pyBrick-DNA: A Python-Based Environment for Automated Genetic Component Assembly

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dc.affiliation.dptoGladys Cavero, Jose Cisneros, Yomali Ferreyra y Alberto Donayre: Departamento de Bioingeniería e Ingeniería Química, Universidad de Ingeniería y Tecnología (UTEC), Barranco, Lima, Perú
dc.affiliation.dptoDaniela Moreno, Yerko Ortiz y Martín Gutiérrez: Escuela de Informática y Telecomunicaciones, Universidad Diego Portales, Santiago, Chile
dc.contributor.authorCavero Rozas, Gladys M.
dc.contributor.authorCisneros Mandujano, Jose M.
dc.contributor.authorFerreyra Chombo, Yomali A.
dc.contributor.authorMoreno Rencoret, Daniela V.
dc.contributor.authorOrtiz Mora, Yerko M.
dc.contributor.authorGutiérrez Pescarmona, Martín E.
dc.contributor.authorDonayre Torres, Alberto J.
dc.contributor.funderUTEC (Perú)
dc.contributor.funderCentroBio UTEC (Perú)
dc.contributor.funderANID (Chile) - FONDECYT proyecto 11220293
dc.date.accessioned2026-02-27T10:30:10Z
dc.date.issued2023-12-14
dc.descriptionEste artículo presenta una herramienta de software escrita en Python (un notebook de Colab) con una GUI que apoya al investigador al automatizar el ensamblaje de componentes genéticos transcripcionales, y constructos de CRISPR con un sgRNA y Cas9. La herramienta permite trabajar con estándares de datos de uso frecuente en la biología sintética como lo son SBOL, GenBank y FASTA. El investigador puede seleccionar las partes que ya estén caracterizadas (por ejemplo desde el registro de iGEM) o bien ingresar secuencias custom. Finalmente, la parte ensamblada se exporta en formato GenBank para poder ser usada por otras herramientas de biología sintética.
dc.description.abstractGenetic component assembly is key in the simulation and implementation of genetic circuits. Automating this process, thus accelerating prototyping, is a necessity. We present pyBrick- DNA, a software written in Python, that assembles components for the construction of genetic circuits. pyBrick-DNA (colab.pyBrick.com) is a user-friendly environment where scientists can select genetic sequences or input custom sequences to build genetic assemblies. All components are modularly fused to generate a ready-to-go single DNA fragment. It includes Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and plant gene-editing components. Hence, pyBrick-DNA can generate a functional CRISPR construct composed of a single-guided RNA integrated with Cas9, promoters, and terminator elements. The outcome is a DNA sequence, along with a graphical representation, composed of user-selected genetic parts, ready to be synthesized and cloned in vivo. Moreover, the sequence can be exported as a GenBank file allowing its use with other synthetic biology tools.
dc.identifier.citationCavero Rozas GM, Mandujano JMC, Chombo YAF, et al. pyBrick-DNA: A Python-Based Environment for Automated Genetic Component Assembly. Journal of Computational Biology. 2023;30(12):1315-1321. doi:10.1089/cmb.2023.0008
dc.identifier.doi10.1089/cmb.2023.0008
dc.identifier.issn1557-8666
dc.identifier.publicationfirstpage1315
dc.identifier.publicationissue12
dc.identifier.publicationlastpage1321
dc.identifier.publicationtitleJournal of Computational Biology
dc.identifier.publicationvolume30
dc.identifier.urihttps://hdl.handle.net/10115/167897
dc.identifier.urlhttps://journals.sagepub.com/doi/full/10.1089/cmb.2023.0008
dc.language.isoen_US
dc.publisherMary Ann Liebert, Inc.
dc.rights.accessRightsinfo:eu-repo/semantics/closedAccess
dc.subjectautomation tool
dc.subjectCRISPR
dc.subjectGenBank
dc.subjectgenetic assembly
dc.subjectgenetic components
dc.subjectsynthetic biology
dc.titlepyBrick-DNA: A Python-Based Environment for Automated Genetic Component Assembly
dc.typeSoftware
dc.typeArticle

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