Y3 BME Automation Group Project : References

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References

References used in our group project: Year 3 BME Group Project 22-23: Automation of Laboratory Protocols

Brochure

  1. 8 Channel Electronic Pipette (GEN2) (2023) Opentrons Labworks Inc. Available at: https://shop.opentrons.com/8-channel-electronic-pipette/ (Accessed: 27 May 2023).
  2. Clarke, L. et al. (2012) A Synthetic Biology Roadmap for the UK. Available at: https://connect.innovateuk.org/web/synthetic-biology-special-interest-group/roadmap-for-synthetic-biology (Accessed: 6 March 2023).
  3. Crunchbase. Inc (2023) Opentrons. Available at: https://www.crunchbase.com/organization/opentrons (Accessed: 1 April 2023).
  4. Fallon, T. and Bryce, D. (2023) LabOP - an open specification for laboratory protocols, that solves common interchange problems stemming from variations in scale, labware, instruments, and automation. Available at: https://ospo.ucsc.edu/project/osre23/ucsd/labop/ (Accessed: 1 April 2023).
  5. Lubio Science (no date) High quality, affordable PCR plates, Lubio Science. Available at: https://www.lubio.ch/applications/consumables/plates (Accessed: 25 April 2023).
  6. Opentrons Labworks Inc (2023) Single Channel Electronic Pipette (GEN2), Opentrons Labworks Inc. Available at: https://shop.opentrons.com/single-channel-electronic-pipette-p20/ (Accessed: 25 April 2023).
  7. Opentrons Labworks Inc (2023) Opentrons, Opentrons Python Protocol API. Available at: https://docs.opentrons.com/v2/index.html (Accessed: 7 May 2023).
  8. Royal Academy of Engineering (2009) Synthetic biology: scope, applications and implications. London: Royal Academy of Engineering.

Final Report

  1. Clarke, L., Adams, J., Sutton, P., Bainbridge, J.W., Birney, E., Calvert, J., Collis, A., Kitney, R., Freemont, P., Mason, P., Pandya, K., Ghaffar, T., Rose, N., Marris, C., Woolfson, D. and Boyce, A., 2012. A Synthetic Biology Roadmap for the UK. [Other] Available at: <https://connect.innovateuk.org/web/synthetic-biology-special-interest-group/roadmap-for-synthetic-biology> [Accessed 6 March 2023].
  2. Royal Academy of Engineering, 2009. Synthetic biology: scope, applications and implications. London: Royal Academy of Engineering.
  3. Gidakovic, S., 2023. Guides: Biology: Protocols and Methods. [online] University of Central Missouri. Available at: <https://guides.library.ucmo.edu/c.php?g=141808&p=8215796> [Accessed 12 February 2023].
  4. Jessop-Fabre, M.M. and Sonnenschein, N., 2019. Improving Reproducibility in Synthetic Biology. Frontiers in Bioengineering and Biotechnology, [online] 7, p.18. https://doi.org/10.3389/fbioe.2019.00018.
  5. Baker, M., 2016. 1,500 scientists lift the lid on reproducibility. Nature, [online] 533(7604), pp.452–454. https://doi.org/10.1038/533452a.
  6. Opentrons, 2023b. The OT-2: Your Personal Pipetting Robot. [online] Opentrons. Available at: <https://opentrons.com/ot-2/> [Accessed 17 March 2023].
  7. Lippi, G. and Rin, G.D., 2019. Advantages and limitations of total laboratory automation: a personal overview. Clinical Chemistry and Laboratory Medicine (CCLM), [online] 57(6), pp.802–811. https://doi.org/10.1515/cclm-2018-1323.
  8. PLOS, 2019. Are biofoundries the solution to synbio democratization? The Official PLOS Blog. Available at: <https://theplosblog.plos.org/2019/05/are-biofoundries-the-solution-to-synbio-democratization/> [Accessed 29 March 2023].
  9. Walsh, D.I., Pavan, M., Ortiz, L., Wick, S., Bobrow, J., Guido, N.J., Leinicke, S., Fu, D., Pandit, S., Qin, L., Carr, P.A. and Densmore, D., 2019. Standardizing Automated DNA Assembly: Best Practices, Metrics, and Protocols Using Robots. SLAS Technology, [online] 24(3), pp.282–290. https://doi.org/10.1177/2472630318825335.
  10. New England BioLabs, 2023. DNA Assembly and Cloning. [online] New England BioLabs. Available at: <https://www.neb.sg/applications/cloning-and-synthetic-biology/dna-assembly-and-cloning> [Accessed 29 March 2023].
  11. New England BioLabs, 2012b. Gibson Assembly. [online] New England BioLabs. Available at: <https://international.neb.com/applications/cloning-and-synthetic-biology/dna-assembly-and-cloning/gibson-assembly> [Accessed 20 March 2023].
  12. Gibson, D.G., Young, L., Chuang, R.-Y., Venter, J.C., Hutchison, C.A. and Smith, H.O., 2009. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nature Methods, 6(5), pp.343–345. https://doi.org/10.1038/nmeth.1318.
  13. New England BioLabs, 2012a. Gibson Assembly® Protocol (E5510). [online] New England BioLabs. Available at:

<https://international.neb.com/protocols/2012/12/11/gibson-assembly-protocol-e5510> [Accessed 30 January 2023].

  1. New England BioLabs, 2020. Golden Gate Assembly. [online] New England BioLabs. Available at: <https://international.neb.com/applications/cloning-and-synthetic-biology/dna-assembly-and-cloning/golden-gate-assembly> [Accessed 20 March 2023].
  2. Engler, C., Kandzia, R. and Marillonnet, S., 2008. A One Pot, One Step, Precision Cloning Method with High Throughput Capability. PLoS ONE, 3(11), p.e3647. https://doi.org/10.1371/journal.pone.0003647.
  3. Bird, J.E., Marles-Wright, J. and Giachino, A., 2022. A User’s Guide to Golden Gate Cloning Methods and Standards. ACS Synthetic Biology, [online] 11(11), pp.3551–3563. https://doi.org/10.1021/acssynbio.2c00355.
  4. New England BioLabs, 2021. Golden Gate Assembly Protocol for Using NEBridge® Golden Gate Assembly Kit (BsaI-HF®v2) (E1601). [online] New England BioLabs. Available at: <https://international.neb.com/protocols/2018/10/02/golden-gate-assembly-protocol-for-using-neb-golden-gate-assembly-mix-e1601> [Accessed 30 January 2023].
  5. Opentrons, 2023a. Opentrons Platform (API and App). [online] Opentrons. Available at: <https://github.com/Opentrons/opentrons> [Accessed 20 February 2023].
  6. Bartley, B., Beal, J., Rogers, M., Bryce, D., Goldman, R.P., Keller, B., Lee, P., Biggers, V., Nowak, J. and Weston, M., 2022. Building an Open Representation for Biological Protocols. https://doi.org/10.1101/2022.07.05.498808.
  7. Bioprotocols Group, 2023. Laboratory Open Protocol Language. [online] Bioprotocols Group. Available at: <https://github.com/Bioprotocols/labop> [Accessed 20 February 2023].
  8. The PyLabRobot authors, 2022. Welcome to PyLabRobot’s documentation! — PyLabRobot documentation. [online] Available at: <https://docs.pylabrobot.org/> [Accessed 2 April 2023].
  9. Opentrons Labworks, Inc, 2023c. Opentrons Python API V2 Documentation. [online] Opentrons. Available at: <https://docs.opentrons.com/v2/index.html> [Accessed 31 March 2023].
  10. Booch, G., Rumbaugh, J. and Jacobson, I., 1996. The Unified Modeling Language for Object-Oriented Development.
  11. Beckett, D. and McBride, B., 2004. RDF/XML Syntax Specification (Revised). [online] W3C Recommendation. Available at: <https://www.w3.org/TR/REC-rdf-syntax/> [Accessed 31 March 2023].
  12. Galdzicki, M., Clancy, K.P., Oberortner, E., Pocock, M., Quinn, J.Y., Rodriguez, C.A., Roehner, N., Wilson, M.L., Adam, L., Anderson, J.C., Bartley, B.A., Beal, J., Chandran, D., Chen, J., Densmore, D., Endy, D., Grünberg, R., Hallinan, J., Hillson, N.J., Johnson, J.D., Kuchinsky, A., Lux, M., Misirli, G., Peccoud, J., Plahar, H.A., Sirin, E., Stan, G.-B., Villalobos, A., Wipat, A., Gennari, J.H., Myers, C.J. and Sauro, H.M., 2014. The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology. Nature Biotechnology, [online] 32(6), pp.545–550. https://doi.org/10.1038/nbt.2891.
  13. Opentrons Labworks, Inc, 2022. Opentrons Protocol Designer BETA. [online] Opentrons Labworks, Inc. Available at: <https://designer.opentrons.com/> [Accessed 1 February 2023].
  14. Bioprotocols Working Group, 2023. About the Bioprotocols Working Group. [online] The Laboratory Open Protocol Language (LabOP). Available at: <https://bioprotocols.github.io/labop/about.html> [Accessed 31 March 2023].
  15. Opentrons Labworks, Inc, 2023a. Labware Library. [online] Opentrons. Available at: <https://labware.opentrons.com/> [Accessed 31 March 2023].
  16. Opentrons Labworks, Inc, 2023b. Labware Library - Custom Labware Creator BETA. [online] Opentrons. Available at: <https://labware.opentrons.com/create/> [Accessed 31 March 2023].
  17. Bartley, B., Beal, J., Bryce, D., Goldman, R.P., Keller, B., Lee, P., Nowak, J., Rogers, M. and Weston, M., 2021. Laboratory Open Protocol language (LabOP) Version 1.0.0-alpha.
  18. Hamilton Company, 2023. Automated Liquid Handlers | Liquid Handling Equipment. [online] Hamilton Company. Available at: <https://www.hamiltoncompany.com/automated-liquid-handling> [Accessed 1 April 2023].
  19. iGEM Foundation, 2022a. DNA Repository Plates and Boxes - parts.igem.org. [online] Available at: <http://parts.igem.org/assembly/plates.cgi?id=6437> [Accessed 6 April 2023].
  20. iGEM Foundation, 2022b. Registry of Standard Biological Parts. [online] Available at: <http://parts.igem.org/Main_Page> [Accessed 6 April 2023].
  21. New England Biolabs Inc., 2022. NEBridge® Golden Gate Assembly Kit (BsaI-HF® v2). [online] New England BioLabs. Available at: <https://international.neb.com/products/e1601-nebridge-golden-gate-assembly-mix-basai-hf-v2#Product%20Information> [Accessed 6 April 2023].
  22. SnapGene, 2023. SnapGene Molecular Cloning Tool. Available at: <https://www.snapgene.com/> [Accessed 7 March 2023].
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