Hacking Away

by Gabrielle DeMarco on July 1, 2011

The great team of web scientists in our Tetherless Research Constellation (TWC) invited me to witness my first hack earlier this week. They had teamed up with the world’s largest publisher of scientific research, Elsevier, to bring hackers from far and wide together at the Rensselaer Technology Park for an all-night hackathon.

When most people outside of the world of bits and bytes think of a “hack,” we picture some misguided young prodigy trying to break into government websites or crash the PlayStation Network. But, hacks are not always destructive. In fact, “to hack” can be very constructive and that was what I saw take form at the first-ever Elsevier/TWC Health and Life Sciences Hackathon. In just 24 short hours, hackers created new applications that literally change the way scientists and doctors can do their work!

The hackathon was opened by our own Tetherless professors Deborah McGuinness and Joanne Luciano. They introduced the group to the work within the constellation and some of the extensive work with open government and health data that the hackers could utilize for their new application ideas. After a few more crash courses, wise words, and rules from Elsevier and others, the hack began.

After working through the night, several hackers stood triumphant.

Tied for second place were Nick Benik and Deon Robinson. Robinson, an RPI sophomore who was only introduced to this kind of technology three weeks ago, developed a very useful app called Mobile Researcher for Android phones. The app transforms any of the thousands upon thousands of scientific journal article on the Elsevier system from text to speech. The app turns them into a media file that can be paused and played over and over again. I can only imagine the multitude of doctoral students who will now fall asleep to the soothing sounds of a paper on protein folding. The application also creates links within each of the papers to definitions of unusual terms, which come up pretty much every other word in most journal papers. The app helps scientists and others bring new life and connections to the standard, static journal article.

Benik who heralds from Harvard Medical School built a program that is a social network for researchers. The application, which would run on the Elsevier SciVerse platform, transforms information about the scientists such as papers published or contact information to pure semantic data. Once in this form it is open to search and analysis in exciting new ways. One example that Benik explained was in the hunt for grant opportunities and collaborators. Searching for an asthma expert to team up with on your smoking research? By using semantic tagging, this application will help that search process.

The winner was RPI doctoral student James McCusker and his GO Browse application. The application provides a very visual new way to search through complex medical data. To exhibit the application, McCusker took the data from a very large medical dataset on the genetics of cancer. The data has been under development for nearly two decades by hundreds of different scientists and doctors around the world. It is now so vast and varied that it can be extremely difficult to sort through. GO Browse uses semantically linked data to create a visualization of data about each type of cancer.

The visualization, which looks like a series of big and small soap bubbles is a new way to see the data regarding each cancer. The biggest bubbles represent facts about that particular cancer that are different from all the other cancers. Through this simple visualization, researchers can quickly sort through millions of words about the cancer in seconds and get to the truly important info that they need – what is it about this particular cancer that makes it different from all others? In such a way new discoveries and connections can be made about the disease in minutes. The application could be applied to any type of data from medical to music. In addition, researchers can click on each of the bubbles to drill down for more information. Articles can be easily sorted through and definitions can be quickly looked up.

As Joanne Luciano told me while preparing for the hackathon, the time for innovative health and medicine applications has come. Applications like these represent an entirely new way of storing and sharing data and open up new pathways to treating patients.

Hopefully all those busy hackers are catching up on all the lost sleep.