StarBiogene and Game 5 of the ALCS

By Justin Riley, Programmer Analyst, OEIT

StarBiogene is a web interface to a set of software tools from the Broad Institute for analyzing genomics data via the web. It enables the user to take part in the analysis of microarray gene expression data without the operational fog of installing, configuring, and loading datasets into the software. Entirely from the web interface, students can select how they want to visualize the data (microarray, heatmap, or clustering views) and also choose from a set of prepackaged datasets to be automatically loaded into the software. StarBiogene then delivers the visualizer along with the requested dataset and launches the software on the client's machine using Java Web Start (tm).

On the week of 10/15-10/20 StarBiogene went into the 7.012 Intro to Biology course at MIT as a homework assignment in the genetics portion of the course. The problem set had the students analyze gene expression data using the visualization software in StarBiogene in order to judge which type of tumor a given patient had. By using the software to understand gene expression levels and the signature patterns they create for different tumor samples, the students were then asked to diagnose a particular tumor based on their findings.

During the same week, the Boston Red Sox were battling the Cleveland Indians in the American League Championship Series (ALCS). With the Red Sox in the ALCS, almost all of Boston was tuned in every night of the series...including MIT students.

The homework for 7.012 was assigned 10/12 and the students had until the 20th to turn in the problem set. The graph below shows the Biogene servers' usage statistics on the week of the homework assignment. The vertical axis shows the number of users and the horizontal axis shows the given day. As is typical, StarBiogene experienced an increasing load as the week moved closer to the homework due date. Interestingly enough though, the maximum load experienced was actually on the day of the homework due date as opposed to the night before. Coincidentally, Game 5 of the ALCS was on 10/18, the night before the homework was due. This implies either that students stayed up late watching Game 5 of the ALCS game and then did the homework afterwards (in the AM) or that the students stayed up late watching Game 5 and waited to do the homework until the day the homework was due.

Despite the “Red Sox Effect” on the homework, StarBiogene was a success. StarBiogene successfully served approximately 324 students in a little under a week without issues. To learn more about StarBiogene you can visit the project website at: http://web.mit.edu/star/biogene. The project page contains links to problem sets and instructions on how to get to and use StarBiogene.