Stanford EE Computer Systems Colloquium

4:15PM, Wednesday, October 31, 2012
Skilling Auditorium, Stanford Campus

RNA nanoengineering through crowd science

Rhiju Das
Stanford Biochemistry & Physics
About the talk:

Internet-scale citizen science projects have successfully solved complex image analysis and molecular modeling challenges. However, these approaches have thus far been limited to computational problems with little or no experimental input. No mechanism has enabled citizen scientists to solve empirical problems requiring continuous wet-lab feedback. We present EteRNA, a 37,000-player "cloud laboratory" that connects citizen scientists with a remote experimental pipeline to attack a fundamental problem in bioengineering: the design of self-assembling RNAs. By taking part in wet-lab experiments, EteRNA players now substantially outperform existing algorithms for designing RNA secondary structures, including complex dendrimer folds and scaffolds for small-molecule sensors. Furthermore, while solving these design puzzles, the Eterna community has proposed general RNA folding rules for a new automated algorithm, and the resulting EterRNAbot design method also outperforms prior algorithms in independent tests. These results show that experimentally driven hypothesis generation - the scientific method itself - can be successfully carried out by a massively multiplayer cloud laboratory.


There is no downloadable version of the slides for this talk available at this time.

About the speaker:

Dr. Das strives to predict how sequence codes for 3D structure in the basic chain-like molecules of Life: RNA, DNA, and proteins. The Das group is creating chemical and computational tools to predict how biomolecules behave, to experimentally map the structures of viral and cellular RNAs, and to design new biomolecule devices. Most recently, the lab's EteRNA project has crowd-sourced cutting-edge experimental research in RNA nanotechnology to tens of thousands of citizen scientists, integrating timely wet-lab feedback into a videogame interface.

Contact information:

Rhiju Das
B421 Beckman Center
279 Campus Drive
Stanford, CA
650 723 5976