Open Source Science: How IT Can Improve Scientific Understanding

June 7th, 2013 | Articles, Job Search | No Comments »

Neurons

Can a mobile app outdo a telescope? Are web apps and 3D graphics engines ready to surpass microscopic imaging? The answers, in some cases, may surprise you.

These days, scientific breakthroughs aren’t exclusively made through the use of conventional tools. Web & mobile apps are becoming more prominent in the research process as IT professionals whip up solutions to augment the work of classically trained biologists, chemists, physicists, and astronomers. Welcome to the age of open source science.

With all the marzipan fluff of certain ravenously consumed apps (I’m looking at you Candy Crush Saga), it can be easy to forget that app developers can do a whole world of good. Scientific applications can bring up important questions, expanding research efforts from that of a cloistered group of white lab coats to the collaborative work of a diversified global community.

Game Changing Brain Puzzles

Mapping the intricate nerve connections of the human brain is the type of daunting task that may be beyond the limits of traditional methods and personnel. That’s why, one group of scientists at the Massachusetts Institute of Technology is testing a web application that may eventually shine some light on the otherwise opaque meandering of those critical connections.

The web application is called EyeWire and gives users the chance to map the branching neural connections found at the back of the eyes of mice. The app allows users to color in nerve cells, a surprisingly challenging task, on a 3D drawing of a slice of tissue. If the project is a success, this team may modify it for the study of the human brain.

Now, it may sound like an odd way to explore our neurons but Sebastian Seung, a neuroscientist with the Institute, says that these types of programs are essential. “There’s no way the professional scientists alone can analyze all of [these nerve connections],” he says, “we need people to help us.” According to Seung, even automated computer programs fall short of the accuracy that human users have when defining the boundaries of these connections.

Essentially, what would have taken a single neuroscientist 570,000,000 years to map the connectivity of the entire brain will – with the 35,000 users and counting registered through EyeWire’s website – take considerably less time. That brings us all the more closer to true neurological understanding.

Catching a Different Kind of Bug

When most developers think of debugging, they don’t imagine their work going towards the eradication of a wriggly, 1 mm long worm. That is the very objective of OpenWorm project.

On this project, microbiologists are calling on the open source IT community to try to simulate and better understand the movements of the roundworm: a microscopic parasite that disproportionately causes big problems. Though they’re made up of a simple number of cells (just under 1,000), these organisms seem to have enough guile to efficiently locate food and reproduce all without being picked off by comparatively larger predators.

They boggle the mind and have pressed scientists to turn to an entire family of IT applications to better decode these creatures.

worm

One is a 3D simulation engine called Geppetto which animates the movements of these squiggly pests. Another is an Enterprise application server called Eclipse Virgo. Together, they have been released as a downloadable, open source prototype which advanced coders can dissect and alter in outside-the-box ways. With this prototype, the project can make exponential strides that were otherwise inconceivable.

Shooting for the Stars

For years, only those in possession of a telescope were capable of mapping out the night sky but as urban centers grow, light pollution is making that a difficult task. Astronomers are looking to grab further intel on stargazing conditions across the globe and using mobile applications to clear up the big picture.

Both Android & iOS platforms sport apps that empower an army of citizen scientists to collect data on the constellations above their heads. Through the Dark Sky Meter and the Loss of the Night App, users can measure light pollution and add to a real-time map that analyzes trends over time and provides researchers with insights on how to control it.

Getting Involved

Best of all, these aren’t the only open source projects in the works that call on the skills of IT professionals. New scientific research projects are starting all the time and calling on the IT community to help collect data and test hypotheses through open source contributions.

Even if you’re just interested in adding to scientific research any way possible, you can get involved with open source initiatives through websites like SciStarter, which regularly identifies scientists in need of an extra hundred hands and minds.

So really, the question maybe not be whether an app can outdo a telescope but whether you can make an app that can outdo a telescope?

by James Walsh

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