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Flapjack: Data Management and Analysis for Genetic Circuit Characterization

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Synthetic Biology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2760))

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Abstract

Flapjack presents a valuable solution for addressing challenges in the Design, Build, Test, Learn (DBTL) cycle of engineering synthetic genetic circuits. This platform provides a comprehensive suite of features for managing, analyzing, and visualizing kinetic gene expression data and associated metadata. By utilizing the Flapjack platform, researchers can effectively integrate the test phase with the build and learn phases, facilitating the characterization and optimization of genetic circuits. With its user-friendly interface and compatibility with external software, the Flapjack platform offers a practical tool for advancing synthetic biology research.

This chapter provides an overview of the data model employed in Flapjack and its hierarchical structure, which aligns with the typical steps involved in conducting experiments and facilitating intuitive data management for users. Additionally, this chapter offers a detailed description of the user interface, guiding readers through accessing Flapjack, navigating its sections, performing essential tasks such as uploading data and creating plots, and accessing the platform through the pyFlapjack Python package.

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References

  1. Yáñez Feliú G, Earle Gómez B, Codoceo Berrocal V, Muñoz Silva M, Nuñez IN, Matute TF, Arce Medina A, Vidal G, Vitalis C, Dahlin J, Federici F, Rudge TJ (2021) Flapjack: data management and analysis for genetic circuit characterization. ACS Synth Biol 10:183–191. https://doi.org/10.1021/acssynbio.0c00554

    Article  CAS  PubMed  Google Scholar 

  2. Vidal G, Vitalis C, Rudge TJ (2021) LOICA: integrating models with data for genetic network design automation. ACS Synth Biol 2021.09.21.460548-2021.09.21.460548. https://doi.org/10.1021/acssynbio.1c00603

  3. McLaughlin JA, Myers CJ, Zundel Z, Mlslrll G, Zhang M, Ofiteru ID, Goñi-Moreno A, Wipat A (2018) SynBioHub: a standards-enabled design repository for synthetic biology. ACS Synth Biol 7:682–688. https://doi.org/10.1021/ACSSYNBIO.7B00403

    Article  CAS  PubMed  Google Scholar 

  4. Vidal G, Vitalis C, Muñoz Silva M, Castillo-Passi C, Yáñez Feliú G, Federici F, Rudge TJ (2022) Accurate characterization of dynamic microbial gene expression and growth rate profiles. Synth Biol 7. https://doi.org/10.1093/SYNBIO/YSAC020

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Author information

Authors and Affiliations

  1. Department of Electrical, Computer, and Energy Engineering, University of Colorado Boulder, Boulder, CO, USA

    Carolus Vitalis

  2. Interdisciplinary Computing and Complex Biosystems, School of Computing, Newcastle University, Newcastle upon Tyne, UK

    Guillermo Yáñez Feliú, Gonzalo Vidal, Macarena Muñoz Silva & Timothy J. Rudge

  3. ANID-Millennium Science Initiative Program Millennium Institute for Integrative Biology (iBio), Santiago, Chile

    Tamara Matúte, Isaac Núñez & Fernán Federici

  4. FONDAP Center for Genome Regulation, Santiago, Chile

    Tamara Matúte, Isaac Núñez & Fernán Federici

  5. Institute for Biological and Medical Engineering Schools of Engineering, Medicine and Biological Sciences Pontificia Universidad Catolica de Chile, Santiago, Chile

    Tamara Matúte, Isaac Núñez & Fernán Federici

Authors
  1. Carolus Vitalis
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  2. Guillermo Yáñez Feliú
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  3. Gonzalo Vidal
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  4. Macarena Muñoz Silva
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  5. Tamara Matúte
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  6. Isaac Núñez
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  7. Fernán Federici
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  8. Timothy J. Rudge
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Corresponding author

Correspondence to Timothy J. Rudge .

Editor information

Editors and Affiliations

  1. Agilent Technologies, Inc, La Jolla, CA, USA

    Jeffrey Carl Braman

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© 2024 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Vitalis, C. et al. (2024). Flapjack: Data Management and Analysis for Genetic Circuit Characterization. In: Braman, J.C. (eds) Synthetic Biology. Methods in Molecular Biology, vol 2760. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3658-9_23

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  • DOI: https://doi.org/10.1007/978-1-0716-3658-9_23

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3657-2

  • Online ISBN: 978-1-0716-3658-9

  • eBook Packages: Springer Protocols

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