User:Lance Martin

Electronic counter review
Electronic counter notebook

Gemini
Gemini notebook

Simulation
Computational modeling notebook

Genetic switches: methylation & feedback regulation
Genetic switches notebook

Recombination switches
Review of recombinases

James Ferrell

 * Timekeeping (James Ferrell)
 * Toggle switch at heart of circadian timekeeping
 * Cell cycle and its switches
 * Feedback loops (James Ferrell)
 * Interlinked positive and negative feedback loops
 * Systems level dissection of the cell cycle

Biological computation

 * Arkin: computation in biochemical networks
 * Chemical implementation of finite state machine
 * Chemical implementation of Turing machine



Basic construction / design principles
[[Media: Principles.ppt]]
 * Summary of reviews by
 * Voight, Endy, Arkin

Computational modeling to aid design
[[Media:Modeling.ppt]]
 * Review of
 * Collins toggle switch
 * Elowitz repressilator



Prior work: implementing recombinase switches

 * Ham & Arkin inversion switch
 * [[Media:Ham&Arkin.ppt]]
 * Harvard/BU 2004 iGem Int/Xis inversion switch & counter
 * Their final presentation
 * [[Media:iGem.ppt]]
 * Notes on this work
 * [[Media:iGemLance.ppt]]

Challenges

 * No spatial addressing of signals in biological systems
 * Many heterogeneous parts implemented, resulting in:
 * Heterogeneity of device physics across circuits
 * Complex properties, making design and modeling hard
 * Large outlays of DNA real-estate may be necessary
 * Large energetic loads on host state