Category Archives: Science

Bioacoustics Science Soundscape

Soundscapes are featured by the NSF!

February 7, 2012 – 8:43 am

The National Science Foundation published yesterday a note featuring our Soundscapes work!

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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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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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Science Sensors Tropical Ecology

I’ll attend the OTS-PASI Embedded Sensors course

July 28, 2010 – 2:11 pm

During the last two weeks of August I will be visiting Costa Rica for an OTS/PASI course on the use of embedded sensors for tropical ecology. Hopefully this kind of course will push forward the use of many kinds of sensors in tropical ecology. There is so much diversity in tropical forests that, in order to better understand these complex ecosystems, we need to use all the tools that are available.

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Bioacoustics Science

World Listening Day this Sunday, July 18

July 12, 2010 – 12:28 pm

This Sunday is the World Listening Day, a day set up to celebrate the practice of listening, raise awareness about issues about sound projects, and design and implement educational initiatives. The date is the birthday of R. Murray Schafer, author of The Soundscape.

Visit their website for more information and lets promote the listening of our world, there is more than car alarms, A/C systems, and noise out there.

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Data Science Software

“Data, data everywhere”

April 21, 2010 – 3:03 pm

I just found a special report from The Economist on data, “Data, data everywhere.” The report deals, in several articles, on the new trend of massive amounts of data available today. They cover mostly the business implications, but also scientific data. For example, the Large Hadron Collider:

[G]enerate 40 terabytes every second—orders of magnitude more than can be stored or analysed. So scientists collect what they can and let the rest dissipate into the ether.

Another quote that got my attention was:

Only 5% of the information that is created is “structured”, meaning it comes in a standard format of words or numbers that can be read by computers.

This means that very little of the data available can be easily imported to other computer systems for analysis. It will become very important to make data available in a way that other computers can use it, otherwise most of the time and cost will go in re-formatting data. It will be kinda like when transferring data from paper to a computer, one more time. We should make raw data available, but also raw data in structured form. A PDF is great for humans, but it sucks when trying to extract data from it. At least something like a comma-separated file should help this process a lot.

Another evident consequence is that scientists, and most notably the next generation, will need to know how to work with large amounts of data. Programming and databases will have to become part of the scientists education, so you better start sooner than later.

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