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Challenges automation sharing manual error data integration - PowerPoint PPT Presentation

Nov 16, 2022 •270 likes •552 views

Challenges automation sharing manual error data integration standardization debugging speed complexity verification time management accuracy execution design trial & error high throughput iterative design specification initial

  2. Challenges automation sharing manual error data integration standardization debugging speed complexity verification time management accuracy execution design trial & error high throughput iterative design specification initial research

  3. Our Vision Apply engineering principles to synthetic biology by utilizing user-centered design to build software tools that foster collaborative problem solving, support complex system design, and enable automation in the lab. BU - Wellesley Software

  4. Outline BU - Wellesley Software

  5. User Centered Design BU - Wellesley Software

  6. A tabletop interface for genomic research Promotes collaborative hypothesis forming

  7. Optimus Primer Multiplatform collaborative primer designer Integrates touch screen environment with Clotho datamodel BU - Wellesley Software

  8. BU - Wellesley Software

  9. Big Picture Part 1 Part 2 Part 1 Part 5 Part 2 Part 1 Part 3 Part 4 Part 3 Part 2 Part 5 BU - Wellesley Software

  10. Invertases Part Invertase Part BU - Wellesley Software

  11. Design Example • 2 genes • Requires 3 distinct invertases • Achieves 8 permutations/ combinations of these genes BU - Wellesley Software

  12. Trumpet Trumpet produces a permutable design using invertases Configurable genetic constructs Structured state space for cellular memory (Ham et al., ‘09) (Friedland ’08) BU - Wellesley Software

  13. BU - Wellesley Software

  14. PuppetShow Flow Spec How does one implement a permutable construct? Plan Manual Side-by- Robot #1 Robot #2 Side Ligation Ligation Ligation volume: 17µL volume: 16.7µL Volume: 20µL Colonies: 300+ Colonies: 300+ Colonies: 300+ Protocol Macro Instruction Action BU - Wellesley Software

  15. eLabNotebook

  16. BU - Wellesley Software

  17. in situ BU - Wellesley Software BU - Wellesley Software

  18. Problem: Tuberculosis Proposed Circuit to Study TB Wang et. al, 2011 Science China Life Sciences

  19. Planning

  20. Wet Lab Results M: MW Ladder 1: Uncut BioBrick FACS Characterization 2: Manual trial 3-5: Robot trials BU - Wellesley Software

  21. Outreach Genekai High School Programs Poster Presentations to the Wellesley Community

  22. Future Work & Conclusion BU - Wellesley Software

  23. In summary… • Collaborative tabletop research tool and primer designer • Developed and automated 2 different algorithms which place invertase sites through Clotho. • Created user-friendly interface for automating protocols to a robot • Successfully tested in the wet lab BU - Wellesley Software

  24. Acknowledgements BU: Daniel Dwyer, Jim Collins, and the Collins Lab, Andrew Krueger, James Galagan, and the Galagan Lab, Gretchen Fougere, Assistant Dean of Outreach and Diversity BBN Technologies: Aaron Aadler JBEI: Josh Gilmore JHU: Jef Boeke, Noah Young MIT: Jonathan Babb and the Weiss Lab, Tiffany Huang, Louis Lamia and the MIT iGEM Team, Joy, Leanna, Paul, Shawn, and Shirley of the MIT iGEM team of 2010 Somerville High School: Chris Angelli UC Berkeley: J. Christopher Anderson Wellesley College: Catherine Summa, Wellesley College Science Center Summer Research, Yui Suzuki and the Suzuki Lab Wyss Institute: Avi Robinson-Mosher

  25. Thank you! Douglas Densmore Orit Shaer Traci Haddock Swapnil Bhatia Megan Strait Suma Jaini Consuelo Margaux Heidi Wang Vanessa Yanez Evelyn Orozco Taili Feng Craig Laboda Michael Lintz Chenkai Liu Valdes Canevari Kelsey Kathy Liu Janoo Casey Grote Michelle Jenhan Tao Alberto Kyle Jones Shannon Alex Pan Tempel Fernandez Ferreirae Purwada Harrington

  26. Questions? BU - Wellesley Software

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