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| Indexado |
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| DOI | 10.1021/ACSSYNBIO.1C00603 | ||||
| Año | 2022 | ||||
| Tipo | artículo de investigación |
Citas Totales
Autores Afiliación Chile
Instituciones Chile
% Participación
Internacional
Autores
Afiliación Extranjera
Instituciones
Extranjeras
Genetic 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.
| Ord. | Autor | Género | Institución - País |
|---|---|---|---|
| 1 | Vidal, Gonzalo | Hombre |
Pontificia Universidad Católica de Chile - Chile
Newcastle Univ - Reino Unido Newcastle University - Reino Unido |
| 2 | Vidal-Cespedes, Carlos | Hombre |
Pontificia Universidad Católica de Chile - Chile
Newcastle University - Reino Unido |
| 3 | Rudge, Timothy J. | Hombre |
Newcastle Univ - Reino Unido
Newcastle University - Reino Unido |
| Fuente |
|---|
| Pontificia Universidad Católica de Chile |
| Institute for Biological and Medical Engineering |
| Newcastle University |
| ANID Fondecyt |
| Agencia Nacional de Investigación y Desarrollo |
| ANID Fondecyt Regular |
| Institute for Biological and Medical Engineering, Pontificia Universidad Catolica de Chile |
| ANID PIA Anillo |
| School of Computing, Newcastle University |
| Agradecimiento |
|---|
| G.V. was supported by a scholarship from the Institute for Biological and Medical Engineering, Pontificia Universidad Catolica de Chile, a scholarship from the School of Computing, Newcastle University, and ANID Fondecyt Regular 11140601. G.V., C.V., and T.J.R. were supported by ANID PIA Anillo ACT192015 and ANID Fondecyt Regular 1211598. The authors thank Chris Myers, Jacob Beal, Tom Mitchell, Guillermo Yanez, and Gabriel Miranda for their helpful comments and discussions. |
| G.V. was supported by a scholarship from the Institute for Biological and Medical Engineering, Pontificia Universidad Católica de Chile, a scholarship from the School of Computing, Newcastle University, and ANID Fondecyt Regular 11140601. G.V., C.V., and T.J.R. were supported by ANID PIA Anillo ACT192015 and ANID Fondecyt Regular 1211598. The authors thank Chris Myers, Jacob Beal, Tom Mitchell, Guillermo Yañez, and Gabriel Miranda for their helpful comments and discussions. |