title: Clarity: an open-source manager for laboratory automation.
abstract: Software to manage automated laboratories, when interfaced with hardware instruments, gives users a way to specify experimental protocols and schedule activities to avoid hardware conflicts. In addition to these basics, modern laboratories need software that can run multiple different protocols in parallel and that can be easily extended to interface with a constantly growing diversity of techniques and instruments. We present Clarity, a laboratory automation manager that is hardware agnostic, portable, extensible, and open source. Clarity provides critical features including remote monitoring, robust error reporting by phone or email, and full state recovery in the event of a system crash. We discuss the basic organization of Clarity, demonstrate an example of its implementation for the automated analysis of bacterial growth, and describe how the program can be extended to manage new hardware. Clarity is mature, well documented, actively developed, written in C# for the Common Language Infrastructure, and is free and open-source software. These advantages set Clarity apart from currently available laboratory automation programs. The source code and documentation for Clarity is available at http://code.google.com/p/osla/.
authors.affiliation: Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02143, USA.
authors.forename: Nigel F
authors.initials: NF
authors.lastname: Delaney
authors.forename: José I
authors.initials: JI
authors.lastname: Rojas Echenique
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Marx
mesh_terms: D057205:Automation, Laboratory / Q000295:instrumentation*; D012371:Robotics; D012984:Software