Engineering biology and automation-Replicability as a design principle.

Applications in engineering biology increasingly share the need to run operations on very large numbers of biological samples. This is a direct consequence of the application of good engineering practices, the limited predictive power of current computational models and the desire to investigate very large design spaces in order to solve the hard, important problems the discipline promises to solve. Automation has been proposed as a key component for running large numbers of operations on biological samples.

Construction of a Calibration Curve for Lycopene on a Liquid-Handling Platform─Wider Lessons for the Development of Automated Dilution Protocols.

Liquid-handling is a fundamental operation in synthetic biology─all protocols involve one or more liquid-handling operations. It is, therefore, crucial that this step be carefully automated in order to unlock the benefits of automation (e.g.

An engineering biology approach to automated workflow and biodesign.

The paper addresses the application of engineering biology strategies and techniques to the automation of laboratory workflow-primarily in the context of biofoundries and biodesign applications based on the Design, Build, Test and Learn paradigm. The trend toward greater automation comes with its own set of challenges. On the one hand, automation is associated with higher throughput and higher replicability.

PASIV: A Pooled Approach-Based Workflow to Overcome Toxicity-Induced Design of Experiments Failures and Inefficiencies.

We present here a newly developed workflow─which we have called PASIV─designed to provide a solution to a practical problem with design of experiments (DoE) methodology: i.e., what can be done if the scoping phase of the DoE cycle is severely hampered by burden and toxicity issues (caused by either the metabolite or an intermediary), making it unreliable or impossible to proceed to the screening phase? PASIV─standing for pooled approach, screening, identification, and visualization─was designed so the (viable) region of interest can be made to appear through an interplay between biology and software.

Removing the Bottleneck: Introducing cMatch - A Lightweight Tool for Construct-Matching in Synthetic Biology.

We present a software tool, called cMatch, to reconstruct and identify synthetic genetic constructs from their sequences, or a set of sub-sequences-based on two practical pieces of information: their modular structure, and libraries of components. Although developed for combinatorial pathway engineering problems and addressing their quality control (QC) bottleneck, cMatch is not restricted to these applications. QC takes place post assembly, transformation and growth.