Extending SynBioHub’s Functionality with Plugins

Mante, Jeanet; Zundel, Zach; Myers, Chris J.

doi:10.1021/acssynbio.0c00056

Cited by 9 publications

(10 citation statements)

References 5 publications

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“…SynBioHub plugins are a way to create modular extensions to the capabilities of the SynBioHub repository. 44 The plugins developed as part of this project allow the integration of SynBioHub into synthetic biology workflows with spreadsheets. A submit plugin was developed for the Excel-to-SBOL converter.…”

Section: Resultsmentioning

confidence: 99%

Excel-SBOL Converter: Creating SBOL from Excel Templates and Vice Versa

Mante

Abam

Samineni

et al. 2022

Preprint

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Standards support synthetic biology research by enabling the exchange of component information. However, using formal representations, such as the Synthetic Biology Open Language (SBOL), typically requires either a thorough understanding of these standards or a suite of tools developed in concurrence with the ontologies. Since these tools may be a barrier for use by many practitioners, the Excel-SBOL Converter was developed to allow easier use of SBOL and integration into existing workflows. The converter consists of two Python libraries: one that converts Excel templates to SBOL, and another that converts SBOL to an Excel workbook. Both libraries can be used either directly or via a SynBioHub plugin. We illustrate the operation of the Excel-SBOL Converter with two case studies: uploading experimental data with the study's metadata linked to the measurements and downloading the Cello part repository.

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Section: Resultsmentioning

confidence: 99%

Excel-SBOL Converter: Creating SBOL from Excel Templates and Vice Versa

Mante

Abam

Samineni

et al. 2022

Preprint

Self Cite

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“…The strict separation between the VisBOL2 front-end and back-end enables other software tools to integrate with VisBOL2 for improved visualization. This is illustrated by VisBOL2 integration into the SynBioHub sequence view plugin 12 (SeqViz). To achieve this integration, the plugin first uses the VisBOL2 back-end to create a backing data structure.…”

Section: ■ Resultsmentioning

confidence: 99%

VisBOL2—Improving Web-Based Visualization for Synthetic Biology Designs

et al. 2021

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VisBOL is a web-based visualization tool used to depict genetic circuit designs. This tool depicts simple DNA circuits adequately, but it has become increasingly outdated as new versions of SBOL Visual were released. This paper introduces VisBOL2, a heavily redesigned version of VisBOL that makes a number of improvements to the original VisBOL, including proper functional interaction rendering, dynamic viewing, a more maintainable code base, and modularity that facilitates compatibility with other software tools. This modularity is demonstrated by incorporating VisBOL2 into a sequence visualization plugin for SynBioHub.

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“…A plugin interface to SynBioHub [12], which enabled rapid development of new functionality for data visualization, submission, and exchange [10].…”

Section: Approachmentioning

confidence: 99%

“…• Advances in biological data representation in the form of enhancements to SBOL2 for comprehensive representation of the design-build-test-learn cycle [5,8] and ultimately the development of SBOL3 [11], which in turn enabled us to accelerate the rate of data standard development and integration. • A plugin interface to SynBioHub [12], which enabled rapid development of new functionality for data visualization, submission, and exchange [10]. • The SBOL Project Dictionary tool [4], which provides a Google Sheets interface for collective "just-in-time" harmonization of terminology across organizations, thus enabling metadata translation and data fusion.…”

Section: Approachmentioning

confidence: 99%

Data Representation in the DARPA SD2 Program

Roehner

Beal

Bartley

et al. 2021

Preprint

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Modern scientific enterprises are often highly complex and multidisciplinary, particularly in areas like synthetic biology where the subject at hand is itself inherently complex and multidisciplinary. Collaboration across many organizations is necessary to efficiently tackle such problems, but remains difficult. The challenge is further amplified by automation that increases the pace at which new information can be produced, and particularly so for matters of fundamental research, where concepts and definitions are inherently fluid and may rapidly change as an investigation evolves. The DARPA program Synergistic Discovery and Design (SD2) aimed to address these challenges by organizing the development of data-driven methods to accelerate discovery and improve design robustness, with one of the key domains under study being synthetic biology. The program was specifically organized such that teams provided complementary types of expertise and resources, and without any team being in a dominant organizational position, such that subject-matter investigations would necessarily require peer-level collaboration across multiple team boundaries. With more than 100 researchers across more than 20 organizations, several of which ran experimental facilities with high-throughput automation, participants were forced to confront challenges around effective data sharing. The default architecture for scientific collaboration is essentially one of anarchy, with ad-hoc bilateral relations between pairs of collaborators or experimental phases. This was by necessity the case during early phases of the SD2 program as well, in which incorporating new tools into pipelines was ad-hoc and time-consuming, and data was generally disconnected from genetic designs and experimental plans. The other typical approach for collaboration is one of "command and control", in which a dominant organization determines the data sharing content and format for all participants. This can be efficient, but tends to be limited in flexibility and extensibility, rendering it unsuitable for research collaboration, as indeed was found when we attempted this approach during the first year of the SD2 program. We addressed these problems with the application of distributed standards to create a "flexible rendezvous" model of collaboration, enabling information flow to track evolving collaborative relationships, improving the sharing and utility of information across the community and supporting accelerated rates of experimentation.

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Extending SynBioHub’s Functionality with Plugins

Cited by 9 publications

References 5 publications

Excel-SBOL Converter: Creating SBOL from Excel Templates and Vice Versa

Excel-SBOL Converter: Creating SBOL from Excel Templates and Vice Versa

VisBOL2—Improving Web-Based Visualization for Synthetic Biology Designs

Data Representation in the DARPA SD2 Program

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