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:

Bradley Voytek Jessica Voytek brainSCANr careMAPr Health2.0

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:

Bradley Voytek Jessica Voytek brainSCANr careMAPr Health2.0

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:

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:

Bradley Voytek brainSCANr

* 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.


First week recap

ResearchBlogging.org Wow, it's only been a week, but brainSCANr has been quite successful!

We don't have a mailing list yet, so if you'd like to keep updated in the meantime, subscribe to our RSS feed or follow Brad on Twitter. You can see what people are saying about our site at the bottom of this post.

And if you haven't seen it yet, Brad's been quoted in a recent New York Times article on the human connectome.

So far we've had just shy of 10,000 pageviews from 75 countries including Kenya and Iran. The top 5 countries by pageviews are the US, UK, Canada, Germany, and Spain. I'm very pleased to see non-English speaking countries on this list.

Bradley Voytek brainSCANr

Social media seems to have played an important part in brainSCANr's spread, with over 30 shares on Facebook, nearly 100 tweets, and 45 points on reddit.

Here's our first glance at user trends and data examination. Because of the nature of our system, we can also examine search trends. Thus far, our top five search terms have been:

  • post-traumatic stress disorder
  • anxiety
  • amygdala
  • happiness
  • depression

as well as some more... interesting searches. Sex and money are popular: terms like "sex", "erection", "money", "neuroeconomics", and so on. Also "Google". Not sure what people are expecting to find, but I have promised friends to get them Google in the brain.

I'm curious as to what kind of neuroscience zeitgeist we can tap into with this platform. Mind you, the search rankings above are a bit skewed because of some direct links to searches from external sites.

For example, Vaughan Bell over at MindHacks wrote about brainSCANr, but he linked directly to the PTSD graph, so that's definitely skewing our rankings.

"Anxiety", "amygdala", "happiness", and "depression" seem to be purely organic searches on our users' part. That said, we do show "happiness" as a search example on our main page, so I'm sure that's skewing things a bit. Also, I wonder if the up-tick in "amygdala" searches aren't motivated by the recent studies about the amygdala that have been getting a lot of press.

By the way, I love the internet. The Bickart study shows how one's amygdala and social network sizes correlate. But the comments sections in the CNN blog I linked to above are where the real magic happens. The story states:

...keep in mind that the brain is plastic, and it's possible that the amygdala does increase in size in response to social activity.

To which a commentor said:

ExCUSE me? The brain is WHAT? Maybe on the Jersey Shore it is, but where I live, the brain is organic matter.

Anyway, we hope to do some more sophisticated analyses once more time passes and we get more data. I'd love to hear some suggestions regarding what kind of analyses we could do!

Bickart KC, Wright CI, Dautoff RJ, Dickerson BC, & Barrett LF (2010). Amygdala volume and social network size in humans. Nature Neuroscience PMID: 21186358

Feinstein JS, Adolphs R, Damasio A, & Tranel D (2010). The Human Amygdala and the Induction and Experience of Fear. Current Biology PMID: 21167712


User comments and suggestions

What a couple of days! Tomorrow I'll do an update on actual usage statistics, but for now I wanted to thank the community and talk a bit about our immediate plans, as well as show you all what people have been saying about brainSCANr.

First, I'm going to be a bit of a broken record for a bit here.

We don't have a mailing list yet, so if you'd like to keep updated in the meantime, subscribe to our RSS feed or follow Brad on Twitter. Because this is a community effort, we wanted to share what people are saying about our site at the bottom of this post.

Bradley Voytek brainSCANr dopamine

Anyway, Jess and I would like to thank everyone for their great feedback, support, suggestions, etc. We've already gotten 40 comments via the site's commenting system. Your suggestions have been great!

Based on users' suggestions, we've now got a list of over 150 new terms we plan on adding to the database after the new year. Mind you, we're both doing this in our spare time, so we can't really devote as much time as we'd like to this project. Nevertheless, we're very dedicated to it.

You'll notice we've got a bit of a teaser above showing our new category for neurotransmitters/neurohormones/etc.

Ladies and gentlemen, the ever-popular: dopamine!

You can see some obvious players here including most of the basal ganglia. There are also strong ties to disease: Parkinson's disease, addiction, depression, and schizophrenia, or to reward, and also a method: PET. This is likely due to the heavy use of PET in studying dopamine binding (such as with raclopride), and other factors.

So stay tuned!

And as promised, here are some great comments from our users, Twitter, etc.

First, some of these are biased from friends of mine, but hey, we'll take the compliments we get :)

"pretty sure that @bradleyvoytek is going to be the next @HansRosling with the brain data visualization that" via @curtischambers

"This is very very cool. Well done! I am always very appreciative when visual perspectives of research are available. Plus this type of thing is fun to sift through. My only wish is that you could provide an option to hide certain categories, or items to help clean up the map a little. But man, this is really great!" via reddit
(Note: we'll be adding that feature soon!)

"This is fantastic! This technology is good for all disciplines, not just neuroscience."
(Note: I've also gotten a lot of these types of comments, and I'd love to expand to other fields.)

"So cool! Brain-data viz. tool for neurogeeks!" via @carlettej

"Congratulations for the work! and specially for the initiative of sharing."

"Your work is making promising connections."

"Many congratulations and thanks for providing such an invaluable source and for helping the neuroscience community to survive the information overload that threatens to engulf us all."

"I think this would be useful if it included neurohormones and names of genes. Another thing that would be really cool would be to have an interactive, manipulable brain "minimap" in the corner where regions can be selected by visually exploring the virtual brain itself, by zooming in and out, selecting particular species, etc. It would be cool to be able to toggle particular protein densities/expression zones as colored overlays."
(Note: such good ideas! We'll do what we can to make these happen!)


"This is great. Really good job. Only one concern, I did not find a legend indicating what the different colors refer to."
(Note: our bad! Legend coming soon...)

"Wow this is great!"

"Awesome site guys!"

"Hi Bradley, Jessica, I just came across your site via a link from a friend, just want to feedback and say I think the concept and the execution of your idea is great."

"Jessica and Brad, Congratulations. This is a really cool tool. A few quick comments of user experience - - there is no legend I could find for the meaning of colors and symbols in the map. I guess users will get it anyway, but still..... If you are really quick, type a term like 'memory' and hit search or enter, you may miss the drop down list that opens, and then you get the Sorry, "memory" was not found' message. It took me a couple of times to understand that I should wait for the list and pick a more specific term. Anyhow, the site is great and I love the clean and simple design."
(Note: we're working on speeding things up and making the searches more organic as well)

"Hi Brad... this is great!! It's a resource that soooo many brain people are looking for not only when they need quick descriptions but even to get a quick summary of prior research on some area, phenomenon or theory. Plus, it looks like you've made it easy enough to use and the design is clean and pretty. Also I love how you made all of your resources and work public. Anyway, I thought maybe you could include the Brodman areas in here - either as stand-alone entries, or maybe joined with their descriptive counterparts (i.e. Broca's = BA45 & BA46). Good look with all of this. Congratulations, it looks great (I mean it)."
(Note: Brodmann areas will be tough... but we're looking into what we can do.)

"Eeeeeeee - I love it :) I'm going to blog about it when I get my Christmas cards done!! Also, can I put in a request for some white matter tracts? I'm really happy to make a list for you or send you a link to a good atlas?? Thanks guys, and congratulations!!"
(Note: we've got the list of white matter tracts, and the next update will include them!)

"Of course I'm sure everyone has their favorite term they'd like to add, but..."
(Note: haha oh my yes...)

"Really cool concept for a tool"

"Here it is! My vote for the best brain site for 2010. Brain function, modules and connections that are all backed by Pubmed articles all at your finger tips. Click on the manuscript link and you will see a pdf of connections in the brain that if you zoom in enough (lots and lots of zooming) you will be amazed at the detail and be able to follow the various connections."

"wow. this is all types of awesome."

So thanks for the feedback everyone! Keep the suggestions (and compliments!) coming. Cheers and happy New Year.


A brainSCANr holiday!

Bradley Voytek brainSCANr

This is the first post in what I hope will be the regularly-updated brainSCANr blog. I'm a huge fan of OkCupid's OkTrends, and since we've got a great way of looking across the more than 20 million articles in PubMed, we think we can do some clever things with it.

Because this is the first post, I think it's only right that we link to our home site: brainSCANr.com.

In future posts I'll be explaining the project a bit more, but in this post I wanted to highlight one of the amusing things my wife and I discovered that we can do with the medical literature.

Turns out, the words "holiday", "Christmas", "Santa", "Hanukkah", and "solstice" actually appear a number of times in the peer-reviewed literature on PubMed. That means we can add them to our database.

Note: this is obviously a silly, fun exercise, but we're not cooking the data at all. Everything we report is exactly as our algorithm found it in the literature. The interpretation of the results is, of course, totally made up for our own amusement.

I was fully prepared to see these terms associated with anxiety, depression, or other such morbid terms that might cause them to show up in the medical literature.

I was pleasantly surprised to find that holiday is most strongly associated with happiness and humor!

Christmas is similar, though it's also paired with hallucinations(?)

Oddly, Hanukkah is only associated with dementia. What's that about?! (Actually, it only appears with one paper, and that paper doesn't really discuss dementia, but it has the keyword associated with it).

Santa is fascinating! Apparently Santa is strongly associated with digit span, reaction time, visual memory, and trail making. I'd imagine those are all very important skills for a man with his occupation. All that counting of kids and their gifts (digit span), speeding around the world in one night (reaction time), remembering all those kids and their homes (visual memory), and finding the optimal route to hit all the houses (trail making). Totally makes sense! (Actually, that's a bit weird that all of those show up... I'm pretty amused).

Finally, solstice. Apparently solstice is all about rhythm, so dance on, my Pagan friends, and enjoy your winter solstice!

Best wishes from the brainSCANr crew (Jessica and Bradley Voytek).

Expect more (real) science from us here after the new year!

In the mean time, follow us here, add us to your RSS, or follow Brad on Twitter to keep up to date!