Plataforma para la automatización de protocolos biológicos

Abstract

Nowadays, the most common way of executing experiments related to synthetic biology is doing them by hand using pipettes, Petri dishes, test tubes, etc. This process not only has a high cost in human resources but also is prone to errors which brings a low reproducibility, automate these experiments would help to ease these problems. Biological protocols are used for describing experiments related to biology. A protocol is a sequence of operations that move small amounts of liquid between test tubes, subject them to certain temperature, centrifuge them...etc. These protocols are usually described in natural language which can cause ambiguities that disables automation. In order to allow it is necessary to describe them using formal languages which can not result in equivocations. Currently, robotic arms and fluidic machines, sets of containers joined by tubes that uses pumps to move liquid between them, are begining to be used for executing biological protocols. Also companies of biology on demand, meaning, sending a protocol to be executed by the company’s specialized robots, has begin to arise. Generally people who execute biological protocols lack advance computation knowledge and programming the automation platforms is hard for them. Besides they do not feel comfortable using formal languages to describe protocol. That is why, in order to make the automation tools more accessible for them, computer applications that assist the biologist upon using those tools are being implemented, like the one designed in this thesis. The main objective of this project is to implement a platform capable of executing biological protocol automatically. The intention is to make the plat- form as flexible as possible that’s why a plugin system has been implemented allowing functionality to be added, modified or removed fast and easily making laboratory automation more attractive to the research community. The system works as follows: first receives a biological protocol described using a formal language and a machine description,that is, a directed graph where the nodes symbolize containers and the edges tubes and pumps that allows the movement of liquid between nodes. After checks if the protocol can be executed over the machine if so the system communicates with the machine components in order to execute the necessary ope- rations.