Background
In 2015, Chaim Gingold released Earth Primer, combined aspects of game play with computer simulations to create a new kind of interactive science book. Earth Primer offers readers a peek into the mind's eye of a geology expert through playful exploration.
Around the same time, Shawn Douglas was building his new research lab down the street at UCSF and searching for ways to improve the process of training new researchers. Upon seeing Earth Primer, Shawn recognized the opportunity to build additional "scientific sandboxes" that would enable students to rapidly build conceptual understanding of experimental methods without spending years of trial and error in the lab. Shawn reached out to Chaim, and they were able initiate a collaboration in early 2018.
Description
Gel electrophoresis enables separation and visualization of biomolecules such as DNA, RNA, or proteins. Like many powerful tools, effective use of gels can be difficult to learn. Gelbox is a simulation tool to help understand the basic relationships between experimental parameters and resulting image data produced by gel electrophoresis.
Gel electrophoresis is routinely used in biology to isolate and characterize molecules. It transforms clear liquids into abstract band patterns that a skilled experimenter can use to interpret the contents of a sample. However, the method is difficult to learn. It requires careful preparation and the interpretation of abstract and often ambiguous data. Moreover, the feedback loop when learning gel electrophoresis is slow—mistakes only become evident upon data collection hours after they occurred, and in practice it's difficult to run more than a couple gels each workday.
Gelbox is a dynamic “scientific sandbox” for visualizing the link between gel band patterns and sample molecules. We sought to capture the notion that gels are easy to mess up, but they do so in predictable ways. Gelbox offers a novel approach to learning gel electrophoresis that complements the *ad hoc* trial-and-error methods routinely used in laboratory settings.
Features
- Run simulated gels instantaneously.
- See the relationship between simulated molecules and a simulated gel.
- Directly manipulate gel bands, and see the molecules change accordingly.
About the Authors
Shawn Douglas is the Principal Investigator at the Douglas Lab at UCSF, in the department of Cellular and Molecular Pharmacology. Prior to joining UCSF, Shawn earned a Ph.D. in Biophysics from Harvard University working in labs of George Church and William Shih, and studied computer science at Yale, working in the lab of Mark Gerstein. The Douglas Lab works in the field of DNA nanotechnology, developing new methods to construct and manipulate biological molecules at the nanometer scale.
Chaim Gingold is a designer and theorist who creates and studies powerful representations for playing with, learning about, and reshaping the world. He designed the Spore Creature Creator, made a playable science book called Earth: A Primer, a magic table called La Tabla that brings inanimate objects to life, and is currently working on a book about the history of SimCity and computer simulation. His Ph.D. in computer science was awarded by the University of California, Santa Cruz, for research on the history of simulation and designing for play.
Contributors
| Shawn Douglas | Concept and Design |
| Chaim Gingold | Design and Programming |
| Jason Brown | App Icon and Video |
| Parsa Nafisi | Calibration gels |
