An interactive programming paradigm for realtime experimentation with remote living matter [article]

Peter Washington, Karina Samuel-Gama, Shirish Goyal, Ashwin Ramaswami, Ingmar H Riedel-Kruse
2017 bioRxiv   pre-print
Recent advancements in life-science instrumentation and automation enable entirely new modes of human interaction with microbiological processes and corresponding applications for science and education through biology cloud labs. A critical barrier for remote life-science experimentation is the absence of suitable abstractions and interfaces for programming living matter. To this end we conceptualize a programming paradigm that provides stimulus control functions and sensor control functions
more » ... realtime manipulation of biological (physical) matter. Additionally, a simulation mode facilitates higher user throughput, program debugging, and biophysical modeling. To evaluate this paradigm, we implemented a JavaScript-based web toolkit, 'Bioty', that supports realtime interaction with swarms of phototactic Euglena cells hosted on a cloud lab. Studies with remote users demonstrate that individuals with little to no biology knowledge and intermediate programming knowledge were able to successfully create and use scientific applications and games. This work informs the design of programming environments for controlling living matter in general and lowers the access barriers to biology experimentation for professional and citizen scientists, learners, and the lay public.
doi:10.1101/236919 fatcat:ak6at64ovverpff6d742iwdcki