Which is a very good description of what I wanted SciPhu to be like (except for maybe the fee, which should be for commercial users only). I have taken the liberty to replace with SciPhu in relevant places in the rest of these bullet points (the original text in brackets):

  • Only those sites meeting the highest standards should be awarded certification.
  • Once a site wins certification from SciPhu (the national scholarly society), it should be permitted to display that stamp of approval prominently.
  • The certification should remain in effect for a specific and limited amount of time (since a site can change rapidly and without notice). The site should regularly seek renewal of its certification.
  • SciPhu (Each disciplinary organization) should issue a resolution recommending that departments construe certification of a site as indicating that it has met the highest standards of scholarship.
  • SciPhu (Each organization) should maintain an online registry of certified sites.

A central site accessible to all is much more efficient than local evaluation bodies. Also the potential to gather a large collection of qualified referees is present only on a truly international site. Such a broad site would also be able to satisfy the open-access requirements in our Web/Science 2.0 future.

The SciPhu blog was set up as a starting point to gather a community of peer-reviewers. Making the blog successful is going to take a long time however, and given this commentary as well as the current interest in different publishing models, it seems wise to try and speed up.

To do this I need help. I need help setting up a good site, – a wiki perhaps. I also need help advertising this to the broader Scientific community and recruit referees. Even with help, achieving success is not going to be a stroll in the park. But without help it is going to be near impossible.

The end result may not end up as originally planned: names, concepts and strategies may/will change on the way, but I strongly believe that this is a path worth traveling.

I also think that Gary A. Olson is to narrowminded when it comes to requirements and scope of such a certification. Doing this online with a large community of referees makes it possible to get peer-review very quickly because reviewers would be accessible around the world 24-7. And there is no reason to limit such reviews to scientific publications. Any news-piece, advertisement or company information with scientific content could get reviewing through a SciPhu-like site. Extending reviewing to non-scientific publication forums is also the commercial opportunity, or business model if you will.

If you are interested in starting a broad and open-minded collaboration on this (and I really hope you are), please leave a comment, send me a mail or even better, join and use The Life Scientists room on FriendFeed for further discussions.

New post on Sciphu.com, the advantages of blog publishing

In Uncategorized on May 19, 2008 at 8:54 am

There’s a new article on SciPhu.com. It’s about pharmacogenetics…..but what I really want to communicate is how superior this way of publishing is:

Here’s what I have experienced while blog-publishing:

1. It is fast. I decided I would publish some data that I already had presented in a talk, since this data wasn’t really fit for a major article. It took me an hour or so to write up and publish the whole thing.

2. One of the reasons it is fast is that it is less rigid in its form. You yourself decide on formatting, wording, whether to use a reference list and how to format this list, or if you would rather have your references as hyperlinks in the text.

3. Papers published on SciPhu.com get hits from google searches. Since the whole text is searchable the hit-probability for people looking for your subject is higher than that on pubmed or any other site where searches are based on title, abstract and keywords. An example is the gel-drying paper which is hit daily by google searches like “SDS-PAGE cracking” or “vacuum drying PAGE” or similar. Although in this case, you could surely search laboratory method web-sites, the fastest way to find your information is probably a google search. This means that any paper published like this has the potential of high visibility. In addition you can get day by day hit statistics, which is probably interesting to many.

4. Communication with referees is interactive and the paper can remain fluid in its format and content. Since publishing like this is rapid it is also bound to be more error-prone. But, by interacting through the comments section, the paper can be continuously revised to correct errors or unclear phrasings. Also the number of referees can be many and since everyone can see the referee-comments, replying to these referees can be done by anyone, not only the authors. Thus, the papers will be less perfect to start off, but may end up better than those in a traditional peer review journal.

5. It is open access and free to everyone. Anyone’s welcome to publish anything as long as it is scientific. This is true scientific democracy.

7. SciPhu.com lacks the “rigid editor” entry point, and it always will.

This publishing solution is not very high tech (but, it may evolve to be), it does not enjoy the recognition that many of the high ranked science journals do (but with active commenting, it can).

As with so many other things in professional life, the potential lies in the numbers. Only if many of us scientists are willing to use publishing channels like these, will it become a success.

This is the age of the web and no-limit communication accessible to all. My recommendation is: Say goodbye to the stale publishing standards of yesterday and come participate in the interactive self-justice of web-publishing.

Launching SciPhu.com

In Uncategorized on April 7, 2008 at 12:55 pm

SciPhu= Science + Phusis

Phusis – An Ancient Greek word often translated as birth or nature (Wikipedia).

SciPhu.com is a blog based, open access and unrestricted publishing model. A hybrid in the spirit of Wikipedia and JustScience.

The idea behind SciPhu-publishing was to be able to publish and peer-review scientific information more efficiently than standard peer-reviewing. We wanted the reviewing process while retaining its scientific credibility, to be faster and less rigid. The answer, we found, is blogger-reviewing (which in this setting is just a fancy name for commenting on blog posts). Blogging is a good starting point since there are so many knowledgeable bloggers out there. While SciPhu may still be developed into a proper web-portal of some sort, the blog based starting point is now launched.

The end goal of SciPhu is to be able to quality control scientific information from any source, so that the twisted reality that sometimes ends up in the popular press (and ultimately in public opinion) can be promptly countered with proper accessible scientific information.

On the way towards this goal, we would like to provide a novel publishing channel for the scientific community. A way of publishing that is completely free of (any kind of) charge, less rigid, more efficient and more interactive than existing publishing models. SciPhu publishing is unlimited open-access and has the potential to reach a broad audience. At the same time, SciPhu aims be a pivotal tool to keep scientific authority intact, free and unpolitical.

Without input from (a lot of) you however, this effort will fail. Therefore, please feel free to contribute scientific content, recommend to friends and collegues or just come by to review/rate someone else’s work.

Invitation:

You are cordially invited to:

  • Write (blog) your own scientific article (or a review of a scientific topic).
  • Referee articles written by others.
  • Participate in scientific publishing in a new format.

You are invited to visit and join the SciPhu publishing community.