libSBOLj 2.0: A Java Library to Support SBOL 2.0

Zhang, Zhen; Nguyen, Tramy; Roehner, Nicholas; Mısırlı, Göksel; Pocock, Matthew; Oberortner, Ernst; Samineni, Meher; Zundel, Zach; Beal, Jacob; Clancy, Kevin J.; Wipat, Anil; Myers, Chris J.

doi:10.1109/lls.2016.2547038

Cited by 4 publications

(5 citation statements)

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“…This pool designer application features a web page interface written in JavaScript and HTML for communication with human users and a representational state transfer application program interface for communication with other applications over the web. The application uses the existing software libraries libSBOLj ( 49 ) for importing and exporting construct designs written in SBOL and Neo4j (Neo Technology Inc., San Mateo, CA, USA) for storing and querying pool extraction data as graphs. The source code for the pool designer application is available open source (BSD license) on GitHub at https://github.com/CIDARLAB/poolDesigner/ .…”

Section: Methodsmentioning

confidence: 99%

Registry in a tube: multiplexed pools of retrievable parts for genetic design space exploration

et al. 2016

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Genetic designs can consist of dozens of genes and hundreds of genetic parts. After evaluating a design, it is desirable to implement changes without the cost and burden of starting the construction process from scratch. Here, we report a two-step process where a large design space is divided into deep pools of composite parts, from which individuals are retrieved and assembled to build a final construct. The pools are built via multiplexed assembly and sequenced using next-generation sequencing. Each pool consists of ∼20 Mb of up to 5000 unique and sequence-verified composite parts that are barcoded for retrieval by PCR. This approach is applied to a 16-gene nitrogen fixation pathway, which is broken into pools containing a total of 55 848 composite parts (71.0 Mb). The pools encompass an enormous design space (1043 possible 23 kb constructs), from which an algorithm-guided 192-member 4.5 Mb library is built. Next, all 1030 possible genetic circuits based on 10 repressors (NOR/NOT gates) are encoded in pools where each repressor is fused to all permutations of input promoters. These demonstrate that multiplexing can be applied to encompass entire design spaces from which individuals can be accessed and evaluated.

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Section: Methodsmentioning

confidence: 99%

Registry in a tube: multiplexed pools of retrievable parts for genetic design space exploration

et al. 2016

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“…The existence of a research community actively working on SBOL development has also been a key aspect of our work. As an example, the development of the SynBIS API encoding the data model uses the libSBOLj Java library [67] to produce SBOL serialisations. In the next version of SynBIS we are planning to use sboljs [68] within our SynBIS front‐end so that it can directly access the data from our new SBOL API without parsing.…”

Section: Discussionmentioning

confidence: 99%

“…All the UML diagrams presented in the paper have been produced by this tool. The SynBIS API implementing our data model has been developed as a RESTful Web Service under Java EE 7 [80]. The generation of the code has been supported by the libSBOLj Java library [67]. …”

Section: Methodsmentioning

confidence: 99%

Data model for biopart datasheets

Murieta

Bultelle

Kitney

2018

Engineering Biology

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This study introduces a new data model, based on the DICOM-SB (see glossary of terms for definition of acronyms) standard for synthetic biology, that is capable of describing/incorporating the data, metadata and ancillary information from detailed characterisation experimentsto present DNA components (bioparts) in datasheets. The data model offers a standardised mechanism to associate bioparts with data and information about component performancein a particular biological context (or a range of contexts, e.g. chassis). The data model includes the raw, experimental data for each characterisation run, and the protocol details needed to reliably reproduce the experiment. In addition, it provides metrics (e.g. relative promoter units, synthesis/growth rates etc.) that constitute the main content of a biopart datasheet. The data model has been developed to directly link to DICOM-SB, but also to be compatible with existing data standards, e.g. SBOL and SBML. It has been implemented within the latest version of the API that enables access to the SynBIS information system. The work should contribute significantly to the current standardisation effort in synthetic biology. The standard data model for datasheets is seen as a necessary step towards effective interoperability between part repositories, and between repositories and BioCAD applications.

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“…The data layer has been developed in Java as a Maven project using libSBOLj (61 ) and can be used as a standalone library.…”

Section: Methodsmentioning

confidence: 99%

Virtual Parts Repository 2: Model-driven design of genetic regulatory circuits

Mısırlı

Yang

James

et al. 2021

Preprint

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Engineering genetic regulatory circuits is key to the creation of biological applications that are responsive to environmental changes. Computational models can assist in understanding especially large and complex circuits where manual analysis is infeasible, permitting a model-driven design process. However, there are still few tools that offer the ability to simulate the system under design. One of the reasons for this is the lack of accessible model repositories or libraries that cater for the modular composition of models of synthetic systems that do not yet exist in nature. Here, we present the Virtual Parts Repository 2, a resource to facilitate the model-driven design of genetic regulatory circuits, which provides reusable, modular and composable models. The repository is service-oriented and can be utilized by design tools in computational workflows. Designs provided in Synthetic Biology Open Language documents are used to derive system-scale and hierarchical Systems Biology Markup Language models. We also present a rule-based modeling abstraction based on reaction networks to facilitate scalable and modular modeling of complex and large designs. This modeling abstraction incorporates design patterns such as roadblocking, distributed deployment of genetic circuits using plasmids and cellular resource dependency. The computational resources and the modeling abstraction presented in this paper allow computational design tools to take advantage of computational simulations and ultimately help facilitate more predictable applications.

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libSBOLj 2.0: A Java Library to Support SBOL 2.0

Cited by 4 publications

References 1 publication

Registry in a tube: multiplexed pools of retrievable parts for genetic design space exploration

Registry in a tube: multiplexed pools of retrievable parts for genetic design space exploration

Data model for biopart datasheets

Virtual Parts Repository 2: Model-driven design of genetic regulatory circuits

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