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
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
Outline BU - Wellesley Software
User Centered Design BU - Wellesley Software
A tabletop interface for genomic research Promotes collaborative hypothesis forming
Optimus Primer Multiplatform collaborative primer designer Integrates touch screen environment with Clotho datamodel BU - Wellesley Software
BU - Wellesley Software
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
Invertases Part Invertase Part BU - Wellesley Software
Design Example • 2 genes • Requires 3 distinct invertases • Achieves 8 permutations/ combinations of these genes BU - Wellesley Software
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
BU - Wellesley Software
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
eLabNotebook
BU - Wellesley Software
in situ BU - Wellesley Software BU - Wellesley Software
Problem: Tuberculosis Proposed Circuit to Study TB Wang et. al, 2011 Science China Life Sciences
Planning
Wet Lab Results M: MW Ladder 1: Uncut BioBrick FACS Characterization 2: Manual trial 3-5: Robot trials BU - Wellesley Software
Outreach Genekai High School Programs Poster Presentations to the Wellesley Community
Future Work & Conclusion BU - Wellesley Software
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
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! 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
Questions? BU - Wellesley Software
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