Specifications of standards in systems and synthetic biology: status and developments in 2020

Schreiber, Falk; Sommer, Björn; Czauderna, Tobias; Golebiewski, Martin; Gorochowski, Thomas E.; Hucka, Michael; Keating, Sarah M.; König, Matthias; Myers, Chris J.; Nickerson, David; Waltemath, Dagmar

doi:10.1515/jib-2020-0022

Cited by 18 publications

(13 citation statements)

References 51 publications

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“…Another area of growing importance in biological engineering is the development and adoption of standards to facilitate improved exchange and reuse of engineered biological parts and systems 99 , as well as data associated with these 100 . Standards are also pervasive in natural biology with an example being the use of a (mostly) common genetic code that aids the exchange and reuse Fig.…”

Section: Toward Evotype Engineeringmentioning

confidence: 99%

Towards an engineering theory of evolution

2021

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Biological technologies are fundamentally unlike any other because biology evolves. Bioengineering therefore requires novel design methodologies with evolution at their core. Knowledge about evolution is currently applied to the design of biosystems ad hoc. Unless we have an engineering theory of evolution, we will neither be able to meet evolution’s potential as an engineering tool, nor understand or limit its unintended consequences for our biological designs. Here, we propose the evotype as a helpful concept for engineering the evolutionary potential of biosystems, or other self-adaptive technologies, potentially beyond the realm of biology.

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Section: Toward Evotype Engineeringmentioning

confidence: 99%

Towards an engineering theory of evolution

2021

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“…Many of these tools are able to exploit increasingly available high-performance computing resources, which is key for moving towards larger dynamical models [38,39,44]. The use of community standards for specifying models and parameter estimation problems [45][46][47] gives easy access to a majority of these tools.…”

Section: Determining Model Parametersmentioning

confidence: 99%

Dynamical models for metabolomics data integration

Lakrisenko,

Weindl

2021

Preprint

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As metabolomics datasets are becoming larger and more complex, there is an increasing need for modelbased data integration and analysis to optimally leverage these data. Dynamical models of metabolism allow for the integration of heterogeneous data and the analysis of dynamical phenotypes. Here, we review recent efforts in using dynamical metabolic models for data integration, focusing on approaches that are not restricted to steady-state measurements or that require flux distributions as inputs. Furthermore, we discuss recent advances and current challenges. We conclude that much progress has been made in various areas, such as the development of scalable simulation tools, and that, although challenges remain, dynamical modeling is a powerful tool for metabolomics data analysis that is not yet living up to its full potential.

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“…The use of SBOLv simplifies the communication of designs and aids both collaboration and reproducibility by removing much of the ambiguity in how core biological parts and their interactions are displayed ( 2 , 3 ). SBOLv fits into a larger standards ecosystem across bioengineering ( 4 ). For example, the SBOL data standard ( 5–7 ) is used to capture detailed information about both the structure and function of a design to facilitate data exchange and enable complex design-build-test-learn workflows ( 8 ), and modeling standards like the Systems Biology Markup Language (SBML) ( 9 ) are used to simulate and test the function of possible designs before they are built.…”

Section: Introductionmentioning

confidence: 99%

paraSBOLv: a foundation for standard-compliant genetic design visualization tools

2021

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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.

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Specifications of standards in systems and synthetic biology: status and developments in 2020

Abstract: AbstractThis special issue of the Journal of Integrative Bioinformatics presents papers related to the 10th COMBINE meeting together with the annual update of COMBINE standards in systems and synthetic biology.

Cited by 18 publications

References 51 publications

Towards an engineering theory of evolution

Towards an engineering theory of evolution

Dynamical models for metabolomics data integration

paraSBOLv: a foundation for standard-compliant genetic design visualization tools

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