LOICA: Integrating Models with Data for Genetic Network Design Automation

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dc.contributor.authorVidal, Gonzalo
dc.contributor.authorVidal-Cespedes, Carlos
dc.contributor.authorRudge, Timothy J.
dc.date.accessioned2025-01-20T21:07:49Z
dc.date.available2025-01-20T21:07:49Z
dc.date.issued2022
dc.description.abstractGenetic design automation tools are necessary to expand the scale and complexity of possible synthetic genetic networks. These tools are enabled by abstraction of a hierarchy of standardized components and devices. Abstracted elements must be parametrized from data derived from relevant experiments, and these experiments must be related to the part composition of the abstract components. Here we present Logical Operators for Integrated Cell Algorithms (LOICA), a Python package for designing, modeling, and characterizing genetic networks based on a simple object-oriented design abstraction. LOICA uses classes to represent different biological and experimental components, which generate models through their interactions. These models can be parametrized by direct connection to data contained in Flapjack so that abstracted components of designs can characterize themselves. Models can be simulated using continuous or stochastic methods and the data published and managed using Flapjack. LOICA also outputs SBOL3 descriptions and generates graph representations of genetic network designs.
dc.fuente.origenWOS
dc.identifier.doi10.1021/acssynbio.1c00603
dc.identifier.issn2161-5063
dc.identifier.urihttps://doi.org/10.1021/acssynbio.1c00603
dc.identifier.urihttps://repositorio.uc.cl/handle/11534/93438
dc.identifier.wosidWOS:000805370400026
dc.issue.numero5
dc.language.isoen
dc.pagina.final1990
dc.pagina.inicio1984
dc.revistaAcs synthetic biology
dc.rightsacceso restringido
dc.subjectgenetic network
dc.subjectgenetic design automation
dc.subjectmodeling
dc.subjectcharacterization
dc.subjectdynamical systems
dc.subjectdesign abstraction
dc.subject.ods03 Good Health and Well-being
dc.subject.odspa03 Salud y bienestar
dc.titleLOICA: Integrating Models with Data for Genetic Network Design Automation
dc.typeartículo
dc.volumen11
sipa.indexWOS
sipa.trazabilidadWOS;2025-01-12
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