A language for modeling and optimizing experimental biological protocols
Automation is becoming ubiquitous in all laboratory activities, leading towards precisely defined and codified laboratory protocols. However, the integration between laboratory protocols and mathematical models is still lacking. Models describe physical processes, while protocols define the steps ca...
| Main Authors: | , , |
|---|---|
| Format: | Journal article |
| Language: | English |
| Published: |
MDPI
2021
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| _version_ | 1797059972405657600 |
|---|---|
| author | Cardelli, L Kwiatkowska, M Laurenti, L |
| author_facet | Cardelli, L Kwiatkowska, M Laurenti, L |
| author_sort | Cardelli, L |
| collection | OXFORD |
| description | Automation is becoming ubiquitous in all laboratory activities, leading towards precisely
defined and codified laboratory protocols. However, the integration between laboratory protocols
and mathematical models is still lacking. Models describe physical processes, while protocols define
the steps carried out during an experiment: neither cover the domain of the other, although they both
attempt to characterize the same phenomena. We should ideally start from an integrated description
of both the model and the steps carried out to test it, to concurrently analyze uncertainties in model
parameters, equipment tolerances, and data collection. To this end, we present a language to model
and optimize experimental biochemical protocols that facilitates such an integrated description,
and that can be combined with experimental data. We provide a probabilistic semantics for our
language in terms of Gaussian processes (GPs) based on the Linear Noise Approximation (LNA) that
formally characterizes the uncertainties in the data collection, the underlying model, and the protocol
operations. On a set of case studies we illustrate how the resulting framework allows for automated
analysis and optimization of experimental protocols, including Gibson assembly protocols |
| first_indexed | 2024-03-06T20:11:11Z |
| format | Journal article |
| id | oxford-uuid:2a9af028-d534-4636-8073-1d7459df9f34 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-06T20:11:11Z |
| publishDate | 2021 |
| publisher | MDPI |
| record_format | dspace |
| spelling | oxford-uuid:2a9af028-d534-4636-8073-1d7459df9f342022-03-26T12:26:06ZA language for modeling and optimizing experimental biological protocolsJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:2a9af028-d534-4636-8073-1d7459df9f34EnglishSymplectic ElementsMDPI2021Cardelli, LKwiatkowska, MLaurenti, LAutomation is becoming ubiquitous in all laboratory activities, leading towards precisely defined and codified laboratory protocols. However, the integration between laboratory protocols and mathematical models is still lacking. Models describe physical processes, while protocols define the steps carried out during an experiment: neither cover the domain of the other, although they both attempt to characterize the same phenomena. We should ideally start from an integrated description of both the model and the steps carried out to test it, to concurrently analyze uncertainties in model parameters, equipment tolerances, and data collection. To this end, we present a language to model and optimize experimental biochemical protocols that facilitates such an integrated description, and that can be combined with experimental data. We provide a probabilistic semantics for our language in terms of Gaussian processes (GPs) based on the Linear Noise Approximation (LNA) that formally characterizes the uncertainties in the data collection, the underlying model, and the protocol operations. On a set of case studies we illustrate how the resulting framework allows for automated analysis and optimization of experimental protocols, including Gibson assembly protocols |
| spellingShingle | Cardelli, L Kwiatkowska, M Laurenti, L A language for modeling and optimizing experimental biological protocols |
| title | A language for modeling and optimizing experimental biological protocols |
| title_full | A language for modeling and optimizing experimental biological protocols |
| title_fullStr | A language for modeling and optimizing experimental biological protocols |
| title_full_unstemmed | A language for modeling and optimizing experimental biological protocols |
| title_short | A language for modeling and optimizing experimental biological protocols |
| title_sort | language for modeling and optimizing experimental biological protocols |
| work_keys_str_mv | AT cardellil alanguageformodelingandoptimizingexperimentalbiologicalprotocols AT kwiatkowskam alanguageformodelingandoptimizingexperimentalbiologicalprotocols AT laurentil alanguageformodelingandoptimizingexperimentalbiologicalprotocols AT cardellil languageformodelingandoptimizingexperimentalbiologicalprotocols AT kwiatkowskam languageformodelingandoptimizingexperimentalbiologicalprotocols AT laurentil languageformodelingandoptimizingexperimentalbiologicalprotocols |