Gene-disease annotation with Mobianga

Over the summer, an enterprising high school student named Nishant Mandapaty approached our research group about doing a project with us.  He found us through the "Crowdsourcing Biology" group that we created for the Google Summer of Code program.  To make a long story short, he has been doing good work for us ever since, quickly learning what he needs to on his own.

His primary contribution so far is a nascent game for collecting gene-disease connections called Mobianga!.  He is planning to submit the results of an experiment using this game to the Intel Science Talent Search, a prestigious national science fair.  But, he needs help if he is going to succeed!  If you know anything about genes and their relationship to disease or are capable of using resources like OMIM, PubMed, and Google find such information he needs you to play a few games!  Even better, invite several of your friends to play a few games.

Help a 17 year old computational biologist reach his dreams, play Mobianga! today!

Mobianga contest at the American Society for Human Genetics annual Meeting

Next week, I will be attending ASHG at the Moscone Center in San Francisco.  I will be presenting a poster (number 3584W) on Wed., Nov. 7 from 3:15-4:15 about game applications in biology.  If you come by and can prove that you have played a game of Mobianga by identifying your name on the leader board I will give you a prize!  I will also be giving out a more substantial prize at the end of the meeting to the top-scoring player as of the morning of Saturday November 10.  Details on the ASHG Mobianga contest will be distributed at my poster.

Technical details

Mobianga! makes use of the human disease ontology to provide the opportunity to easily annotate genes at varying levels of granularity.  For each gene challenge, you start at the top of the hierarchy (e.g. choose between 'disease of cellular proliferation' and 'disease of mental health') and you work your way down to specific diseases.  At each step you earn points based on an algorithm that assesses the precision of the annotation and degree of consensus among prior players in a manner similar to the Herdit game for music tagging recently published in PNAS.  

The game is implemented as a Python-powered Web Application that runs in the Google App Engine.  The code is open source and he would welcome collaborators.  The game is intended to eventually run smoothly on phone-sized browsers (the name Mobianga came from 'the mobile annotation game'), but this optimization has not yet been achieved.  Anyone that wants to help, please get in touch.

Ack .. PhD comic hits home again..

 As time goes on I'm shocked to see myself transition fully into Mike from the PhD comic..  Thanks (I think) for spotting this one Richard!

graddatical

Graddatical : a short period of study-related travel taken by a graduate student.

During the long and winding course of graduate school, I've been lucky to have the opportunity to take two graddaticals - the second of which is just finishing up today.  As I've defined it above, a graddatical is an opportunity for a graduate student to, in increasing order of importance:

1. take advantage of the main perk of student life - the relative freedom from strict time and location constraints (which is typically discussed in relation to the lack of money with which to frivolously enjoy that freedom)
2. take a break from your current surroundings which, particularly in the Nth years, may start to have the look and feel of a prison chamber regardless of the beauty of the campus or the character of your associates
3. spend time working closely with experts in your field who you would normally only ever interact with over email (if they bothered to respond to you)

The value of this last attribute of the graddatical really can't be overstated.  Though my personal path through the PhD jungle has probably been even more meandering than most, I think its safe to say that many students may find that their research takes them in many unexpected directions that can end up leaving them feeling somewhat, shall we say, intellectually lonely.  For example, you may come into and even select your graduate program thinking that you are going to be working on computational vaccine design, then follow a trail that leads you through machine learning through the semantic Web into classification theory; and from there wind up working on things that only people who manage libraries for a living actually care or know anything about.  Needless to say, its likely that you are now the only one in your lab and possibly your department and possibly even your city that cares about the semantic underpinnings of the Dewey Decimal system and thus find yourself with no one to talk to about your work.  A graddatical is what you need.

To have a successful graddatical:

1. identify some one who seems to be interested in what you are interested in and seems to know a lot more about it than you do
2. find a way to get to know them - ideally through a strong network connection like your supervisor
3. ask if you can come visit their lab/office for a week (most people will be happy to let you come hang out - if they aren't, you don't want to waste your graddatical on them)
4. make cheap travel arrangements..  this may be tricky but can almost always be done.  Keys for getting there are to either a) pick  somewhere that isn't too far or b) pick somewhere that is not too far from a conference you can get funded to attend somehow.  Another financial and fun related consideration is to request lodging on the couch of graduate students in the lab you are visiting.  Again, you will be amazed how welcoming people can be and it will make your experience both cheaper and more enjoyable.

Now, students of the world, go forth and get graddatical!