An Exciting Ferris Wheel of Science: New Features!

BrainSCANr’s circular graph has gotten a face lift and some new features. Jess has been busy the last few weeks adding some interactive elements to the circular graph. We’ve tossed the force directed graph in favor of a more geometric hyper tree. Visitors can still move nodes around by dragging and dropping them into new positions, but we’ve also added some new interactions as well.

Filter by category
Click a category in the circular graph’s key to remove that category from the graph.

Double-click to search
Double click the label of a node to search brainSCANr for that node. Note: you have to double click the label and not the node or it won’t work (we’re working on it).

Hover for clarity
Hover your mouse over a node to see that node’s connections highlighted as well as that node’s probable association with the search term and category. You will also see that node’s corresponding bar highlighted in the new...

...Histogram of probable association!
To better visualize the relative probable association of terms to the search term we’ve added a bar chart histogram to the circular graph. Hover your mouse over a bar to see the term, and probable association, you’ll also see the that term’s node highlighted in the circular graph.

Paper rejected and Health2.0

Sorry for the silence these last few weeks! With Jess back in school and Brad back from break, we've had to refocus on our "real world" work again.

To give a brief few updates, the brainSCANr manuscript was not even sent out for review (hooray!) so we decided to do a few presubmission inquiries at journals to see if it's even of interest to anyone. We're sure the paper will find a home, we're just not sure where.

Also, we've set up a Google Group for discussion. You can join it here:
http://groups.google.com/group/brainscanr



This past Saturday, Brad and Jess spent all day at the Health2.0 Developer Challenge (aka the "code-a-thon") at the Googleplex. This event was intended to pair researchers, developers, designers, and folks from the health industry to provide rapid prototypes to address social and person issues in health and medicine.

Neither of us really knew what to expect when we got there, but it ended up being a really cool experience. We started with Brad giving a brief presentation to the crowd about brainSCANr and why we built it. This piqued the interest of a few people in the crowd, and soon we were off in a group discussing some other possibilities with data-mining PubMed.

After about an hour, we were met by Alex from MEDgle (another great heath data mining service), who recognized Brad from Twitter.

We quickly decided on a tool to map where the primary research on health topics was being performed, and one of the members of the group (Sean) dubbed this "careMAPr".

You can see the rapid demo prototype here:
http://www.brainscanr.com/health_mapr/index.html



Right now this only works for ADHD for the USA, but the idea would be to allow anyone to enter any search term, and we would query PubMed for that topic. From the results we can identify where the primary research is being conducted. The user could even search by year to highlight only researchers who have recently published on a topic, for example.

The problem that we are trying to address with this site is how to connect the lay community with research specialists. The use case scenario we presented was this: imagine you are a parent whose child was recently diagnosed with ADHD. Maybe your kid was prescribed a drug as part of their treatment. But maybe your child also has another disease, and you want to know about research looking at the relationship between that disease and ADHD.

Right now, the best most people have is to do some Google searching (which can result in very dubious or even misleading information). You can talk to a psychiatrist, but maybe that doctor doesn't really know much about ADHD. How can you find a clinician in your area who does? We hoped that our site might serve as such a resource.

Anyway, the project was very fun, and we were all pretty surprised with how much we managed to put together in just a few hours. We're not sure if we're going to see this one through the the finish, but we hope to.

What do people think about the idea? Any suggestions?

Big update!

First of all, if you want to discuss site issues, please join the mailing list for general discussion:
http://groups.google.com/group/brainscanr/subscribe

It's been 3 weeks since we launched, and we've gotten a ton of feedback and made a lot of changes based on your suggestions. We've gotten over 15,000 views and over 100 user-submitted questions and comments. We've also submitted the paper for publication (so wish us luck).

Our biggest changes are as follows:



* Hierarchical view: you can view the links as either the original circular graph, or as a tree. This is a neat way to follow a path: click on a leaf in the tree to view its associaitons. The tree only pre-loads data five levels deep. Also, due to database issues, you can only view the hierarchical graph *after* the circular graph fully loads, If you click on the hierarchical view link before the circular loads, you'll need to reload the page.

* Lots of new terms! We've added white matter tracts, neurochemicals (hormones, transmitters, etc.), drugs, as well as other user-submitted suggestions for each category for a total of 627 terms and nearly 200,000 associations. You see see the full terms list here: http://www.brainscanr.com/Terms

* You can no search by common acronyms as well (e.g., "ACC" for anterior cingulate cortex)

* You can see publications that show associations between the search term and whichever term you select in the list below the graph.

* Click and drag objects: you can move the graph and nodes around, move the legend off the page, etc.

* Finally, lots of users have suggested adding a filter by association strength or category, a way to export images, or a way to remove the gray links between terms in the circular view. We're working on all of this, we promise! My wife is doing this work in her free time, so bear with us.

Anyway, thanks to everyone for making this such a hit, and thanks to our friends who helped: Amitai Shenhav, Curtis Chambers, Avgusta Shestyuk, and Kirstie Whitaker.