Software Usage in the Sciences: What do you use?

It comes as no surprise that computer software is widely used in scientific experimentation. The power of analysis afforded by computation has revolutionized and accelerated scientific progress to a truly astounding extent over the past 30 years (and even more so in the last 10). While technology pervades most every aspect of our lives, including how we cook, exercise, and relate to others via social media, the changes effected by software and computing power in the sciences (and industrial research and development) for the advancement of scientific endeavors, technological innovation and economic growth are most valuable for humanity, and should be the most well published.

Using JoVE search to find techniques using algorithms

Perhaps it’s just me, but these things may go without saying. More interesting than these broad statements is an understanding of specific ways that software and other computer based technologies are being used in experimentation, scientific visualization and sharing of ideas. This is an ever-expanding quest, as technologic advancement and the semantic web are progressing at a blistering pace. However, to begin to understand one small aspect of how software is used in the sciences, I turned to a JoVE search.

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This Month in JoVE

Want a preview what’s happening in JoVE?

In the October 2011 issue, we follow researchers into the Atlantic ocean as they study the movement of jellyfish in their natural environment. Over in Graz, Austria, scientists use an electron microscope to analyze the how a viral infection can change the structure of a leaf.

Click on the jellyfish to watch "This Month in Jove"

Back in California, researchers measure the cognitive impairments in rats treated with radiotherapy, or x-ray treatment. Radiotherapy is given to a person’s head to prevent or delay the spread of cancer to the brain, and the cognitive impairments in rats are similar to those found in cancer survivors.

Also in California, scientists demonstrate how to genetically manipulate human induced pluripotent stem cells— cells that can develop into any adult cell type.

In addition to the video articles featured in the video, this month JoVE will also present methods for measuring physical responses from people under stress, tracking the bursting of bacteria following infection, and visualizing the olfactory bulb through a window in the cranium.

Please note that this posts links to some articles that are not yet published. Keep checking back to see new articles throughout the month!

JoVE for the Developing World

Word that JoVE will now be offering free subscriptions to institutions in the developing world is making its way around the globe!

Award-winning science writer David Bradley, who is based in Cambridge, UK, recently wrote about JoVE on his blog Sciencebase:

JoVE Around the World

JoVE is hoping to address scientific information inequality across the globe and has now made free subscriptions to Journal of Visualized Experiments through the HINARI initiative to developing nations in South America, Asia and Africa.

JoVE was originally developed to increase productivity in biological research, and is the only science video journal indexed in PubMed so far. The journali publishes video articles demonstrating advanced experiments performed in major laboratories (including Harvard, MIT, Stanford and Yale).

According to it creators: “Seeing experiments, rather than translating text, saves scientists and students time and money when learning new research techniques.” They add that, “Access to this visual content is especially important in developing countries.”

JoVE for the devloping world.

Show and Tell— Sharing Science by Video

David Wheat wrote about JoVE and our recent partnership with HINARI on his blog, Science in Action. Wheat, who holds a degree in biology and started blogging in 2004, writes about science and math in plain English. Notable posts include “Why is Urine Yellow?” and “Do Cow Farts Cause Global Warming?

Here is what he had this to say about JoVE:

Show and Tell— Sharing Science by Video

The Journal of Visualized Experiments (JoVE) makes hands-on science available by video. Real scientists demonstrate their experiments on line to accompany their publications. A picture being worth a thousand words, and a video being worth at least a thousand pictures, this novel channel gives fellow researchers (and budding scientists!) around the world clearer access to experimental procedures. Now JoVE is offering free access to developing-country researchers.

Those of us who have tried to figure out just how research was done by reading the often-cryptic “Materials and Methods” sections of scientific publications can appreciate the value of this approach.

JoVE has teamed up with the Health InterNetwork Access to Research Initiative (HINARI) of the World Health Organization to provide this free access. Here is a press release about the initiative.

Many schools and libraries in developing countries cannot afford to subscribe to scientific journals, which are among the most expensive of periodicals (and highly profitable to their publishers). See this blog post by George Monbiot about the high cost of access to the scientific literature. I agree with his complaint that these very high pay walls prevent the wide dissemination of information that is essential to progress in science, and to its understanding by the public. “Secret” science is a sin, especially in our digitally connected world.

To keep reading, please click here.