Hardware, Software, and Wetware Codesign Environment for Synthetic Biology

Abstract

Synthetic biology is the process of forward engineering living systems. These systems can be used to produce biobased materials, agriculture, medicine, and energy. One approach to designing these systems is to employ techniques from the design of embedded electronics. These techniques include abstraction, standards, modularity, automated design, and formal semantic models of computation. Together, these elements form the foundation of “biodesign automation,” where software, robotics, and microfluidic devices combine to create exciting biological systems of the future. This paper describes a “hardware, software, wetware” codesign vision where software tools can be made to act as “genetic compilers” that transform high-level specifications into engineered “genetic circuits” (wetware). This is followed by a process where automation equipment, well-defined experimental workflows, and microfluidic devices are explicitly designed to house, execute, and test these circuits (hardware). These systems can be used as either massively parallel experimental platforms or distributed bioremediation and biosensing devices. Next, scheduling and control algorithms (software) manage these systems’ actual execution and data analysis tasks. A distinguishing feature of this approach is how all three of these aspects (hardware, software, and wetware) may be derived from the same basic specification in parallel and generated to fulfill specific cost, performance, and structural requirements.

The Laboratory Automation Protocol (LAP) Format and Repository: A Platform for Enhancing Workflow Efficiency in Synthetic Biology

“…12 These workflows involve collaboration among various disciplines, encompassing design, mathematical modeling, genetic engineering, and result analysis, all working toward a shared objective. Currently, there is significant room for improvement at the convergence of software, hardware, and wetware, 13 which paves the way for laboratory automation in synthetic biology laboratories, assisting in addressing future challenges. 14−16 At the heart of open-source automation is the utilization of program scripts, which are sets of instructions that encode molecular biology protocols.…”