Automated robotic liquid handling assembly of modular DNA devices

Recent advances in modular DNA assembly techniques have enabled synthetic biologists to test significantly more of the available "design space" represented by "devices" created as combinations of individual genetic components. However, manual assembly of such large numbers of devices is time-intensive, error-prone, and costly. The increasing sophistication and scale of synthetic biology research necessitates an efficient, reproducible way to accommodate large-scale, complex, and high throughput device construction. Here, a DNA assembly protocol using the Type-IIS restriction endonuclease based Modular Cloning (MoClo) technique is automated on two liquid-handling robotic platforms. Automated liquid-handling robots require careful, often times tedious optimization of pipetting parameters for liquids of different viscosities (e.g. enzymes, DNA, water, buffers), as well as explicit programming to ensure correct aspiration and dispensing of DNA parts and reagents. This makes manual script writing for complex assemblies just as problematic as manual DNA assembly, and necessitates a software tool that can automate script generation. To this end, we have developed a web-based software tool, http://mocloassembly.com, for generating combinatorial DNA device libraries from basic DNA parts uploaded as Genbank files. We provide access to the tool, and an export file from our liquid handler software which includes optimized liquid classes, labware parameters, and deck layout. All DNA parts used are available through Addgene, and their digital maps can be accessed via the Boston University BDC ICE Registry. Together, these elements provide a foundation for other organizations to automate modular cloning experiments and similar protocols. The automated DNA assembly workflow presented here enables the repeatable, automated, high-throughput production of DNA devices, and reduces the risk of human error arising from repetitive manual pipetting. Sequencing data show the automated DNA assembly reactions generated from this workflow are ~95% correct and require as little as 4% as much hands-on time, compared to manual reaction preparation

Automated sequence and motion planning for robotic spatial extrusion of 3D trusses

While robotic spatial extrusion has demonstrated a new and efficient means to fabricate 3D truss structures in architectural scale, a major challenge remains in automatically planning extrusion sequence and robotic motion for trusses with unconstrained topologies. This paper presents the first attempt in the field to rigorously formulate the extrusion sequence and motion planning (SAMP) problem, using a CSP encoding. Furthermore, this research proposes a new hierarchical planning framework to solve the extrusion SAMP problems that usually have a long planning horizon and 3D configuration complexity. By decoupling sequence and motion planning, the planning framework is able to efficiently solve the extrusion sequence, end-effector poses, joint configurations, and transition trajectories for spatial trusses with nonstandard topologies. This paper also presents the first detailed computation data to reveal the runtime bottleneck on solving SAMP problems, which provides insight and comparing baseline for future algorithmic development. Together with the algorithmic results, this paper also presents an open-source and modularized software implementation called Choreo that is machine-agnostic. To demonstrate the power of this algorithmic framework, three case studies, including real fabrication and simulation results, are presented.Comment: 24 pages, 16 figure

Octree-based production of near net shape components

Near net shape (NNS) manufacturing refers to the production of products that require a finishing operation of some kind. NNS manufacturing is important because it enables a significant reduction in: machining work, raw material usage, production time, and energy consumption. This paper presents an integrated system for the production of near net shape components based on the Octree decomposition of 3-D models. The Octree representation is used to automatically decompose and approximate the 3-D models, and to generate the robot instructions required to create assemblies of blocks secured by adhesive. Not only is the system capable of producing shapes of variable precision and complexity (including overhanging or reentrant shapes) from a variety of materials, but it also requires no production tooling (e.g., molds, dies, jigs, or fixtures). This paper details how a number of well-known Octree algorithms for subdivision, neighbor findings, and tree traversal have been modified to support this novel application. This paper ends by reporting the construction of two mechanical components in the prototype cell, and discussing the overall feasibility of the system

A computer-based product classification and component detection for demanufacturing processes

This is an Author's Accepted Manuscript of an article published in International Journal of Computer Integrated Manufacturing, 24(10), 900-914, 2011 [copyright Taylor & Francis], available online at: http://www.tandfonline.com/10.1080/0951192X.2011.579169.The aim of this paper is to propose a novel computer-based product classification, component detection and tracking for demanufacturing and disassembly process. This is achieved by introducing a series of automated and sequential product scanning, component identification, image analysis and sorting – leading to the development of a bill of material (BOM). The produced BOM can then be associated with the relevant disassembly/demanufacture proviso. The proposed integrated image sorting and product classification (ISPC) approach can be considered as a step forward in automation of demanufacturing activities. The ISPC model proposed in this paper utilises and builds on the state-of-the-art technology and current body of research in computer-integrated demanufacturing and remanufacturing (CIDR). An appraisal of the latest research material and the factors that inhibit CIDR methods inpractice are presented. A novel solution for the integration of imaging and material identification techniques toovercome some of the existing shortcomings of automated recycling processes is proposed in this paper. The proposed product scanning and component detection ISPC software consists of four distinct models: the repertory database, the search engine, the product-attributes updater and the image sorting and classification algorithm. The software framework that integrates the four components is presented in this paper. Finally, an overall assessment of applying ISPC at various stages of CIDR processes concludes the article.University of Ibadan MacArthur Foundation Gran