establishing baseline performance scores for the cagen robust gene response challenge
DESCRIPTION
Establishing Baseline Performance Scores for the CAGEN Robust Gene Response Challenge. Shaunak Sen Caltech CMS Oct 11, 2011. CAGEN - C ritical A ssessment of G enetically E ngineered N etworks Systematize the design of genetic networks (robustness, connectability ) - PowerPoint PPT PresentationTRANSCRIPT
Slide 1
Establishing Baseline Performance Scores for the CAGEN Robust Gene Response ChallengeShaunak Sen Caltech CMS Oct 11, 2011CAGEN - Critical Assessment of Genetically Engineered Networks
Systematize the design of genetic networks (robustness, connectability)
- Facilitate applications, for ex. in agriculture, medicineCAGEN Challenge #1 : Robust Gene ResponseDetectable: >10 fold inductionRobust: Low variability across cells & temperaturesFast: Quick responseTimeIPTG AdditionYFP induction1 X0>10 X0SpeedLow VariabilityINPUTOUTPUTInduce OUTPUT (YFP) in response to INPUT (IPTG), so that,Critical Assessment of Selected DesignsChallenge SpecificationsSelf Assessment by ParticipantsPurpose: Establish Baseline PerformancePurposeEstablish Baseline PerformanceANNOUNCEMENTSELECTIONPerformance metric to score robustness and speed of designs
Worst CaseTime integral of square errorNormalizing factor(equilibrium amplitude of reference trace)
Time (hours)Protein Levels (nM)simulationr(t)yj(t)j=215xPxXSingle cell dynamics are measured for a simple reference design, for different temperaturesYFPPinducibleE. coli30 C32 C34 C#1???#2???yfpPlacIPTG#1cI-yfpPlacIPTG#2MoviesYFPPinducible
Reference trace exhibits > 10x inductionTime (minutes)Mean Fluorescence (a.u.)No inductionCamera Bgd.Cell division10x inductionPerformance scores for inducible protein expression circuits
Time (minutes)Mean Fluorescence (a.u.)yfpPlacIPTG#1Reference trace (32 C)Traces at 32 CTraces at 34 CTraces at 30 C
Time (minutes)Mean Fluorescence (a.u.)cI-yfpPlacIPTG#2Reference trace (34 C)Traces at 34 CTraces at 30 CS = 0.27S = 0.29Population level metric to estimate performance score
Time (minutes)Protein Levels (nM)Count
Population Dynamics/Flow Cytometry
Time (hours)Protein Levels (nM)simulationr(t)yj(t)j=215Single-Cell Dynamics/ Microscopy
Future WorkRefined single-cell measurements using fluidics
Simulation/Eric KlavinsCritical Assessment of Selected DesignsChallenge SpecificationsSelf Assessment by ParticipantsBaseline for Critical AssessmentBenefit #1.Exact induction timemeasurement.Benefit #2:Similar decay timemeasurement.