US-IALE Meeting

I received notification recently that I’ve received the NASA-MSU Professional Enhancement Award to attend the US-IALE 2010 Meeting. So it’s a good chance if you want to meet and talk some ideas.

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R Bloggers – the network

Just as the name implies, R Bloggers is a compendium of over 40 blogs that deal with different aspects of R.

It looks like a gold mine.

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What the Antartic waters sound like

Gizmodo recently featured an interesting scientific project that records the sounds from under the ice shelf in Antarctica. The best thing is that the sound is transmitted (almost) live on the Internet.

Two options for listening are available:

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My technology tools

Talking the other day with a labmate I suggested him some tools I’m using. I thought it could help someone else to make a list of some of the technological tools I use everyday. Some may help you, some may not be for you, but the main lesson here is this: technology is supposed to help us, not hinder. If you feel trapped by a particular gadget or software, look for alternatives.

  • Operating system (Ubuntu Linux) – I won’t go into the Mac vs PC debate here. I’m using Ubuntu Linux 95% of the time. The other 5% is for games and software that can not be run anywhere else, like ArcGIS. Each release of Ubuntu is easier to use. In particular, version 9.10 includes a “Software Center” that allows you to search easily for programs or descriptions. You can download a “live CD,” which is a CD-ROM image you can burn to a CD-R and then boot directly from the CD; you will be using Ubuntu without making any change to your computer. Worth a try.
  • Data in the cloud (Dropbox) – One of the most impressive and simple working applications to store files in the cloud is Dropbox. It automatically keeps file synchronized and keeps a history of the file changes. I am using their free account (2GB) to store files that I am working on or might need for reference on working projects. Note: I still have some referrals for an extra 250MB for free, just use this link.
  • Note keeping (Tiddlywiki) – A few months ago I began a search for a note-taking application to replace a notebook. The reason was simple: convenience. I tried using MediaWiki, but it was too much overhead for just me and it required a live Internet connection. Now I’m using Tiddlywiki, which works like a local wiki that is completely contained in a single file. The file is loaded locally, so no network connection is needed. It uses a combination of CSS and JavaScript to allow to use tags, links, and search of your notes. I keep the file in the Dropbox folder.
  • Task tracking (MonkeyGTD) – A system based on TiddlyWiki that lets you manage tasks based on the Getting Things Done program. You can find more info here.
  • Office applications (OpenOffice) – Most users do not need all the extras that MS Office has, OpenOffice opens and edits all MS Office formats and the best thing is that is free and open source. Some features may not be present, but for most students it will be enough.
  • Data analysis and statistics (R) – One of the most important open-source scientific tools is R, which is based on S-Plus. It was even featured in a New York Times article. Check the Comprehensive R Archive Network for packages, tutorials, and many publications.
  • Password management (KeePassX) -Too many passwords, not much memory to keep them. KeePassX is a password manager that will allow you to keep many passwords and other information encrypted with a single password. I like it because it also has a password generator with many options.
  • Document encryption (Truecrypt) – To protect my documents in my laptop in case it is stolen, I have all my documents inside an encrypted partition using Truecrypt. It is a free and open-source encryption software that only uses strong methods. It is a must-have to reduce the risk of identity theft.
  • Update: Literature management (Aigaion) – In this digital age, PDFs are a convenience but it is still complicated to keep them organized. I’ve been using Aigaion for a while, it runs on PHP/MySQL and can import literature in several formats as well as hold the PDF files for each paper.

I hope this list helps someone else.

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A web-based sound archive management and visualization system

About two years ago we started a project in which we we collecting several hundred recordings each week at different sites. In an instant, browsing this archive became a problem due to the difficulty in browsing files that we need to listen and look at their spectrograms to make sense. Back then I started to work on a web-based system to manage and browse the archive. What was then is now an open-source and free software system available in version 1.0: Pumilio.

The system is written mostly in PHP, with some Python scripts and Javascript. PHP provides the main interaction and communication with the MySQL database. Python is used to analyze the structure of the sound files and generate spectrogram and waveform images. Javascript, in particular the JQuery framework, provide some checks, notices and interactivity. The system has two sound players, one is based on Prototype and Soundmanager2 and was made by Freesound.org. The other is the JW Player.

A bit further into the project, we needed a way to select regions in the spectrograms. I designed a way to do it from a web browser with a bit of Javascript code, using the JCrop plugin, in addition to the PHP code.

Future enhancements include options for ultrasonic and infrasonic recordings, more tools, and improved archive and metadata management tools. If you are interested in testing it there is a demo available or you can download the current version from SourceForge.

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Finding the nearest point using only SQL

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Amphibians are not so wimpy after all

One of the most over-used reasons amphibians are endangered is that they are more sensitive to environmental changes and contaminants than other groups, making them “canaries” for the environment. This reason is mentioned without evidence and only backed with the reasoning that they have permeable skin and many are exposed to more environments due to their amphibious life history. A recent paper by Jacob L. Kerby, Kathryn L. Richards-Hrdlicka, Andrew Storfer, and David K. Skelly, tested this idea, apparently for the first time, by comparing the response of amphibians to toxins like pesticides and heavy metals.

The study found that amphibians are not more sensitive in at least three of the groups evaluated, which calls into question the justification of portraying them as canaries for the environment. Hopefully this study will force some to test their justifications, since, in my opinion, amphibian declines have been exaggerated in some cases by abusing poor quality data. Better data sets and better analyses will yield possible answers and research questions while poor quality research will only lead to more confusion.

Kerby, Jacob L., Kathryn L. Richards-Hrdlicka, Andrew Storfer, and David K. Skelly. 2009. An examination of amphibian sensitivity to environmental contaminants: are amphibians poor canaries? Ecology Letters 12: 1-8. doi: 10.1111/j.1461-0248.2009.01399.x

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An interesting discussion on the p-value

The p-value is one of those important concept in statistics that we all get mixed up (unless you are a statistician I guess). ScienceNow (from AAAS) did an interview with Victor De Gruttola, chair of biostatistics at the Harvard School of Public Health, talking about what the p-value is, how to think about it and how to use it. The interview is the result of a discussion on the results of an AIDS vaccine trial, but the implications of the p-value cover most science.

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New automated recorder from Wildlife Acoustics

SM2Wildlife Acoustics have released a new version of their Song Meter automated digital recorder. Among the most interesting features are an even lower power consumption and twice the storage space.

It’ll be interesting to see where they take these boxes in the future.

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Mechanism of chytridiomycosis, caused by Batrachochytrium dendrobatidis, proposed

One of the most proposed causes for the declining amphibian populations has been the disease chytridiomycosis, which is caused by the skin infection by the fungus Batrachochytrium dendrobatidis. Although evidence for some populations linking the decline with the fungus has been limited, the mechanism by which the disease may kill the frogs was unknown, until now. A group of researchers from Australia and United States have published a paper in Science indicating that the fungus inhibits the transport of electrolytes, which ends up killing the frog.

Further studies should confirm and refine their findings.

Jamie Voyles, Sam Young, Lee Berger, Craig Campbell, Wyatt F. Voyles, Anuwat Dinudom, David Cook, Rebecca Webb, Ross A. Alford, Lee F. Skerratt, and Rick Speare. 2009. Pathogenesis of Chytridiomycosis, a Cause of Catastrophic Amphibian Declines. Science 326: 582. DOI: 10.1126/science.1176765.

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