PHD explains open access and why it is necessary

Check out this video that explains what open access is and why it is so necessary.



Narrated by Nick Shockey and Jonathan Eisen and illustrated by  Jorge Cham, the genius behind PHD (Piled Higher and Deeper).

Posted in Data, Open Science, Papers, Science | Leave a comment

SeaBASS and career paths

A couple of weeks ago I participated in SeaBASS 2012, the BioAcoustics Summer School, a week-long course on marine bioacoustics that was offered for the second time at Penn State University. The course was sponsored by the Applied Research Laboratory at Penn State, the Office of Naval Research, the National Oceanic and Atmospheric Administration, and the Acoustical Society of America.

SeaBASS was a great opportunity to learn about the latest discoveries on marine bioacoustics and the questions many groups are trying to answer. In addition, we got to meet several researchers and graduate students from all over the world. I even had the chance to meet another Puerto Rican researcher that was going to her field site in Panama right after the course to work with bottlenose dolphins.

The course featured both lectures on theory and practical aspects, like problems dealing with the marine environment, calibration, and some cool hardware several research groups are using. There were also hands-on training on several software packages, like MMPE, Raven and Ishmael. It covered themes from basic acoustics in water to how marine mammals listen. Of course, there are many unknowns in all areas, it is our job to answer the questions that still remain. If you are interested, or are currently working, in the area, consider applying for the next time the course is offered.

One of the nights, the course featured a career paths panel, something that I hope most short courses start doing. In particular in this job market, where jobs in science are not what they used to be, it was quite inspiring to get a glimpse of how established researchers have dealt with their own careers. The one common theme across all presenters was that they did not end up where they originally planned. Some opportunities appeared to them, some others were chosen to solve conflicts with their family or significant other. In the end, we all learned that we must have our eyes open for when opportunities arise, even if they are not what we had planned.

Posted in Bioacoustics, Science, Sensors, Software | Leave a comment

I made the mistake of paying for Microsoft Office

My university, Purdue, has been offering discounted licenses of several software products. Some of these licenses carried restrictions like having to delete it after you graduate. This one is annoying but it makes sense, after all the idea is to hook the students, who are not earning money. Another restriction was that between Purdue and, in this case, Microsoft, they could unilaterally decide to end their agreement and void whatever license you paid for. I made this mistake. My advisor insists on using Microsoft Office, so I decided to buy myself a student copy to save some time when working with him on documents and presentations. Never again.

To my knowledge, Purdue has not made this announcement public. According to the licensing manager, less than 8,000 licenses for Microsoft products were sold last year (out of 48,000 students). Apparently, the rest of the students are using other alternatives, like Google Docs and pre-installed versions in their laptops. Interestingly, Open Office, now LibreOffice (a free and open source office suite), is not mentioned and it is not installed in the campus’ computers.

So, according to the agreement (I never thought that this would happen), my copy of MS Office will end this Summer. This is why people hate companies like Microsoft that restrict their users for no reason. There is no refund. There is no option other than paying, twice, for another student license for MS Office – or resort to piracy. There is also no institutional push for a standard, be it docx or odt, creating a mess of conflicting formats after pushing for years the Microsoft way.

If you create documents with the software of these type of companies, the moment you stop paying you have no way to access your documents and data. This is why open standards must be a priority in research and the academia. There is no reason to keep giving money to these companies that have such little regards to their users. I don’t mind paying for good software or services, what I do mind is when that software is taken from my hands for no reason other than greed.

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“Is silence going extinct?” in the New York Times

Last week, the New York Times had a story on the problem of noise and how hard it is to find a quiet spot, even in National Parks. My advisor got interviewed for the piece and it also features some cool sounds.

Posted in Science, Soundscape | Leave a comment

Soundscapes are featured by the NSF!

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

Posted in Bioacoustics, Science, Soundscape | Leave a comment

Will 2012 be the year of open science publishing?

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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New paper on our software to manage sound archives

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 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:10.1890/0012-9623-93.1.71PDF. Full textPumilio Website.

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Special Issue of Landscape Ecology: Soundscape Ecology

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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New publications on Soundscape Ecology from our lab

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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Paper calls into question the chytridiomycosis hypothesis for amphibian declines

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.

Posted in Declining Amphibian Populations, Science | 2 Comments