General rightsThis document is made available in accordance with publisher policies. Please cite only the published version using the reference above. Full terms of use are available: http://www.bristol.ac.uk/pure/about/ebr-terms Keywords: visualization; standardization; SBOLv; bio-design automation; synthetic biology 2 Abstract DNAplotlib (www.dnaplotlib.org) is a computational toolkit for the programmable visualization of highly customizable, standards-compliant genetic designs. Functions are provided to aid with both visualization tasks and to extract and overlay associated experimental data. High-quality output is produced in the form of vector-based PDFs, rasterized images, and animated movies. All aspects of the rendering process can be easily customized or extended by the user to cover new forms of genetic part or regulation. DNAplotlib supports improved communication of genetic design information and offers new avenues for static, interactive and dynamic visualizations that map and explore the links between the structure and function of genetic parts, devices and systems; including metabolic pathways and genetic circuits. DNAplotlib is crossplatform software developed using Python and released under the MIT license.
3Engineering disciplines rely on standardized pictorial representations of parts and their interconnections to create schematics that clearly communicate how they are pieced together and to enable the reliable construction of large complex systems. In bioengineering, DNA sequences are often synthesized to create genetic constructs that probe or perturb the natural function of a cell or implement novel capabilities. Unlike more established engineering disciplines, the way that a genetic design is visually represented can vary significantly between labs and across different areas of the field. This leads to ambiguities that hinder data exchange, understanding, and the effective reuse of this research.The Synthetic Biology Open Language Visual 1 (SBOLv) initiative was started to help alleviate this problem, defining a set of agreed symbols for commonly used genetic elements. In addition, other schemes such as the Systems Biology Graphical Notation 2 (SBGN) have been developed to more broadly standardize the graphical notation used to describe biological processes. The importance of these standardized approaches has also been recognized by publishers, with a major synthetic biology journal (ACS Synthetic Biology) adopting the use of SBOLv symbols when presenting genetic design information 3 .Although these initiatives will help accelerate adoption of these standards, they rely on the availability of supporting tools to enable the production of compliant diagrams. Some tools do exist to generate SBOLv visualizations from genetic design information, either through graphical point-and-click interfaces (e.g., VectorNTI 4 , TinkerCell 5 , GenoCAD 6 , DeviceEditor 7 and SBOL Designer) or text-based inputs (e.g., Pigeon 8 and VisBOL 9 ). These are effective for small numbers of constructs, but lack the ...