![]() ![]() It will become imperative for researchers to share complete descriptions of their methods in a form that can be consistently replicated in other laboratories. ![]() ![]() As fields such as synthetic biology attempt to synthesize living systems as a composition of many parts, we will need to execute lengthy protocols with great precision. Second, the complexity of biology protocols is increasing dramatically. In order to leverage such technologies for biological experimentation, it will be necessary to express the protocols in a format that is not only comprehensible by humans, but also by machines. The increasing density of microfluidic devices has been compared to Moore's Law, with recent products supporting up to 9,216 parallel reactions. First, we are witnessing immense advances in laboratory automation systems. However, due to recent technology trends, the practice of describing protocols with free-flowing English-language text is quickly becoming inadequate and obsolete. We invite other researchers to leverage BioCoder to improve the precision and completeness of their protocols, and also to adapt and extend BioCoder to new domains.įor decades, biologists have relied on written descriptions of protocols to guide their experiments in the laboratory. Our experience suggests that this practice is tractable and offers many benefits. Our vision is to change the way that experimental methods are communicated: rather than publishing a written account of the protocols used, researchers will simply publish the code. ConclusionsīioCoder represents the first practical programming system for standardizing and automating biology protocols. BioCoder is freely available for download at. We argue that BioCoder exposes and resolves ambiguities in existing protocols, and could provide the software foundations for future automation platforms. We have implemented over 65 protocols in BioCoder the most complex of these was successfully executed by a biologist in the laboratory using BioCoder as the only reference. In addition to being suitable for automation, BioCoder converts the code into a readable, English-language description for use by biologists. We have developed BioCoder, a C++ library that enables biologists to express the exact steps needed to execute a protocol. Our goal in this paper is to improve both the reproducibility and automation of biology experiments by using a programming language to express the precise series of steps taken. However, there is increasing benefit to formalizing the descriptions of protocols, as laboratory automation systems (such as microfluidic chips) are becoming increasingly capable of executing them. Published descriptions of biology protocols are often ambiguous and incomplete, making them difficult to replicate in other laboratories. ![]()
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