Your protocols will be assimilated

The Aquarium Project

A study in 2012 found that six of fifty-three selected 'landmark' papers in cancer biology were reproducible. Another found that retractions, due to errors or otherwise, are increasingly frequent. The bar for what makes a scientific result has either lowered, or the complexity of science has increased to where the last century's methods no longer apply. Attempting to build on scientific results in the life sciences, researchers in engineering have begun to explore the study of engineering life itself, only to find that said results do not hold. Even when a result is valid, the methods are poorly explained, purposefully not explained, or simply buried in some researcher's head.

The Aquarium Project aims to fix this problem by providing the means to specify, as precisely as possible, how to obtain a result. Researchers encode protocols in Plankton, specifying how to manipulate items in the Aquarium inventory (test tubes, pipettors, 96 well plates, etc) using a combination of formal statements, informal descriptions, and photographs. Protocols are parameterized by "tuning knobs" (such as incubation times or reagent concentrations) that can be varied when the protocols are scheduled. The researcher strings together protocols into processes specified in Oyster, specifying how the output samples of one protocol become the inputs to other protocols, and how protocols can be scheduled, parallelized, and controlled.

Protocols and processes are scheduled and presented to technicians on touchscreen monitors placed throughout the lab. Every step is logged: who performed the step, which items were used, what data was gathered by which instruments, and how long it took. Color and depth sensing video cameras aimed at the technician, and other sensors sprinkled throughout the lab, record the details of each step and are used to annotate an automatically generated a lab notebook. The data can be used to debug and improve the experiment. More importantly it provides a complete, executable description of the results obtained -- one that could be used by any lab running Aquarium to reproduce the result!