Challenges automation sharing manual error data integration - - PowerPoint PPT Presentation

Challenges

data design execution

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

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.

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Our Vision

Outline

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User Centered Design

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A tabletop interface for genomic research Promotes collaborative hypothesis forming

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Optimus Primer

Multiplatform collaborative primer designer Integrates touch screen environment with Clotho datamodel

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Part 1 Part 2

Part 1 Part 3

Part 2 Part 5

Part 1 Part 2 Part 3 Part 4 Part 5

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Big Picture

Part Part

Invertase

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Invertases

• 2 genes
• Requires 3 distinct

invertases

• Achieves 8

permutations/ combinations of these genes

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Design Example

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Trumpet

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

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PuppetShow Flow

How does one implement a permutable construct?

Spec Plan Protocol Macro Instruction Action

Robot #1 Ligation volume: 17µL Colonies: 300+ Robot #2 Ligation volume: 16.7µL Colonies: 300+

Manual Side-by- Side Ligation Volume: 20µL Colonies: 300+

eLabNotebook

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in situ

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Problem: Tuberculosis

Wang et. al, 2011 Science China Life Sciences

Proposed Circuit to Study TB

Planning

FACS Characterization

Wet Lab Results

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M: MW Ladder 1: Uncut BioBrick 2: Manual trial 3-5: Robot trials

Outreach

Genekai Poster Presentations to the Wellesley Community High School Programs

Future Work & Conclusion

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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

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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

Thank you!

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

Questions?

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