Highly-automated, high-throughput replication of yeast-based logic circuit design assessments.

We describe an experimental campaign that replicated the performance assessment of logic gates engineered into cells of Saccharomyces cerevisiae by Gander et al. Our experimental campaign used a novel high-throughput experimentation framework developed under Defense Advanced Research Projects Agency's Synergistic Discovery and Design program: a remote robotic lab at Strateos executed a parameterized experimental protocol. Using this protocol and robotic execution, we generated two orders of magnitude more flow cytometry data than the original experiments. We discuss our results, which largely, but not completely, agree with the original report and make some remarks about lessons learned. Graphical Abstract.

Intent Parser: A Tool for Codification and Sharing of Experimental Design.

Communicating information about experimental design among a team of collaborators is challenging because different people tend to describe experiments in different ways and with different levels of detail. Sometimes, humans can interpret missing information by making assumptions and drawing inferences from information already provided. Doing so, however, is error-prone and typically requires a high level of interpersonal communication. In this paper, we present a tool that addresses this challenge by providing a simple interface for incremental formal codification of experiment designs. Users interact with a Google Docs word-processing interface with structured tables, backed by assisted linking to machine-readable definitions in a data repository (SynBioHub) and specification of available protocols and requests for execution in the Open Protocol Interface Language (OPIL). The result is an easy-to-use tool for generating machine-readable descriptions of experiment designs with which users in the DARPA SD2 program have collected data from 80 208 samples using a variety of protocols and instruments over the course of 181 experiment runs.

In vivo fluorescent imaging of the mouse retina using adaptive optics.

In vivo imaging of the mouse retina using visible and near infrared wavelengths does not achieve diffraction-limited resolution due to wavefront aberrations induced by the eye. Considering the pupil size and axial dimension of the eye, it is expected that unaberrated imaging of the retina would have a transverse resolution of 2 microm. Higher-order aberrations in retinal imaging of human can be compensated for by using adaptive optics. We demonstrate an adaptive optics system for in vivo imaging of fluorescent structures in the retina of a mouse, using a microelectromechanical system membrane mirror and a Shack-Hartmann wavefront sensor that detects fluorescent wavefront.