[Insight-users] The Insight Journal: Zen and The Art of taking researchers out of the Dark Ages of scientific publishing
Luis Ibanez
luis.ibanez at kitware.com
Thu May 22 13:52:26 EDT 2008
Hi Ali,
Thanks a lot for your comments.
We are very happy that you have brought up this point.
The Insight Journal was conceived as a vehicle for taking
our field out of the Dark Ages of obsessive publishing and
zealous closeness to the Bright Future of the Openness
that the information Age has made possible for us to enjoy.
In that quest, the Insight Journal took on many features
that, at the time, were revolutionary in the context of
scientific publishing.
Let's list some of them:
0) Full electronic publication (no-paper)
1) Not requiring copyright transfer from authors
2) Using Creative Commons by Attribution licenses to
allow redistribution and the creation of derivative works
3) Requiring verification of reproducibility
which implies to require authors to make available
- source code
- data
- parameters
4) Performing open/public non-anonymous peer-review
5) Allowing any reader to be a reviewer
6) Publicly rating reviewers
7) Allowing authors to post revisions (corrections
and improvements) to their papers.
8) Performing continuous peer-review.
(A paper is never "accepted" or "rejected" it is
simply in continuous state of being rated).
Items (1) and (2) are the cure against the Copyright obsession
that Authors, Journals, Scientific and Technical Societies and
Conferences have been infected with.
The purpose of scientific publishing is to disseminate information.
Ubiquitous Copyright cripples the dissemination of information in the
Internet Age, when almost any operation requires to "copy" data from
one computer to another. Copyright is a collection of exclusive rights,
but nobody is "forced" to exercise the rights. We can simply take the
stands of: "My Paper is Copyrighted, but I let anybody to copy it,
distribute it, create derivative works, and perform public displays
of it".
Item (3) is simple and pure scientific honesty and transparency.
A publication that can not be reproduced, is not a scientific
publication. It is just "advertisement". The practical requirement
for reproducing reports in our domain, is to have available the
source code, data and parameters required to run an algorithm.
Items (4)(5) come down to *really* implementing peer-review.
Our peers are all the readers of a Journal. They are the same kind
of people who publish in a Journal. Peer-review MUST NOT be restricted
to "domain experts" because they lack the natural receptivity for
revolutionary ideas.
Items (6) is a safeguard to prevent bad reviewers to taint the
record of a good publication.
Item (7) is the result of placing readers at the top of the priorities
of a Journal. What we want is to make sure that readers have the best
information available to them. If an author makes a mistake in a paper,
then it is in the best interest of readers to allow an encourage the
author to make corrections in the paper and to post the corrected
version. Since the cost of keeping both versions online is negligible,
then there is no problem in maintaining multiple versions available and
letting readers access all of them.
Item (8) is the recognition that some publications may be
"ahead of their time", and their importance may not be recognized
at the moment they are submitted, but maybe two or three years later
as the field advances in a certain direction. Item (0) made possible
to do this, because we are not subject to the artificial deadlines
associated with having to "go to press".
-----
All that being said,
The disastrous diseased state in which our field has been pushed by
the "publish or perish" obsession, and the greediness of Journals and
Scientific Societies for generating revenue out of restricting the
dissemination of information, is so profound that it is very hard to
convince everybody to move out of the current Darkness towards the
Openness of the Information Age.
Our best hope was that the current generation of undergrads and graduate
students would adopt these methodologies as the natural mechanism for
sharing technical information, and that, as the older generations
retire in the coming 10 to 25 years, the scientific community will
be naturally renewed with an open minded population, free of the
fears and complexes associated with the absurd idea of our time that
"information is a form of property".
Surprisingly, the appreciation for these new approach to publishing
has not been limited to the youngest generations, and we have been
fortunate to see that scientists who are honestly interested in the
advancement of the field have been driven to adopt some of the features
of the Insight Journal.
The challenge, however, is that not everybody in our community is
ready for this transition. Some are attracted to some of the Insight
Journal features, but still afraid of other features.
For example: Nobody, (to my knowledge) have complained about the
papers being online, authors retaining copyright or using Creative
Commons licenses.
Some, however, are concerned about open-peer reviews,
Others are resisting to sharing their source code and data (and the
reasons behind the resistance may require another long email to be
analyzed properly).
We have faced therefore a question of
"fundamentalism" versus "pragmatism"
And the question is:
Do we force everybody to adopt the ten or so features of the
Insight Journal, and we create a binary partition of the field
into those who are hopelessly lost in the Dark Ages of physical
paper publishing, and those who have evolved and adopted the
technologies of the Information Age.
or
Do we welcome shades of gray, and encourage Conferences and Workshops
to adopt *at least* some of the features of the Insight Journal.
We decided to take the second option.
Mainly with the hope that, once this larger population get exposed
to the efficiency of information dissemination provided by the
Insight Journal, they may overcome their fears and be more willing
to adopt the other features.
Your email is indeed a great milestone in the right direction.
When readers of Journals *request*, and later *REQUIRE*, and later
*DEMAND* that papers must include the full disclosure of all the
elements that are required for reproducing the work, (e.g. source
code, data, parameters) then we have a good opportunity to move the
field forward.
Please *continue sending email* to the authors of papers who decided
not to share their source code, data and parameters. Please cc those
emails to the ITK users list.
Please *send email* to the organizers of Workshops who decided to
hold a "paper-only" event, without any trace of reproducibility
verification. Please cc those emails to the ITK users list.
Please *send email* to the funding agencies that supported these
authors. Whether they are public or private, it is important for them
to hear that the times are changing and that there is a demand for
scientific transparency, that must overcome the decadent practice of
just publishing for the sake of raising a metric of 'intellectual
production'.
Keep in mind, however, that the authors who submitted to these
workshops, did so under the rules set forward by the workshop
organizers, and therefore, were not expected or required to
share their source code, data and parameters.
What we face here is a vicious circle situation, in which Workshop
organizers didn't dare to require full disclosure of reproducibility
for fear of scaring authors to publish/participate in their workshop.
Authors, not being required to evolve, decided to fall back on the
traditional method of sending a PDF only publication.
It is of the utmost importance that readers of the Insight Journal
let authors and workshop organizers know that
* Obscure publishing is not acceptable anymore
* Lack of reproducibility is not an honest way to publish
Keep those emails coming.
Regards,
Luis
-------------
Ali - wrote:
> Julien,
>
> Thanks for clarifying this. It would be also helpful to hear from people
> from the other point of view.
>
> It is appreciated that it took them a long time and lots of energy or
> some considrable funding to achieve what they reported and they feel
> unsafe to publish it as open source. Having said that, if it took them N
> months to implement the idea, and if I am interested to extend the idea,
> it will also take me about N months to re-implement it -- the paper
> does NOT make it easier for other people to re-implement. This
> substantially decreases the chance of re-using ideas.
>
>
> -Ali
>
>
> >
> > Ali,
> >
> > I very much agree with you and we certainly don't want to go away from
> > the Insight Journal philosophy. I'm glad we are thinking along the same
> > lines.
> >
> > So now for the long story. MICCAI workshop papers are not going to be
> > included in the conference proceedings, therefore you would probably
> > never have heard about these papers, unless someone put them on a
> > website, etc... For this reason, we proposed to host the papers for
> > these workshops on the Insight Journal, so that people can access them,
> > publicly review them and interact with the authors.
> > We have strongly encouraged (and are still encouraging) authors to
> > submit code, data and other materials as part of their submission, but
> > we are not enforcing it for these workshops.
> >
> > > I do not see much point in publishing something like: 'if
> > > you do such and such steps, in principle, you should get such and such
> > > results'. Almost anyone can claim this on paper, but, where is the
> > > implementation?
> >
> > That's what traditional publishing has been doing for years. It is a
> > matter of trust and scientific ethics.
> > The Insight Journal is trying to promote open-science and "converting"
> > people is not that easy, we just hope that offering the IJ to these
> > workshops is going to be a first step and will benefit the scientific
> > community.
> >
> > Julien
> >
> > Ali - wrote:
> > > Julien,
> > >
> > > I was not aware of that, I had the idea that it is the policy of
> Insight
> > > Journal to publish the obvious dependencies of the paper, such as the
> > > code, as well. I do not see much point in publishing something
> like: 'if
> > > you do such and such steps, in principle, you should get such and such
> > > results'. Almost anyone can claim this on paper, but, where is the
> > > implementation?
> > >
> > > I honestly do not see the point of publishing in this style, can
> someone
> > > make this clear to me about code-less papers? Is this all about
> > > copyright? Isn't Insight Journal all about 'copyme'?
> > >
> > >
> > > -Ali
> > >
> > >
> > >
> > > >
> > > > Hi Ali,
> > > >
> > > > Thanks for the report. The PDF should be at least part of the zip
> > > archive.
> > > >
> > > > The Insight-Journal is being used for some of the workshops at the
> > > > upcoming MICCAI conference (Sept 2008). Some workshops don't require
> > > > submission of the source code (as much as we wanted them to),
> therefore
> > > > source code might not be present. Feel free to review the paper and
> > > > request the source code to the authors :)
> > > >
> > > > You can download the paper at: http://hdl.handle.net/1926/1371
> > > >
> > > > Julien
> > > >
> > > > Ali - wrote:
> > > > > The following paper comes with empty zip files. Is this a system
> > > error or is the paper supposed to lack the corresponding code?
> > > > >
> > > > >
> > > > > -Ali
> > > > >
> > > > >
> > > > > Hello,
> > > > > A new submission has been added to the Insight Journal.
> > > > >
> > > > > Title: Cardiac motion estimation using multi-scale feature points
> > > > > Author(s): Becciu, Alessandro
> > > > > Abstract:
> > > > > Heart illnesses influence the functioning of the cardiac muscle
> and
> > > are the major causes of death in
> > > > > the world. Optic flow methods are essential tools to assess and
> > > quantify the contraction of the cardiac
> > > > > walls, but are hampered by the aperture problem. Harmonic phase
> > > (HARP) techniques measure the
> > > > > phase in magnetic resonance (MR) tagged images. Due to the regular
> > > geometry, patterns generated by
> > > > > a combination of HARPs and sine HARPs represent a suitable
> > > framework to extract landmark features.
> > > > > In this paper we introduce a new aperture-problem free method to
> > > study the cardiac motion by tracking
> > > > > multi-scale features such as maxima, minima, saddles and corners,
> > > on HARP and sine HARP tagged
> > > > > images.
> > > > >
> > > > > Download the paper at: http://hdl.handle.net/1926/1371
> > > > > Review the paper at: http://insight-journal.org
> > > <http://insight-journal.org/>
> > > > >
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