User:Lance Martin: Difference between revisions

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==Electronic memory & logic devices==
[[Image:Electronic Devices.jpg|thumb|right|Abstraction hierarchy]]


===Devices===
*Transistors
**[[Media:Transistor Detail.ppt]]
*Logic gates
*Latches
*D-type flip-flops
*JK flip-flops


===Summary presentation===
[[Media:Electronic_Memory_&_Logic_Devices.ppt]]


==Electronic counters & system architecture==
[[Image:Counter Architecture.jpg|thumb|right|Decision tree]]


===Architectures===
==Projects==
*Cascade
*Asynchronous
*Synchronous


===Summary presentation===
===Electronic counter review===
[[Media:Electronic_Counters.ppt]]
[http://openwetware.org/wiki/Endy:Notebook/Electronic_counters Electronic counter notebook]


==Native biological memory & logic==
===Gemini===
[http://openwetware.org/wiki/Endy:Notebook/Gemini Gemini notebook]
 
===Simulation===
[http://openwetware.org/wiki/Endy:Notebook/Computational_modeling#Steps_in_flipee_mechanism_for_modeling Computational modeling notebook]
 
===Genetic switches: methylation & feedback regulation===
[http://openwetware.org/wiki/Endy:Notebook/Genetic_switches:_feedback%2C_methylation%2C_%26_more Genetic switches notebook]
 
===Recombination switches===
[http://openwetware.org/wiki/Endy:Notebook/Review_of_recombinases Review of recombinases]
 
==Assorted items of interest==
[[Image:Inversion.jpg|thumb|right|A biological bit]]
[[Image:Inversion.jpg|thumb|right|A biological bit]]


===Basic requirements===
===James Ferrell===
*Reliably holds state
*Timekeeping (James Ferrell)
*Controllable state change
**[http://www.sciencemag.org/cgi/content/summary/318/5851/757?ck=nck Toggle switch at heart of circadian timekeeping]
*Many additional application-specific requirements
**[http://www.nature.com/nature/journal/v454/n7202/full/454288a.html Cell cycle and its switches]
*Feedback loops (James Ferrell)
**[http://www.sciencemag.org/cgi/content/abstract/321/5885/126 Interlinked positive and negative feedback loops]
**[http://www.ncbi.nlm.nih.gov/pubmed/16122424 Systems level dissection of the cell cycle]


===Systems===
===Biological computation===
*Recombination
*[http://www.citeulike.org/user/dylan77/article/1281370 Arkin: computation in biochemical networks]
**Types of enzymes
*[http://www.pnas.org/content/89/1/383.abstract Chemical implementation of finite state machine]
*** [[Media:Recombinases.ppt]]
*[http://www.pnas.org/content/88/24/10983.abstract Chemical implementation of Turing machine]
**Kinetic modeling recombinase mechanism
*** [[Media:Mechanism.ppt]]
*DNA methylation
*Others?
**Feedback loops
**Bi-stable networks


==Design of engineered biological memory & logic==
[[Image:Process.jpg|thumb|right|Design process]]
[[Image:Process.jpg|thumb|right|Design process]]


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


===Computational modeling===
===Computational modeling to aid design===
*Review of
*Review of
**Collins toggle switch
**Collins toggle switch
Line 64: Line 54:
[[Media:Modeling.ppt]]
[[Media:Modeling.ppt]]


==Publications==
[[Image:PriorWork.jpg|thumb|right|Some engineered biological memory & logic systems]]
<!-- Replace the PubMed ID's ("pmid=#######") below with the PubMed ID's for your publications.  You can add or remove lines as needed -->
 
<biblio>
===Prior work: implementing recombinase switches===
#Paper1 pmid=6947258
*Ham & Arkin inversion switch
#Paper2 pmid=13718526
**[[Media:Ham&Arkin.ppt]]
// leave a comment about a paper here
*Harvard/BU 2004 iGem Int/Xis inversion switch & counter
#Book1 isbn=0879697164
**Their final presentation
</biblio>
***[[Media:iGem.ppt]]
**Notes on this work
***[[Media:iGemLance.ppt]]


==Useful links==
===Challenges===
*[[OpenWetWare:Welcome|Introductory tutorial]]
*No spatial addressing of signals in biological systems
*[[Help|OpenWetWare help pages]]
*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

Latest revision as of 09:52, 6 April 2009

I am a new member of OpenWetWare!





Projects

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

Assorted items of interest

A biological bit

James Ferrell

Biological computation

Design process

Basic construction / design principles

  • Summary of reviews by
    • Voight, Endy, Arkin

Media: Principles.ppt

Computational modeling to aid design

  • Review of
    • Collins toggle switch
    • Elowitz repressilator

Media:Modeling.ppt

Some engineered biological memory & logic systems

Prior work: implementing recombinase switches

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
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