scholarly journals paraSBOLv: A Foundation for Standard-Compliant Genetic Design Visualization Tools

2021 ◽  
Author(s):  
Charlie J Clark ◽  
James Scott-Brown ◽  
Thomas E Gorochowski
Keyword(s):  
Synthetic Biology ◽  
Design Process ◽  
Physical System ◽  
Computational Tools ◽  
Design Information ◽  
Complex Design ◽  
Visualization Tools ◽  
Synthetic Biology Open Language ◽  
Machine Readable ◽  
Python Package

Abstract Diagrams constructed from standardized glyphs are central to communicating complex design information in many engineering fields. For example, circuit diagrams are commonplace in electronics and allow for a suitable abstraction of the physical system that helps support the design process. With the development of the Synthetic Biology Open Language Visual (SBOLv), bioengineers are now positioned to better describe and share their biological designs visually. However, development of computational tools to support the creation of these diagrams is currently hampered by an excessive burden in maintenance due to the large and expanding number of glyphs present in the standard. Here, we present a Python package called paraSBOLv that enables access to the full suite of SBOLv glyphs through use of machine-readable parametric glyph definitions. These greatly simplify the rendering process while allowing extensive customization of the resulting diagrams. We demonstrate how adoption of paraSBOLv can accelerate the development of highly specialized biodesign visualization tools or even form the basis for more complex software by removing the burden of maintaining glyph specific rendering code. Looking forward, we suggest that incorporation of machine-readable parametric glyph definitions into the SBOLv standard could further simplify the development of tools to produce standard-compliant diagrams and integration of visual standards across fields.

scholarly journals A standard-enabled workflow for synthetic biology

2017 ◽  
Vol 45 (3) ◽  
pp. 793-803 ◽  
Author(s):  
Chris J. Myers ◽  
Jacob Beal ◽  
Thomas E. Gorochowski ◽  
Hiroyuki Kuwahara ◽  
Curtis Madsen ◽  
...  
Keyword(s):  
Systems Biology ◽  
Synthetic Biology ◽  
Markup Language ◽  
Design Tools ◽  
Data Standards ◽  
Data Repositories ◽  
Simulation Tools ◽  
Systems Biology Markup Language ◽  
Visualization Tools ◽  
Synthetic Biology Open Language

A synthetic biology workflow is composed of data repositories that provide information about genetic parts, sequence-level design tools to compose these parts into circuits, visualization tools to depict these designs, genetic design tools to select parts to create systems, and modeling and simulation tools to evaluate alternative design choices. Data standards enable the ready exchange of information within such a workflow, allowing repositories and tools to be connected from a diversity of sources. The present paper describes one such workflow that utilizes, among others, the Synthetic Biology Open Language (SBOL) to describe genetic designs, the Systems Biology Markup Language to model these designs, and SBOL Visual to visualize these designs. We describe how a standard-enabled workflow can be used to produce types of design information, including multiple repositories and software tools exchanging information using a variety of data standards. Recently, the ACS Synthetic Biology journal has recommended the use of SBOL in their publications.

scholarly journals SBOL Visual 2 Ontology

2020 ◽  
Author(s):  
Göksel Misirli ◽  
Jacob Beal ◽  
Thomas E. Gorochowski ◽  
Guy-Bart Stan ◽  
Anil Wipat ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Web Service ◽  
Visual Representation ◽  
Biological Ontologies ◽  
Visualization Tools ◽  
Synthetic Biology Open Language

AbstractStandardising the visual representation of genetic parts and circuits is vital for unambiguously creating and interpreting genetic designs. To this end, an increasing number of tools are adopting well-defined glyphs from the Synthetic Biology Open Language (SBOL) Visual standard to represent various genetic parts and their relationships. However, the implementation and maintenance of the relationships between biological elements or concepts and their associated glyphs has to now been left up to tool developers. We address this need with the SBOL Visual 2 Ontology, a machine-accessible resource that provides rules for mapping from genetic parts, molecules, and interactions between them, to agreed SBOL Visual glyphs. This resource, together with a web service, can be used as a library to simplify the development of visualization tools, as a stand-alone resource to computationally search for suitable glyphs, and to help facilitate integration with existing biological ontologies and standards in synthetic biology.Graphical TOC Entry

scholarly journals SEVA 3.0: an update of the Standard European Vector Architecture for enabling portability of genetic constructs among diverse bacterial hosts

2019 ◽  
Vol 48 (D1) ◽  
pp. D1164-D1170 ◽  
Author(s):  
Esteban Martínez-García ◽  
Angel Goñi-Moreno ◽  
Bryan Bartley ◽  
James McLaughlin ◽  
Lucas Sánchez-Sampedro ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Bacterial Species ◽  
Web Based ◽  
Genomic Engineering ◽  
Bioinformatic Tools ◽  
Synthetic Biology Open Language ◽  
User Friendly ◽  
Machine Readable ◽  
Genetic Constructs

Abstract The Standard European Vector Architecture 3.0 database (SEVA-DB 3.0, http://seva.cnb.csic.es) is the update of the platform launched in 2013 both as a web-based resource and as a material repository of formatted genetic tools (mostly plasmids) for analysis, construction and deployment of complex bacterial phenotypes. The period between the first version of SEVA-DB and the present time has witnessed several technical, computational and conceptual advances in genetic/genomic engineering of prokaryotes that have enabled upgrading of the utilities of the updated database. Novelties include not only a more user-friendly web interface and many more plasmid vectors, but also new links of the plasmids to advanced bioinformatic tools. These provide an intuitive visualization of the constructs at stake and a range of virtual manipulations of DNA segments that were not possible before. Finally, the list of canonical SEVA plasmids is available in machine-readable SBOL (Synthetic Biology Open Language) format. This ensures interoperability with other platforms and affords simulations of their behaviour under different in vivo conditions. We argue that the SEVA-DB will remain a useful resource for extending Synthetic Biology approaches towards non-standard bacterial species as well as genetically programming new prokaryotic chassis for a suite of fundamental and biotechnological endeavours.

scholarly journals SynBiopython: an open-source software library for Synthetic Biology

2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Jing Wui Yeoh ◽  
Neil Swainston ◽  
Peter Vegh ◽  
Valentin Zulkower ◽  
Pablo Carbonell ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Open Source ◽  
Open Source Software ◽  
Development Projects ◽  
Software Library ◽  
Current State ◽  
Starting Point ◽  
Common Problems ◽  
Data Tracking ◽  
Python Package

Abstract Advances in hardware automation in synthetic biology laboratories are not yet fully matched by those of their software counterparts. Such automated laboratories, now commonly called biofoundries, require software solutions that would help with many specialized tasks such as batch DNA design, sample and data tracking, and data analysis, among others. Typically, many of the challenges facing biofoundries are shared, yet there is frequent wheel-reinvention where many labs develop similar software solutions in parallel. In this article, we present the first attempt at creating a standardized, open-source Python package. A number of tools will be integrated and developed that we envisage will become the obvious starting point for software development projects within biofoundries globally. Specifically, we describe the current state of available software, present usage scenarios and case studies for common problems, and finally describe plans for future development. SynBiopython is publicly available at the following address: http://synbiopython.org.

Human versus Artificial Intelligence: A Data-Driven Approach to Real-Time Process Management During Complex Engineering Design

2021 ◽  
pp. 1-38
Author(s):  
Joshua Gyory ◽  
Nicolas F Soria Zurita ◽  
Jay Martin ◽  
Corey Balon ◽  
Christopher McComb ◽  
...  
Keyword(s):  
Real Time ◽  
Design Process ◽  
Process Management ◽  
Superior Performance ◽  
Team Members ◽  
Engineering Teams ◽  
Complex Design ◽  
Data Driven Approach ◽  
Complex Engineering ◽  
Process Managers

Abstract Managing the design process of teams has been shown to considerably improve problem-solving behaviors and resulting final outcomes. Automating this activity presents significant opportunities in delivering interventions that dynamically adapt to the state of a team in order to reap the most impact. In this work, an Artificial Intelligent (AI) agent is created to manage the design process of engineering teams in real time, tracking features of teams' actions and communications during a complex design and path-planning task with multidisciplinary team members. Teams are also placed under the guidance of human process managers for comparison. Regarding outcomes, teams perform equally as well under both types of management, with trends towards even superior performance from the AI-managed teams. The managers' intervention strategies and team perceptions of those strategies are also explored, illuminating some intriguing similarities. Both the AI and human process managers focus largely on communication-based interventions, though differences start to emerge in the distribution of interventions across team roles. Furthermore, team members perceive the interventions from the both the AI and human manager as equally relevant and helpful, and believe the AI agent to be just as sensitive to the needs of the team. Thus, the overall results show that the AI manager agent introduced in this work is able to match the capabilities of humans, showing potential in automating the management of a complex design process.

A Database Tool for Managing Customer and Design Information During Product Definition

1994 ◽  
Author(s):  
Dileep V. Khadilkar ◽  
John A. Gershenson ◽  
Larry A. Stauffer
Keyword(s):  
Life Cycle ◽  
Design Process ◽  
Research Program ◽  
New Product ◽  
Design Engineering ◽  
Ongoing Research ◽  
Design Information ◽  
Product Definition

Abstract We developed a new database tool to manage information during the product definition process. This tool is a result of an ongoing research program to coordinate marketing and design engineering efforts in new product developments, and consider the related life cycle issues early in the design process. The database tool facilitates a methodology that integrates customer and design information, and allows reuse of this information during redesign problems. This paper presents the development, implementation, and an example use of the database tool.

Comparison of Computational Tools for Protein-Protein Interaction (PPI) Mapping and Analysis

2013 ◽  
Vol 63 (1) ◽  
Author(s):  
Geok Wei Leong ◽  
Sheau Chen Lee ◽  
Cher Chien Lau ◽  
Peter Klappa ◽  
Mohd Shahir Shamsir Omar
Keyword(s):  
Protein Interactions ◽  
Network Visualization ◽  
Database Integration ◽  
File Format ◽  
Output File ◽  
Ppi Network ◽  
Protein Protein Interactions ◽  
Computational Tools ◽  
Protein Protein Interaction ◽  
Visualization Tools

Several visualization tools for the mapping of protein-protein interactions have been developed in recent years. However, a systematic comparison of the virtues and limitations of different PPI visualization tools has not been carried out so far. In this study, we compare seven commonly used visualization tools, based on input and output file format, layout algorithm, database integration, Gene Ontology annotation and accessibility of each tool. The assessment was carried out based on brain disease datasets. Our suggested tools, NAViGaTOR, Cytoscape and Gephi perform competitively as PPI network visualization tools, can be a reference for future researches on PPI mapping and analysis. 

A Validator and Converter for the Synthetic Biology Open Language

2017 ◽  
Vol 6 (7) ◽  
pp. 1161-1168 ◽  
Author(s):  
Zach Zundel ◽  
Meher Samineni ◽  
Zhen Zhang ◽  
Chris J. Myers
Keyword(s):  
Synthetic Biology ◽  
Synthetic Biology Open Language

scholarly journals Building Capabilities Through Democratic Dialogues

Design Issues ◽  
2018 ◽  
Vol 34 (4) ◽  
pp. 80-95 ◽  
Author(s):  
Liesbeth Huybrechts ◽  
Katrien Dreessen ◽  
Ben Hagenaars
Keyword(s):  
Design Process ◽  
Participatory Design ◽  
Design Approach ◽  
Railway Track ◽  
Alternative Futures ◽  
Design Processes ◽  
Self Organized ◽  
Complex Design ◽  
Developing Strategies

Designers are increasingly involved in designing alternative futures for their cities, together with or self-organized by citizens. This article discusses the fact that (groups of) citizens often lack the support or negotiation power to engage in or sustain parts of these complex design processes. Therefore the “capabilities” of these citizens to collectively visualize, reflect, and act in these processes need to be strengthened. We discuss our design process of “democratic dialogues” in Traces of Coal—a project that researches and designs together with the citizens an alternative spatial future for a partially obsolete railway track in the Belgian city of Genk. This process is framed in a Participatory Design approach and, more specifically, in what is called “infrastructuring,” or the process of developing strategies for the long-term involvement of participants in the design of spaces, objects, or systems. Based on this process, we developed a typology of how the three clusters of capabilities (i.e., visualize, reflect, and act) are supported through democratic dialogues in PD processes, linking them to the roles of the designer, activities, and used tools.

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