Open Science Papers Science

Will 2012 be the year of open science publishing?

January 17, 2012 – 1:07 pm

The Research Works Act (HR 3699) seems to have launched a wave of criticism that may finally end the publishers unfair profit of science. This bill pretends to prohibit the federal government, which funds a lot of research, from forcing publishers to make scientific papers available for free. Right now the NIH has a policy that says all funded research must be available for free one year after publication.

The problem lies in that the publishers dictate a, usually ridiculous, price to access research that has been paid for by funds from the government or private foundations. The questions that everyone, scientists and taxpayer, need to ask are:

  • What are they bringing to the table?
  • Why do we have to put up with them?
  • Why are they making a lot of profit from our work while our libraries spend millions and keep cutting subscriptions?

The economics of the current model are not justified, an analysis revealed that we could publish all papers in the world using the PLoS ONE model and costs with just the profits of the two largest publishers: Elsevier and Springer. The HR 3699 has brought a lot of discussion because it will only benefit the publishers, not the scientists and definitely not the taxpayers.

Please join the discussion and contact your Congress representative.

Some other articles of interest:

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Bioacoustics Papers Science Software Soundscape Ubuntu

New paper on our software to manage sound archives

December 15, 2011 – 12:25 pm

The paper describing our software Pumilio has just been published in the Bulletin of the Ecological Society of America. Pumilio is a web-based sound archive and analysis tool.

Pumilio was created out of necessity. Our lab was collecting a lot of sound data and there was no system that could help us manage that amount of data. In addition, we used at least two operating systems (Windows and Linux) and some collaborators even use Mac. On top of that, some of us used Chrome, while some used Firefox. We started just putting files in folders in a network share. After a few hundred files there is no way of keeping track. Plus, we were wasting time each time we had to open a file in Audacity or Raven to see its spectrogram.

One of the first instances of this system was a simple database that would display rows of spectrograms with a Flash mp3 player on the bottom of each. Similar to the “gallery” view of the current version of Pumilio. The problem was generating all those spectrograms. Using R was easy, but took too long to write the png files. The function specgram() in Python crashed with our files (15 minutes). After a while, I stumbled upon a Python script written by the people of Freesound.org. This was a very fast script and I took it and implemented it.

Afterwards it was all step by step. A JavaScript plugin built to crop images over the web became a selection tool for zooming in a sound and filtering.

The main idea is to make it easy to navigate a sound archive using any modern computer. This means using cross-browser tools to allow the use of any modern browser. Blueprint enables a consistent CSS, JQuery takes care of most of the JavaScript and some of the styling.

Screenshots of Pumilio:

Main Menu

Browsing the archive

All the data of a sound file

The software is available for free under an open source license from the project website.

Villanueva-Rivera, Luis J. and Bryan C. Pijanowski. 2012. Pumilio: A Web-Based Management System for Ecological Recordings. Bulletin of the Ecological Society of America 93:71–81. doi:10.1890/0012-9623-93.1.71. PDF. Full text. Pumilio Website.

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Bioacoustics Papers Science Soundscape

Special Issue of Landscape Ecology: Soundscape Ecology

November 28, 2011 – 9:04 am

The journal Landscape Ecology featured a special issue on Soundscape Ecology in their November 2011 number with Bryan C Pijanowski and Almo Farina as guest editors. The issue featured nine research articles with an editorial by the guest editors.

The issue is opened with a preface by Barry Truax and Gary W. Barrett.

Springer has free access to this journal until December 31, 2011.

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Papers Soundscape

New publications on Soundscape Ecology from our lab

September 9, 2011 – 10:03 am

As part of an upcoming Special Issue on Soundscape Ecology in the journal Landscape Ecology, our lab has some papers available already online. These papers range from an introduction to the area, an introduction to working with sounds and soundscapes, and viewing soundscapes as a resource in need of management:

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Declining Amphibian Populations Science

Paper calls into question the chytridiomycosis hypothesis for amphibian declines

August 17, 2011 – 9:37 am

A new paper published in PLoS ONE by Matthew Heard, Katherine F. Smith, and Kelsey Ripp have called into question the hypothesis that chytridiomycosis is causing amphibian declines. The threat by this disease seems to have been exaggerated since there are few species for which the fungus is a threat.

When the new version of the Red List for amphibians was published a few years ago, under the name the Global Amphibian Assessment, I asked the same questions. Why assign chytridiomycosis as a risk for species for which there is no evidence? Even worse, it was listed as a threat to species for which there was evidence they were immune to the disease!

A figure in the paper is very revealing, out of the species that have listed chytridiomycosis as a threat, very few have any kind of evidence.

It seems that chytridiomycosis became the default cause for any kind of decline found in an amphibian population. This is a problem because conservation programs will waste time, money, and resources in controlling a disease without need. In addition, the uncertainty will not help to protect species that do need some help.

Hopefully this kind of publication will halt the alarm and put things into perspective. Scientists need to start proving that the disease is a real threat, they have had more than enough time.

Heard M, Smith KF, Ripp K, 2011 Examining the Evidence for Chytridiomycosis in Threatened Amphibian Species. PLoS ONE 6(8): e23150. doi:10.1371/journal.pone.0023150

Updated on 23nov11 to fix some grammar.

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Bioacoustics Papers Science Sensors Soundscape

New scientific field will study ecological importance of sounds

March 1, 2011 – 1:20 pm

PRESS RELEASE

Luis J. Villanueva-Rivera, from right, Bryan Pijanowski and Sarah Dumyahn collect data from a remote listening post that records sounds from the surrounding area. (Purdue Agricultural Communication photo/Tom Campbell)

WEST LAFAYETTE, Ind. – A Purdue University researcher is leading an effort to create a new scientific field that will use sound as a way to understand the ecological characteristics of a landscape and to reconnect people with the importance of natural sounds.

Soundscape ecology, as it’s being called, will focus on what sounds can tell people about an area. Bryan Pijanowski, an associate professor of forestry and natural resources and lead author of a paper outlining the field in the journal BioScience, said natural sound could be used like a canary in a coal mine. Sound could be a critical first indicator of environmental changes.

Pijanowski said sound could be used to detect early changes in climate, weather patterns, the presence of pollution or other alterations to a landscape.

“The dawn and dusk choruses of birds are very characteristic of a location. If the intensity or patterns of these choruses change, there is likely something causing that change,” Pijanowski said. “Ecologists have ignored how sound that emanates from an area can help determine what’s happening to the ecosystem.” read more »

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Data Science

Special Issue of Science on Data

February 23, 2011 – 8:55 am

The 11 February issue of Science was a Special Issue that contained a section on data. Seems to be an interesting overview, with perspectives from climate research, ecology, and other areas. The most troubling figure, from the introduction, was:

Just one of each five researchers have funding for data curation. This is a recipe for wasted efforts, increased redundancy, and wasted research opportunities.

The online issue’s table of contents is here.

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Cloud Computing Ubuntu

Installing a graphical desktop to Ubuntu on Amazon EC2

February 17, 2011 – 9:29 am

Amazon’s EC2 service offers an interesting diversity of cloud computing. From less than a dollar an hour, you can run a powerful virtual machine on their hardware. View my previous post on setting up an Ubuntu machine with R.

I was interested in playing some with this infrastructure, and now installing a graphical interface, GNOME, on a Ubuntu machine. After setting up an Ubuntu 10.10 machine from these instructions, set up remote access with these instructions: read more »

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Cloud Computing R Ubuntu

Getting Started with Ubuntu and R on Amazon’s EC2 cloud

February 14, 2011 – 10:52 am

Amazon EC2 is their “cloud” service, which means that you can run a virtual machine on their hardware. They have many basic VMs, which they call AMI, that you can use to start and setup your machine with the configuration and software that you need.

New accounts, since October 2010, on Amazon Web Services can have a year of free services of the basic varieties of their services. For example, they offer 5GB on the S3 storage and a “micro” virtual machine on their EC2 platform. The micro has a single Xeon E5430 2.66GHz CPU, 613 MB of RAM and 8GB of disk space. It is not much, but you can use it to play and learn to use EC2. You can also setup a machine configuration and then save it as an image (AMI) to create more powerful machines from that configuration. read more »

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Open Science Software

Publish your computer code: it is good enough

January 18, 2011 – 7:34 am

I just found this column in Nature discussing the need for scientists to publish the code they used. I’m still amazed that this is not getting more attention. If a proper-written Methods section is mandatory in a paper, why not the code that produced the results?

Among the excuses for not publishing the code (and the reasons why they are not valid most of the time) that the column identifies are:

  • It is not common practice.
  • People will pick holes and demand support and bug fixes.
  • The code is valuable intellectual property that belongs to my institution.
  • It is too much work to polish the code.

Even when the Methods section may be enough to be able to reproduce your results, why condemn someone else to go through the whole process of debugging some code to make it work? The code may not be pretty, may require some obscure software, or may be more convoluted than it has to be, but it is incredibly valuable and a time-saver for researchers. This kind of code is also very useful for students, it lets them learn how research is done in their area.

Of course, this requires some planning and careful file management, hopefully universities and societies will start promoting code publishing to make this practice more common.

Barnes, Nick. 2010. Publish your computer code: it is good enough. Nature 467: 753. doi:10.1038/467753a

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