Team:Penn/PennApps

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modeling

PennApps


Synthetic Biology holds its roots in electrical engineering and computer science, however, most engineers in these fields have had little exposure to Synthetic Biology. To reach out to hundreds of fellow computer scientists and build an open source methylation analysis software along the way, the mmbers of Penn iGEM participated in PennApps, the largest college hackathon. PennApps is attended by approximately 1,000 top student hackers from around the world. Over the course of 48 hours, teams work to design an app from start to finish. At the demo round, all the teams – over 200 in total – present their apps to fellow hackers, interested students, and representatives from the tech industry. The Penn iGEM team represented synthetic biology at an event predominantly attended by computer science students, and PennApps attendees were excited to see a new computer program with a scientific application.

Our booth is busy! Danny and Josh simultaneously present the app to two interested onlookers.

Josh explains the math behind the software.

Our final product was a gel analysis app which automates the process of interpreting DNA bands run through gel electrophoresis. This app, the Magellin Software Package, complements our digestion assay and reports the extent of on-target and off-target methylation, greatly simplifying data analysis for the experimenter. Unlike other gel analysis programs, MaGellin interprets plasmid sequences, understands methylation patterns, and assesses targeted methylation based on a gel image.

Learn more about the MaGellin Software Package on our software page.

The MaGellin Software Package is a robust platform that can easily be adjusted for other gel analysis problems, such as interpreting COBRA and quantifying PCR yields. Our code is open-source, and we encourage researchers to adapt it to various needs. We would like to collaborate with other iGEM teams to expand the range of gel analysis tasks this software performs.

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