Synthetic biology – the state of play

Kitney, R.I.; Freemont, Paul S.

doi:10.1016/j.febslet.2012.06.002

Cited by 83 publications

(58 citation statements)

References 28 publications

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“…Application-specific data can be embedded in SBOL documents in the form of annotations, enabling the exchange of information that is not captured explicitly by the SBOL data model. Other standards that are useful for synthetic biologists include DICOM-SB, which adds features such as raw measurement data [20,21], the Systems Biology Markup Language (SBML) [22], CellML [23] and Kappa [24], both of which allow the easy representation and exchange of dynamic models of biological parts.…”

Section: Research Articlementioning

confidence: 99%

Constructing synthetic biology workflows in the cloud

Mısırlı

Madsen

Murieta

et al. 2017

Engineering Biology

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Abstract:The synthetic biology design process has traditionally been heavily dependent upon manual searching, acquisition and integration of existing biological data. A large amount of such data is already available from Internetbased resources, but data exchange between these resources is often undertaken manually. Automating the communication between different resources can be done by the generation of computational workflows to achieve complex tasks that cannot be carried out easily or efficiently by a single resource. Computational workflows involve the passage of data from one resource, or process, to another in a distributed computing environment. In a typical bioinformatics workflow, the predefined order in which processes are invoked in a synchronous fashion and are described in a workflow definition document. However, in synthetic biology the diversity of resources and manufacturing tasks required favour a more flexible model for process execution. Here, the authors present the Protocol for Linking External Nodes (POLEN), a Cloud-based system that facilitates synthetic biology design workflows that operate asynchronously. Messages are used to notify POLEN resources of events in real time, and to log historical events such as the availability of new data, enabling networks of cooperation. POLEN can be used to coordinate the integration of different synthetic biology resources, to ensure consistency of information across distributed repositories through added support for data standards, and ultimately to facilitate the synthetic biology life cycle for designing and implementing biological systems.

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Section: Research Articlementioning

confidence: 99%

Constructing synthetic biology workflows in the cloud

Mısırlı

Madsen

Murieta

et al. 2017

Engineering Biology

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“…Finally, one has to consider that effective techniques to ensure biological safety in critical application contexts have to be rapidly available, because some applications are already well advanced (Folcher and Fussenegger 2012;Kitney and Freemont 2012). Hence, with regard to the drawbacks mentioned above, it is worth exploring more feasible approaches.…”

Section: Trophic and Semantic Containment: Systems On An Unnatural Basismentioning

confidence: 99%

Hazards, Risks, and Low Hazard Development Paths of Synthetic Biology

Giese

Gleich

2014

Risk Engineering

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In early stages of research and innovation a precise investigation of technological risks, as well as the analysis of particular beneficial features, is confronted with a lack of knowledge about exact process or product qualities, application contexts and intentions of users. Therefore, an appropriate identification of anticipated risks, accompanied by the achievements of synthetic biology, should rather focus on basic properties and functionalities of the objects of synthetic biology which will be exploited in future products and processes. Accordingly, the aim of this chapter is to determine major risk factors of synthetic biology creations with a focus on the technology itself. In consideration of the demand to cover these risks by appropriate counter measures, the question is raised, whether there are suitable strategies to achieve a high level of safety. In this regard, the discussion will be extended to feasible alternatives, e.g. by introducing trophic and semantic isolation strategies for synthetic organisms as an approach to overcome major drawbacks of classical biosafety mechanisms. Finally, functional reduction, a concept which is already aspiring to achieve efficient biosynthesis, is suggested as a measure for the reduction of risk-related functionalities. This strategy is worth further investigation if the full potential of synthetic biology is to be obtained in a safe and sustainable way.

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“…BBC, 2010). In practice, however, it is important to note that the potential range of applications available for use in the short term remains more prosaic (Kitney & Freemont, 2012), and it is long term future developments which are the object of speculation (Kaiser, 2012;Vincent, 2013). Indeed, Bubela et al (2012, p.132) have noted that "maintaining the trust of the public and policy regulators is paramount….Hype and exaggerated claims are counterproductive to developing adaptive and ethically sound regulatory models responsive to stakeholder concerns".…”

Section: Introductionmentioning

confidence: 99%