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[Axiom-developer] Where literate programming could have a huge impact

From: daly
Subject: [Axiom-developer] Where literate programming could have a huge impact
Date: Tue, 10 Jan 2012 21:26:52 -0500

Publish the code and the data as well as the results.
People should be able to reproduce results without
contacting the original authors.

We really do need to raise the level of scholarship
in software and software-related science.


>From Alfredo Portes:


Scientists, Share Secrets or Lose Funding: Stodden and Arbesman
2012-01-10 00:00:13.0 GMT

     (For more Bloomberg View, click on VIEW <GO>.)

By Victoria Stodden and Samuel Arbesman
     Jan. 10 (Bloomberg) -- The Journal of Irreproducible
Results, a science-humor magazine, is, sadly, no longer the only
publication that can lay claim to its title. More and more
published scientific studies are difficult or impossible to
     It’s not that the experiments themselves are so flawed they
can’t be redone to the same effect -- though this happens more
than scientists would like. It’s that the data upon which the
work is based, as well as the methods employed, are too often
not published, leaving the science hidden.
     Many people assume that scientists the world over freely
exchange not only the results of their experiments but also the
detailed data, statistical tools and computer instructions they
employed to arrive at those results. This is the kind of
information that other scientists need in order to replicate the
studies. The truth is, open exchange of such information is not
common, making verification of published findings all but
impossible and creating a credibility crisis in computational
     Federal agencies that fund scientific research are in a
position to help fix this problem. They should require that all
scientists whose studies they finance share the files that
generated their published findings, the raw data and the
computer instructions that carried out their analysis.
     The ability to reproduce experiments is important not only
for the advancement of pure science but also to address many
science-based issues in the public sphere, from climate change
to biotechnology.

                    Too Little Transparency

     Consider, for example, a recent notorious incident in
biomedical science. In 2006, researchers at Duke University
seemed to have discovered relationships between lung cancer
patients’ personal genetic signatures and their responsiveness
to certain drugs. The scientists published their results in
respected journals (the New England Journal of Medicine and
Nature Medicine), but only part of the genetic signature data
used in the studies was publicly available, and the computer
codes used to generate the findings were never revealed. This is
unfortunately typical for scientific publications.
     The Duke research was considered such a breakthrough that
other scientists quickly became interested in replicating it,
but because so much information was unavailable, it took three
years for them to uncover and publicize a number of very serious
errors in the published reports. Eventually, those reports were
retracted, and clinical trials based on the flawed results were
     In response to this incident, the Institute of Medicine
convened a committee to review what data should appropriately be
revealed from genomics research that leads to clinical trials.
This committee is due to release its report early this year.
     Unfortunately, the research community rarely addresses the
problem of reproducibility so directly. Inadequate sharing is
common to all scientific domains that use computers in their
research today (most of science), and it hampers transparency.
     By making the underlying data and computer code
conveniently available, scientists could open a new era of
innovation and growth. In October, the White House released a
memorandum titled “Accelerating Technology Transfer and
Commercialization of Federal Research in Support of High-Growth
Businesses,” which outlines ways for federal funding agencies to
improve the rate of technology transfer from government-financed
laboratories to the private business sector.

                      Technology Transfer

     In this memo, President Barack Obama called on federal
agencies to measure the rate of technology transfer. To this
end, agencies such as the National Institutes of Health and the
National Science Foundation should require that scientists who
receive federal funds publish full results, including the data
they are based on and all the computer steps taken to reach
them. This could include providing links to Internet sites
containing the data and codes required to replicate the
published results.
     Exceptions could be made when necessary -- some information
might need to be kept confidential for national-security
reasons, for example. But standard practice for scientific
publication should be full transparency.
     Leaving this up to the scientific community isn’t
sufficient. Nor is relying on current federal rules. Grant
guidelines from the NIH and the NSF instruct researchers to
share with other investigators the data generated in the course
of their work, but this isn’t enforced. The NIH demands that
articles resulting from research it finances be made freely
available within a year of publication. But even if this policy
were extended to all government-financed studies, the data and
computer codes needed to verify the findings would still remain
     As Jon Claerbout, a professor emeritus of geophysics at
Stanford University, has noted, scientific publication isn’t
scholarship itself, but only the advertising of scholarship. The
actual work -- the steps needed to reproduce the scientific
finding -- must be shared.
     Stricter requirements for transparency in publication would
allow scientific findings to more quickly become fuel for
innovation and help ensure that public policy is based on sound

     (Victoria Stodden is an assistant professor of statistics
at Columbia University. Samuel Arbesman is a senior scholar at
the Ewing Marion Kauffman Foundation. The opinions expressed are
their own.)

Read more opinion online from Bloomberg View.

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For more on science: NI SCIENCE <GO>

--Editors: Mary Duenwald, David Henry.

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To contact the writers of this article:
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Samuel Arbesman at address@hidden

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