The Kitware Blog

Open Access: Stop the Research Works Act!

Luis Ibanez — Sun, 22 Jan 2012 21:28:31 -0500

The "Research Works Act" is a proposed legislation that will forbid
US Federal Agencies from requiring the public dissemination of the
results of Publicly funded research.

If passed, this legislation will destroy the NIH Public Access policy,
and preclude the adoption of similar Public Access policies by other
Federal Agencies.

More here at the Association of Research Libraries:

http://www.arl.org/sparc/media/blog/12-0106.shtml

A new bill, The Research Works Act (H.R.3699), designed to roll back the NIH Public Access Policy and block the development of similar policies at other federal agencies has been introduced into the U.S. House of Representatives. Co-sponsored by Darrell Issa (R-CA) and Carolyn Maloney (D-NY), it was introduced on December 16, 2011, and referred to the Committee on Oversight and Government Reform.

Essentially, the bill seeks to prohibit federal agencies from conditioning their grants to require that articles reporting on publicly funded research be made accessible to the public online.

The bill text is short and to the point. The main point reads:

"No Federal agency may adopt, implement, maintain, continue, or otherwise engage in any policy, program, or other activity that -- (1) causes, permits, or authorizes network dissemination of any private-sector research work without the prior consent of the publisher of such work; or (2) requires that any actual or prospective author, or the employer of such an actual or prospective author, assent to network dissemination of a private-sector research work."

Supporters of public access to the results of publicly funded research need to speak out against this proposed legislation. Contact Congress to express your opposition today, or as soon as possible.

It has been clarified that the bill interprets "private-sector research" to include all the papers that institutions produce under Federal funding support.

The proposed bill is backed by the Association of American Publishers,

however, several members of the association have indicated that they
do not support this Act.

In particular

You can join in opposing the Act

by signing the following Petition:

http://www.thepetitionsite.com/207/support-the-open-access-movement-stop-the-research-works-act/

TEDxCambridge - Hugo Campos fights for the right to open his heart's data

Luis Ibanez — Thu, 19 Jan 2012 18:23:35 -0500

http://www.youtube.com/watch?v=oro19-l5M8k

WIKIPEDIA Blackout to protest SOPA and PIPA

Luis Ibanez — Tue, 17 Jan 2012 21:14:35 -0500

From:

http://wikimediafoundation.org/wiki/Press_releases/English_Wikipedia_to_go_dark

<quote>

On January 18, 2012, in an unprecedented decision, the Wikipedia community has chosen to blackout the English version of Wikipedia for 24 hours, in protest against proposed legislation in the United States — the Stop Online Piracy Act (SOPA) in the U.S. House of Representatives, and PROTECTIP (PIPA) in the U.S. Senate. If passed, this legislation will harm the free and open Internet and bring about new tools for censorship of international websites inside the United States.

Over the course of the past 72 hours, over 1800 Wikipedians have joined together to discuss proposed actions that the community might wish to take against SOPA and PIPA. This is by far the largest level of participation in a community discussion ever seen on Wikipedia, which illustrates the level of concern that Wikipedians feel about this proposed legislation. The overwhelming majority of participants support community action to encourage greater public action in response to these two bills. Of the proposals considered by Wikipedians, those that would result in a "blackout" of the English Wikipedia, in concert with similar blackouts on other websites opposed to SOPA and PIPA, received the strongest support.

“Today Wikipedians from around the world have spoken about their opposition to this destructive legislation," said Jimmy Wales, founder of Wikipedia. "This is an extraordinary action for our community to take - and while we regret having to prevent the world from having access to Wikipedia for even a second, we simply cannot ignore the fact that SOPA and PIPA endanger free speech both in the United States and abroad, and set a frightening precedent of Internet censorship for the world."

We urge Wikipedia readers to make your voices heard. If you live in the United States, find your elected representative in Washington (https://www.eff.org/sopacall). If you live outside the United States, contact your State Department, Ministry of Foreign Affairs or similar branch of government. Tell them you oppose SOPA and PIPA, and want the internet to remain open and free.

http://en.wikipedia.org/wiki/Wikipedia:SOPA_initiative/Action#Summary_and_conclusion

http://opinion.latimes.com/opinionla/2012/01/more-opponents-for-pipa-and-sopa-emerge-on-the-right.html

Inscight Podcast - RFI response on Public Access to Federally Funded Research

Luis Ibanez — Mon, 09 Jan 2012 15:44:19 -0500

The Inscight Podcast

http://inscight.org/

just posted a new episode:

http://inscight.org/2012/01/08/episode-22-public-access-to-federally-funded-research/

On the response to two Request for Information (RFI) that the
US Office of Science and Technology Policy has posted in order
to gather feedback on how to improve Public Access to the Data
and Peer-Reviewed publications resulting from Federally Funded Research.

We talked recently about these RFI in our previous blog post:
http://www.kitware.com/blog/home/post/220

The RFIs are due on January 12th.

We will be wrapping up our public open response
on January 10th, by the end of the day.

This Podcast episode included the participation of:

Alan Ruttemberg (special guest)
Cameron Neylon (special guest)
Marcus Hanwell
Luis Ibanez (moderator)

The discussion touched very interesting topics, including:

Public funding of scientific research
Licensing of scientific articles and data
Career incentives for researchers
The culture of scientific research

Background

Alan Ruttenberg is Director of Clinical and Translational Data Exchange at the State University of New York at Buffalo. Until recently he was Principal Scientist at Creative Commons, working on the Science Commons, where he developed the Neurocommons, a large scale Semantic Web knowledge base of biological information. He co-chaired the (Web Ontology Language) OWL Working Group, and is a coordinating editor of the (Open Biological and Biomedical Ontologies) OBO Foundry, helping coordinate efforts to enable web scale data integration across the whole of biomedical science.

Cameron Neylon is a biophysicist and well known advocate of opening up the process of research. He is a co-author of the Panton Principles for open data in science, Founding Editor in Chiefof Open Research Computation as well as being an academic editor for PLoS ONE. He was named as a SPARC Innovator in July 2010 and is a proud recipient of the Blue Obelisk for contributions to open data. He writes regularly at his blog, Science in the Open(http://cameronneylon.net).

Marcus Hanwell is a R&D Engineer at Kitware, where he leads the Open Chemistry project. He is involved in the development of open source, cross platform scientific visualization and analysis software. Marcus is a strong believer in open science, open data and open source and proud member of Blue Obelisk. He works on Avogadro, Titan, VTK, ParaView, CMake, KDE and several other large open source projects.

Join Us: Shaping the Future of Federal Public Access Policy

Luis Ibanez — Wed, 04 Jan 2012 08:22:42 -0500

The Office of Science and Technology Policy (OSTP) is requesting public feedback to draft future policies on public access to data and peer-reviewed publications resulting from Federally Funded Scientific Research (FFSR).

To this end, OSTP has posted two Requests for Information (RFI) and responses are due by January 12, 2012.

At Kitware, we have decided to respond to both RFIs the "Open Source Way".

We have posted the draft of our responses in the two public documents below:

and we now invite you to join us in refining and extending the answers to both RFIs. The documents are open for editing by anyone with the link.

Please join us in improving the feedback that we are providing to OSTP, or if you are satisfied with the current content of the documents, please join us by signing the response at the end of each document.

If you want to suggest large changes to the document, please coordinate with others by using the annotation tools that you will find in the top menu bar.

We will close down edits on January 10th, to format the final document responses and submit them to OSTP by January 12th.

Also, watch for an upcoming inSCIght podcast on this topic, open access and federally funded research, which should be available sometime this week.

More about the Office of Science and Technology Policy:

OSTP's Mission

The mission of the Office of Science and Technology Policy is threefold:

To provide the President and his senior staff with accurate, relevant, and timely scientific and technical advice on all matters of consequence;
To ensure that the policies of the Executive Branch are informed by sound science; and
To ensure that the scientific and technical work of the Executive Branch is properly coordinated so as to provide the greatest benefit to society.

Strategic Goals and Objectives

Ensure that Federal investments in science and technology are making the greatest possible contribution to economic prosperity, public health, environmental quality, and national security.
Energize and nurture the processes by which government programs in science and technology are resourced, evaluated, and coordinated.
Sustain the core professional and scientific relationships with government officials, academics, and industry representatives that are required to understand the depth and breadth of the Nation’s scientific and technical enterprise, evaluate scientific advances, and identify potential policy proposals.
Generate a core workforce of world-class expertise capable of providing policy-relevant advice, analysis, and judgment for the President and his senior staff regarding the scientific and technical aspects of the major policies, plans, and programs of the Federal government.

Europe: Open Data Strategy

Luis Ibanez — Tue, 13 Dec 2011 19:10:03 -0500

The European Commission has launched an

Open Data Strategy for Europe

which is expected to deliver a €40 billion boost
to the EU's economy each year.

...

Commission Vice President Neelie Kroes said:

"We are sending a strong signal to administrations today."

"Your data is worth more if you give it away. "

"So start releasing it now: use this framework to join the
other smart leaders who are already gaining from
embracing open data."

"Taxpayers have already paid for this information,
the least we can do is give it back to those who
want to use it in new ways that help people and
create jobs and growth.”

In this short video release:
http://www.youtube.com/watch?v=MlcFKPyiRuw

Vicepresident Kroes states:

"The European Commission will be releasing its own data for Free
So, let's open up the rest of Europe public sector
let's deliver a single market for database products and services."

This article in The Guardian

http://www.guardian.co.uk/world/datablog/2011/dec/13/eu-open-government-data

further analyses the significance of the announcement:

"Firstly, the European Commission will lead the way
by pioneering open data policies and practises that
it would like to see adopted by EU member states.
"Eating your own dogfood", as software developers
affectionately call it.

They will open up documents and datasets from
across dozens of institutions"

"Secondly the Commission will put up €100 million
in financial support for research into "data-handling
technologies".

The European initiative include legislation proposals
for making data "Open by Default":

"...An 'open by default' rule for all 'public documents'
which will mean that they "can be re-used for any
purpose, commercial or non-commercial".
Though this isn't spelled out, 'documents' is probably
intended in a broad sense to cover datasets, as in the
current text of the Directive. The basic message is:
'if you can make it public, it should be open for everyone
to reuse'.

The announcement included a call to immediate action
for embracing Open Data, and raising awareness of its
importance.

UK Government Embraces Open Access

Luis Ibanez — Thu, 08 Dec 2011 20:17:32 -0500

The Guardian reports today:

http://www.guardian.co.uk/science/2011/dec/08/publicly-funded-research-open-access

that the UK Government has adopted the policy of making the outcome
of publicly-funded research to be published in Open Access venues.

In a report published on Monday:

"Innovation and Research Strategy for Growth"

http://www.bis.gov.uk/assets/biscore/innovation/docs/i/11-1387-innovation-and-research-strategy-for-growth.pdf

The Government states:

(page 76)

"Expanded Access to Research Publications and Data
6.6 The Government, in line with our overarching commitment to transparency and open
data, is committed to ensuring that publicly-funded research should be accessible
free of charge. Free and open access to taxpayer-funded research offers significant
social and economic benefits by spreading knowledge, raising the prestige of UK
research and encouraging technology transfer. At the moment, such research is
often difficult to find and expensive to access. This can defeat the original purpose of
taxpayer-funded academic research and limits understanding and innovation. We
have already committed, in our response to Ian Hargreaves’s review of intellectual
property, to facilitate data mining of published research. This could have substantial
benefits, for example in tackling diseases. But we need to go much further if, as a
nation, we are to gain the full potential benefits of publicly-funded research."

(Page 77)

"6.7 There are many successful international examples of open access research. At
Harvard, academics often grant the university a non-exclusive irrevocable right to
distribute their scholarly output for non-commercial use. Their articles are than
stored, preserved and made freely available through the Digital Access to
Scholarship at Harvard (DASH). The UK has various similar examples of good
practice:
• many universities and subject communities have their own digital open access
repositories;
• the independent Wellcome Trust ensure all research they fund is made freely
available in UKPubMed, supported by the Medical Research Council, an online
resource; and
• the British Medical Journal has been open access since 1998, with authors
making a payment to cover the costs of publication, including peer review."

"6.8 Government will work with partners, including the publishing industry, to achieve
free access to publicly-funded research as soon as possible and will set an example
itself.

• We have helped establish an independent working group chaired by Janet
Finch to consider how to improve access to research publications, including
publicly-funded research. This will report in early 2012.

• The Royal Society is considering how to improve the sharing and disclosing
of research data, both within the research community and beyond. It will report
in early 2012.

• Alan Langlands is chairing a task force to advise on improving the
accessibility of data within Government and its agencies, which will advise
on data linkage, conditions of access and data quality. This will report during 2012."

"6.9 The Research Councils expect the researchers they fund to deposit published
articles or conference proceedings in an open access repository at or around the
time of publication. But this practice is unevenly enforced. Therefore, as an
immediate step, we have asked the Research Councils to ensure the researchers
they fund fulfil the current requirements. Additionally, the Research Councils have
now agreed to invest £2 million in the development, by 2013, of a UK ‘Gateway
to Research’. In the first instance this will allow ready access to Research Council
funded research information and related data but it will be designed so that it can
also include research funded by others in due course. The Research Councils will
work with their partners and users to ensure information is presented in a readily
reusable form, using common formats and open standards."

In the US, we have an opportunity to catch up with the progressive initiative
of the British, by replying to the Requests for Information on:

Public Access to Peer-Reviewed Scholarly Publications
Resulting From Federally Funded Research

http://www.kitware.com/blog/home/post/197

http://www.federalregister.gov/articles/2011/11/04/2011-28623/request-for-information-public-access-to-peer-reviewed-scholarly-publications-resulting-from

The Insight Journal Reaches 500 Published Articles!

Julien Jomier — Wed, 07 Dec 2011 14:41:53 -0500

The Insight Journal just received its 500th paper on November 30th!

This marks a milestone on the progress of Open Science and the promotion of Reproducibility in Scientific Research. The wide adoption of the Insight Journal by the ITK community is evidence that progress is possible, and that a community of committed individuals can trigger and sustain change.

The idea of the Insight Journal originated from the initial experience of implementing many image analysis algorithms in ITK, and realizing how insufficient traditional journal publications are when it comes to specifying the software implementation of any algorithm. At the time, it was quite evident that something has been lost in the practice of scientific research: The fundamental rule by which a researcher should communicate the outcome of her research work by describing it in enough detail for anyone else to be able to replicate it. The popularization of software as a day-to-day tool in the practice of scientific research has not been followed by a corresponding modernization in the means of publishing scientific results. The standard publication venues were still: 10 pages papers at single space, two columns with black and white static images, and it took two years for them to go from submission to publication.

The Insight Journal was conceived as a quantum leap in technical and scientific publications, by asking the fundamental question of "What would you need in order to replicate the work described by the authors? ". When attempting to answer this question, very quickly it became evident that we needed: (a) all source code, (b) input data, and (c) parameters; used in the computation of the original work, and that all these materials should be made available to both reviewers and readers.

The Journal readily adopted, what was at the time the nascent Open Access movement, and chose to enable authors to keep the copyright of their papers, and license them for any one to use, under the terms of the Creative Commons by Attribution License.

The Journal also implemented an infrastructure for systematically testing the source code accompanying every submitted paper. Since every paper is expected to be submitted with source code, data and parameters, it becomes possible for the Insight Journal infrastructure to extract the source code from a paper submission, configure and build the code, and then proceed to run it on the input data that is also provided by the authors along with the paper. The results of the entire process are then posted online as a first review of the paper.

Another novelty of the Insight Journal was to revert the order of publication and review. That is, instead of waiting for a paper to be reviewed before it gets to be published, in the Insight Journal, the paper is first published online (within 24 hours after submission), and then it is open for public peer-review by the community. The reviews are public and non-anonymous, and evolve into a forum-like conversation. Authors are also allowed and encouraged to post revisions to their papers, in particular as a response to comments posted by the reviewers.

With the visionary support of the National Library of Medicine, in the form of A2D2 funding, the Insight Journal came online in 2005. The first fully open-access, reproducible article was published in July 2005. Now, six years later, the Insight Journal has reached 500 published articles. This represents an average of over 80 published papers a year.

With 2,480 registered users, and 819 community reviews, the Insight Journal has become an integral part of the ecosystem surrounding the Insight Toolkit. This is the direct mechanism for community members to share their developments with their peers. This level of adoption clearly shows that there is a community that truly appreciates the importance of reproducibility in the practice of scientific research, and understands that the main purpose of publishing is to share information with their peers, not to be used as a surrogate for measuring productivity.

Over the past five years, the Insight Journal has become a central place for open-access and has been hosting open-access articles for the MICCAI conferences and other events. We have also extended the Insight Journal to other open-source communities with the VTK Journal and are looking to extend it further.

Continuing on this success we have recently made several improvements to the Insight Journal. In particular we are trying to keep the website up to date with the latest technology and integrate authors and readers suggestions. We are looking forward to adding another 500 articles to the Journal.

The Insight Journal was made possible thanks to the visionary support Dr. Terry Yoo, at the National Library of Medicine via the following grants and support contracts:

A2D2 Journal - 2005
ITK Maintenance Contract 2006-2009 - N01-LM-4-3508
ITK Maintenance Contract 2009-2010 - HHSN276200900852P
ITK Maintenance Contract 2010-2011 - HHSN276201000516U

This committed support to the creation of Reproducible Research Journals preceded the current renaissance of appreciation for reproducibility in Science.

Once is not Enough

Luis Ibanez — Sat, 03 Dec 2011 11:51:11 -0500

This Week's issue of Science magazine carries a Special Issue on

Data Replication & Reproducibility

This issue...

Open Science Now!

Luis Ibanez — Mon, 14 Nov 2011 12:44:12 -0500

In this TED talk,

http://www.ted.com/talks/michael_nielsen_open_science_now.html

Michael Nielsen builds up the argument for Open Science.
He eloquently identifies the root of the problem:

"If you are a young researcher...
You may think that the [...] Wiki is a wonderful idea, in principle,
but you also know that writing a single mediocre paper
will do more for your career and your job prospects than
a long series of brilliant contributions to such a site."

Nielsen continues analyzing the misalignment between the goals
and principles of scientific research and the incentives and
reward structures used to motivate and evaluate scientists:

"...Scientist are not paid or rewarded for sharing data.
...It is all about publishing papers."

This statement illustrates the great irony of the problem:
That "Publishing" is what gets in the way of "Sharing",
or to make it more evident, what is wrong with this situation is that:
"Publishing" gets in the way of making data "Public."

"Publishing", which should have been the mechanism for "making public" the information gathered during the scientific research process, is frequently the reason why scientists will NOT share information generously and efficiently. Scientists are motivated to keep information to themselves until they manage to exchange it for "productivity points" in the process of publishing papers in high reputation journals, or even in not-so-high-reputation ones.

Nielsen raise his concerns about the status quo:

"There is so much knowledge that is still locked up"
"Scientists hold the computer code they write"
"They hold their best ideas"

His talk concludes with raising our hopes by identifying the
mechanisms by which we could change the status quo:

"We would like to change the culture of science.
We want to change the values of individual scientists
so they start to feel it is part of their job to share their
data and share their best ideas".

In particular, he makes the Economic connection with funding:

"Any publicly funded science should be open science"

This is perfect timing to remind us that the Science and Technology Policy Office, the organization that advises the President of the United States on Science Policy matters, is asking for your feedback on whether Federally funded
research should result in Open Access papers, and Open Data sharing.

http://www.kitware.com/blog/home/post/197

The two corresponding Requests for Information links are:

Public Access to Digital Data
Resulting From Federally Funded Scientific Research

http://www.federalregister.gov/articles/2011/11/04/2011-28621/request-for-information-public-access-to-digital-data-resulting-from-federally-funded-scientific#p-4

Public Access to Peer-Reviewed Scholarly Publications
Resulting From Federally Funded Research

http://www.federalregister.gov/articles/2011/11/04/2011-28623/request-for-information-public-access-to-peer-reviewed-scholarly-publications-resulting-from

The deadline for responses is January 12, 2012.

The Kitware Blog

Open Access: Stop the Research Works Act!

TEDxCambridge - Hugo Campos fights for the right to open his heart's data

WIKIPEDIA Blackout to protest SOPA and PIPA

Inscight Podcast - RFI response on Public Access to Federally Funded Research

Join Us: Shaping the Future of Federal Public Access Policy

OSTP's Mission

Strategic Goals and Objectives

Europe: Open Data Strategy

UK Government Embraces Open Access

Public Access to Peer-Reviewed Scholarly Publications Resulting From Federally Funded Research

The Insight Journal Reaches 500 Published Articles!

Once is not Enough

Open Science Now!

Public Access to Digital Data Resulting From Federally Funded Scientific Research

Public Access to Peer-Reviewed Scholarly PublicationsResulting From Federally Funded Research

Public Access to Peer-Reviewed Scholarly Publications
Resulting From Federally Funded Research

Public Access to Digital Data
Resulting From Federally Funded Scientific Research

Public Access to Peer-Reviewed Scholarly Publications
Resulting From Federally Funded Research