Open Science talk at the 2014 NIAID bioinformatics festival

Dan is giving a talk today at the 2014 NIAID bioinformatics festival.  The meeting is being live streamed from the NIH campus. If you’d like a preview, the slides are now available on slideshare.

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New PLOS Open data policy

PLOS one logoPLOS has announced some changes to their publishing policies, and these changes are great news.  The new PLOS policies will go a significant way towards encouraging open data and open source.  Although the announcement itself is somewhat vague on the subject of source code, the actual PLOS One Sharing Policy is excellent:

…if new software or a new algorithm is central to a PLOS paper, the authors must confirm that the software conforms to the Open Source Definition, have deposited the following three items in an open software archive, and included in the submission as Supporting Information:

  • The associated source code of the software described by the paper. This should, as far as possible, follow accepted community standards and be licensed under a suitable license such as BSD, LGPL, or MIT (see http://www.opensource.org/licenses/alphabetical for a full list). Dependency on commercial software such as Mathematica and MATLAB does not preclude a paper from consideration, although complete open source solutions are preferred.
  • Documentation for running and installing the software. For end-user applications, instructions for installing and using the software are prerequisite; for software libraries, instructions for using the application program interface are prerequisite.
  • A test dataset with associated control parameter settings. Where feasible, results from standard test sets should be included. Where possible, test data should not have any dependencies — for example, a database dump.

However, the one loophole is that they allow for code that runs on closed source platforms in “common use by the readership”  (e.g. MATLAB), although it must run without dependencies on proprietary or otherwise unobtainable ancillary software.  That “common use” loophole could potentially be a mile wide in some fields.  Is Gaussian a common use platform in computational chemistry and therefore exempt from this new policy?   If so, the policy is a bit toothless.  I’d like to see the limits and bounds of the “common use” loophole more clearly stated.

The announcement makes PLOS ONE a much more attractive place to send our next paper.

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On the Science “Sting”

Science magazine (a closed-access publisher) does a “sting” on crappy OA journals (and boy are there lots of these), and Michael Eisen points out how this sting is more about how crappy peer review is at catching bad science (even at Science).  Here’s the best quote from Eisen’s response:

“To suggest – as Science (though not Bohannon) are trying to do – that the problem with scientific publishing is that open access enables internet scamming is like saying that the problem with the international finance system is that it enables Nigerian wire transfer scams.

There are deep problems with science publishing. But the way to fix this is not to curtain open access publishing. It is to fix peer review.”

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A Bechdel test for scientific workshops

After attending two recent scientific conferences, one which was gender balanced, and one which was so gender-imbalanced that it engendered snarky out-of-band twitter comments, it struck me that we might need a Bechdel Test for scientific workshops.  The Bechdel test is a simple test for movies.  To pass the test, a movie has to have:

  1. at least two [named] women in it,
  2. who talk to each other,
  3. about something besides a man.

Seems simple, right?  You’d be amazed at just how few popular movies pass the test, including some set in universes that were originally designed for equality. (I’m talking about you, Star Trek reboot.)

Here’s an analogous test for scientific workshops or conference symposia.  Does the workshop have:

  1. at least two female invited speakers,
  2. who are asked questions by female audience members,
  3. about their research.

Again, this seems simple, right?  But you’d be shocked how few scientific conference symposia or workshops can live up to this standard.  I suspect this depends strongly on specific research fields. 

Rigoberto Hernandez has been talking about advancing science through diversity for quite a while.  I finally got to hear him speak about the OXIDE project on this latest trip, and he’s got a lot of great things to say about how diversity can strengthen science. I think one great way to help is to point out the good conferences we attend which live up to this standard.

Rigoberto also happened to be one of the organizers of the gender-balanced conference, which was also one of the best meetings I’ve ever attended.

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OpenScience comes of age

In 1998, Open Science seemed like a pretty obvious projection of basic scientific principles into the digital age.  I didn’t think the ideas would meet much, if any, resistance from the scientific community.   And in October 1999, Brookhaven National Lab sponsored a meeting called Open Source / Open Science that, in retrospect, was a pretty utopian gathering.  There were a lot of the current OpenScience community members present at the meeting (notably Brian Glanz and Greg Wilson).   It felt like everyone would be convinced to do Open Source & Open Data science in short order.

The past 14 years have been instructive in just how long it can take to make cultural changes in the scientific community.

So, it was an amazing experience to be present when the Office of Science and Technology Policy (OSTP) announced the Champions of Change for Open Science.  These are 13 incredible individuals and organizations with great stories about sharing their science.  It feels like we’ve made significant motion on implementing policies that are friendly to Open Science.   I should note that we’re particularly happy to see OSTP use the phrase Open Science, and not the more narrow terms: Open Data or Open Access.  I’m hopeful that Open Source will also be part of science policy going forward.

openscipostersThere was a second group who got the opportunity to present at this event at a poster session later that day.  I haven’t seen the list publicized elsewhere, but these are some sharp folks who deserve recognition for their work.  I’m going to highlight some of these in the coming week.  Here’s the list of posters:

  1. Richard Judson & Ann Richard from the National Center for Computational Toxicology presented on “ACToR & DSSTox: EPA Open Information Tools for Chemicals in the Environment”
  2. Tom Bleier, Clark Dunson & Michael Lencioni from the QuakeFinder project presented on “Electromagnetic Earthquake Forecasting Research”
  3. David C. Van Essen from WUSTL presented on the “Human Connectome Project
  4. Heather Piwowar & Jason Priem presented a poster on “ImpactStory: Open Carrots for Open Science”
  5. Jean-Claude Bradley (Drexel) and Andrew Lang (Oral Roberts University) presented a poster on “Open Notebook Science“.
  6. Dan Gezelter (that’s me) presented on “The OpenScience Project“.
  7. John Wilbanks from Sage Bionetworks presented on “Portable Legal Consent – Let Patients Donate Data to Science
  8. Matt Martin from the National Center for Computational Toxicology presented on “ToxRefDB & ToxCastDB: High-Throughput Toxicology Resources”
  9. Brian Athey and Christoph Brockel presented on “The tranSMART Platform: Accelerating Open Science, Data Analytics and Data Sharing”
  10. Alexander Wait Zaranek, Ward Vandewege & Jonathan Sheffi from Clinical Future, Inc. presented on “Transparent Informatics: A Foundation for Precision Medicine

It was an intense day, and I’m delighted that Open Science has finally come of age.

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Open Science Champions of Change

Congratulations to new White House “Champions of Change” for Open Science - all well-deserved!   It is fantastic to see Open Science getting public and welcome recognition from OSTP. A number of other great people from the Open Science movement will be at the ceremony at the White House today.    I’ll be there to give the aforementioned Open Science poster.  I’m looking forward to connecting with some people, including a few who I haven’t seen since the OpenSource/OpenScience conference at Brookhaven National Labs way back in 1999.

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OpenAPIs for scientific instrumentation?

382119_573424529339454_1784469895_nAn interesting question from Dale Smith:  Are there OpenAPIs for remote sensing and monitoring of scientific instruments?  Dale pointed us at this very cool RSOE EDIS alert map as an example of what could be possible with distributed consumer-grade sensors that had OpenAPIs.   I can imagine a number of very cool things that could be done with distributed weather or earth motion sensors.  Are there software tools out there that make querying these sensors easy?

(One suggestion,  however, would be for the RSOE EDIS to look for a slightly less ominous-sounding motto).

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OpenScience poster

OpenSciencePoster.001

I’m giving a poster in a few days about openscience.org, and it has been a very long time since I’ve had to make a poster.  This one turned out quite text-heavy, but I wanted to make a few arguments that seemed difficult or impossible to translate into graphics.   A PDF (9.3 MB) of the draft is available by clicking the image on the right…

Comments and suggestions, as always, are quite welcome.

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Great OpenScience news today

Lots of fantastic OpenScience happenings in the news today:

  • The G8 Science ministers support open data in science with one of the strongest statements I’ve seen: “To the greatest extent and with the fewest constraints possible publicly funded scientific research data should be open…”    See more on this at the Open Knowledge Foundation blog.
  • Mozilla has opened the Mozilla Science Lab, and appointed two great people to run it.  Kaitlin Thaney managed the science program at Creative Commons and has been named the director, and Greg Wilson, who has been involved in Software Carpentry from the beginning has also been appointed to the team.
  • Yesterday’s US Supreme Court ruling that genes cannot be patented is a clear Open Science victory.   I’m not sure how to parse the cDNA portion of the ruling, however. More details on the decision here.
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Playing with MultiGraph

multigraph-logo72x72I’ve been playing around with a cool JavaScript library called MultiGraph which lets you interact with graphical data embedded in a blog post.   The data format is a simple little xml file called a “MUGL“.   Here’s a sample that took all of about 10 minutes to create:

Note that you can pan and zoom in on the data.   For those readers who are interested, this data is the Oxygen-Oxygen pair distribution function, \(g_{OO}(r)\), for liquid water that was inferred from X-ray scattering data from  G. Hura, J. M. Sorenson,  R. M. Glaeser, and  T. Head-Gordon, J. Chem. Phys. 113(20), pp. 9140-9148 (2000).

Inserting this into the blog post involved uploading two files, the javascript library itself and the MUGL file. After those were in place, there were only two lines that needed to be added to the blog post:
<script type="text/javascript" src="http://www.openscience.org/blog/wp-content/uploads/2013/05/multigraph-min.js"></script>
<div class="multigraph" data-height="300" data-src="http://www.openscience.org/blog/wp-content/uploads/2013/05/gofrmugl.xml" data-width="500"></div>

One thing that would be nice would be a way to automate the process of going from an xmgrace file directly to the MUGL format.

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