Language & tools for context-aware biology

Abstract

Current biological research workflows make use of disparate, poorly integrated systems that cause large mental burden on the scientist leading to mistakes on often long, complex and costly experimental procedures. The lack of open tools to assist in the collection of distributed experimental conditions and data is largely responsible making protocols difficult to debug and laboratory practice hard to learn. In this thesis, we describe an open Protocol Descriptor Language (PDL) and system to enable a context-rich, quantitative approach to biological research. We detail the development of a closed-loop pipetting technology and a wireless, sample temperature sensor that integrate with our Protocol Description platform enabling novel, real-time experimental feedback to the researcher thereby reducing mistakes and increasing overall scientific reproducibility.