Chandra Clarke

Award-winning entrepreneur. Author. Professional Optimist.

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Join the fight against malaria

April 18, 2012 By Chandra Clarke Leave a Comment

AnophelesGambiaemosquito
Ouch! (Photo credit: Wikimedia Commons)

Some diseases get more headlines than others, for reasons having to do with news cycles, politics, and interest groups. One disease that ought to be getting much more press is malaria.

Malaria is typically spread by mosquitos, and is common in tropical and subtropical climates. Estimates on spread and mortality vary greatly, in part because poorer (and harder to track) populations tend to suffer disproportionately from the affliction. However, the World Health Organization’s 2011 World Malaria Report suggests that at least 655,000 people died from malaria in 2010, while a 2012 study in The Lancet suggests that the figure is actually closer to 1,238,000.

From a citizen science perspective, you can help combat malaria by helping researchers understand it. By downloading the BOINC client (explained in this post), you can contribute computer time to the Malaria Control project.

The project is designed to model the best ways to fight malaria, by analyzing databases of health system descriptions, intervention costing, and vector bionomics, and testing various approaches in simulations. The goal is to find the most effective way to fight the disease while reducing costs, and more importantly, reducing the risk of creating new, resistant strains of malaria.

To participate, simply download and install the BOINC client, and then set your configuration options in the software to dedicate time to the Malaria Control project. Your computer will do the rest.

The Malaria Control project is managed by the Swiss Tropical Institute, and is supported by the Bill and Melinda Gates Foundation.

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Grabens, cracks, and straight rilles, oh my!

April 13, 2012 By Chandra Clarke Leave a Comment

The NASA Lunar Reconnaissance Orbiter
The NASA Lunar Reconnaissance Orbiter (Photo credit: Wikipedia)

Our Moon is a thing of quiet grey beauty, and it has fascinated us for centuries. Those of you who can’t get their fill of looking at it at night should check out Moon Zoo, a project designed to review the many hundreds of images generated by the Lunar Reconnaissance Orbiter.

Much like the previously discussed Moon Mappers, Moon Zoo asks you to find and classify craters using a simple point-and-click interface. This project goes one step further, and also asks you to compare two images to determine which has the most boulders in the aptly-named “Boulder Wars” exercise. You can also highlight features of interest, like the grabens, cracks, and straight riles of my title.

Moon Zoo has a couple of nice extras. With the My Moon Zoo feature, you can effectively zoom out and see exactly where you’ve ‘visited’ when you’ve reviewed images of various craters and features; this is a good way to get some context and perspective. The Live! feature allows you see what’s happening on Moon Zoo in real time: an Earth map is displayed next to a Moon map, and both automatically scroll to show you that, for instance, UserJane from Vancouver is viewing images from the Ocean of Storms. It’s fun to watch the action for a while, as it gives you a real sense of participating in a group activity.

The site’s “moonometer” notes that to date, Moon Zoo players have reviewed more than 3 million images, which is the equivalent of 301 Chicagos, or .024 Australias. Just in case you were wondering what the Chicago to Australia conversion rate was.

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Scientific progress goes BOINC

April 11, 2012 By Chandra Clarke Leave a Comment

The new BOINC logo. Русский: Логотип BOINC с и...
The BOINC logo. (Photo credit: Wikipedia)

By far the easiest way to get involved with a citizen science project is to let your computer do all the work: sign up for a so-called distributed computing project, install and configure some software, and voila! You’re contributing valuable CPU time to an important cause, and you don’t even have to break a sweat.

Today, I’m going to talk a bit about the concept of distributed computing, why it’s important, and then I’ll point you to one of the major platforms being used to do distributed computing.

Prior to the advent of distributed computing, researchers with big projects requiring a lot of computer power had to try to score time on their university’s super computer. As you might imagine, competition for a time slot was fierce: there were lots of problems requiring lots of computer cycles, and resources were limited. You could wait weeks or months for a slot that might or might not be long enough to accomplish your project goals, and heaven forbid something should go wrong with the system in the meantime, as that would mean further delays.

Then along came the rise of personal computing. While home computers certainly aren’t super computers, they are reasonably powerful, and more to the point, unless the user is actively playing an intensive PC game or rendering 3d movies, the CPU is actually idle most of the time. Someone lit upon the idea of harnessing all of those idle CPU cycles, and “distributed computing” was born.

The concept is this: break up a very large project into millions of smaller tasks, and then hand off those tasks to thousands of computers.You still need a decent server to communicate with all the remote devices, and a robust software program to coordinate all of those tasks, but both of these were cheaper to implement than additional super computer time.

The most popular distributed computing platform is called BOINC. The short form stands for the Berkeley Open Infrastructure for Network Computing, and it was originally developed to support the SETI@home project (a program designed to analyze radio signals, searching for signs of extra terrestrial intelligence). First started in 2002, the platform currently has more than 295,000 volunteers running the program on just under 1 million computers. That might sound like a lot, and indeed it provides projects with a fairly spectacular amount of computational power. However, it’s really only scratching the surface of what’s available. Think of it: how many computers do you have in your home alone? How many are in your office?

BOINC currently supports just over 40 projects, which I’ll cover in separate posts. But you don’t have to wait for me… go ahead and check out the software and see if there’s something you’d like to help out!

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Skip FarmVille: play Phylo instead

April 4, 2012 By Chandra Clarke Leave a Comment

 

Phylo (video game)
The Phylo home page

Phylo is a nifty Flash-based game designed to help researchers figure out multiple sequence alignments (MSAs).

MSAs are ways of aligning DNA or RNA to discover areas that are similar. By looking at alignments, biologists may be able to detect shared evolutionary origins, functionally important sites, or mutation events. In addition to explaining the evolution of a genome, they may be able to  trace the source of certain genetic diseases. While computers can certainly be used to try to find patterns, humans also have excellent pattern-detection abilities, and Phylo harnesses that with the game interface.

To play the game, you look at two strips of material, represented by colour-coded blocks. Your goal is to change the position of the blocks (by dragging them) to maximize the number of matches between the two strips. It’s trickier than it looks; you may have to introduce gaps, or remove gaps and play with it for a while to get it right. There’s a video explaining how it works here; there’s also a PDF explanation and a slide show.

The data collected will be incorporated into computer models and used by researchers at McGill University in Canada.

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