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]]


===References===
[http://books.google.com/books?id=bkOMDgwFA28C&dq=horowitz+and+hill+the+art+of+electronics&printsec=frontcover&source=bn&hl=en&ei=zDfISdS4NoG0sAOax5V2&sa=X&oi=book_result&resnum=7&ct=result Horowitz & Hill]
[http://hyperphysics.phy-astr.gsu.edu/Hbase/Electronic/etroncon.html#c1 Electronics tree]
[http://www.allaboutcircuits.com/vol_4/chpt_3/5.html Very strong overview of circuits: DC, AC, Semi-conductors, Digital]


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


===Architectures===
===Electronic counter review===
*Cascade
[http://openwetware.org/wiki/Endy:Notebook/Electronic_counters Electronic counter notebook]
*Asynchronous
*Synchronous


===Summary presentation===
===Gemini===
[[Media:Electronic_Counters.ppt]]
[http://openwetware.org/wiki/Endy:Notebook/Gemini Gemini notebook]


===References===
===Simulation===
[http://www.allaboutcircuits.com/vol_4/chpt_11/3.html Synchronous counters]
[http://openwetware.org/wiki/Endy:Notebook/Computational_modeling#Steps_in_flipee_mechanism_for_modeling Computational modeling notebook]


==Native biological memory & logic==
===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 for memory & logic===
===James Ferrell===
*Big picture
**Reliably holds state
**Controllable state change
*Then, degenerates into many application-specific requirements
**What are the applications for memory and logic in biological systems?
**How do naturally evolved mechanisms break down between combinatorial and sequential logic?
**Need a chart listing all mechanisms with associated cellular applications, requirements, timescale ...
 
===Native systems===
*Recombination
**[http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.biochem.73.011303.073908 Nice overview]
**Serine Recombinases
*** [http://www3.interscience.wiley.com/journal/118923247/abstract?CRETRY=1&SRETRY=0 Diversity in Ser recombinases]
*** [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0040186&ct=1 BxB1 directionality]
*** [[Media:Recombinases.ppt]]
**Tyrosine Recombinases
*** [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-45S48WH-F&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=db485e9dbaa8d2b7c4b57104b4de03bb Kinetic analysis of Flp and Cre]
*** [[Media:Mechanism.ppt]]
*DNA methylation
**[http://en.wikipedia.org/wiki/Epigenetics Epigenetics]
**[http://en.wikipedia.org/wiki/DNA_methylation DNA methylation]
**[http://en.wikipedia.org/wiki/Genomic_imprinting#Imprinting_mechanisms Genomic imprinting]
*Error prone DNAp
**[http://www.pnas.org/content/100/17/9727.abstract Targeted gene evolution]
*DSB & repair
**[http://www.nature.com/nbt/journal/v23/n8/abs/nbt1125.html Zinc finger gene targeting]
**[http://www.nature.com/nature/journal/v435/n7042/abs/nature03556.html Zinc finger human gene correction]
*Timekeeping (James Ferrell)
*Timekeeping (James Ferrell)
**[http://www.sciencemag.org/cgi/content/summary/318/5851/757?ck=nck Toggle switch at heart of circadian timekeeping]
**[http://www.sciencemag.org/cgi/content/summary/318/5851/757?ck=nck Toggle switch at heart of circadian timekeeping]
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*[http://www.pnas.org/content/88/24/10983.abstract Chemical implementation of Turing machine]
*[http://www.pnas.org/content/88/24/10983.abstract Chemical implementation of Turing machine]


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


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[[Media:Modeling.ppt]]
[[Media:Modeling.ppt]]


==Past engineered biological memory & logic devices/systems==
[[Image:PriorWork.jpg|thumb|right|Some engineered biological memory & logic systems]]
[[Image:PriorWork.jpg|thumb|right|Some engineered biological memory & logic systems]]


===Of particular interest to us===
===Prior work: implementing recombinase switches===
*Ham & Arkin inversion switch
*Ham & Arkin inversion switch
**[[Media:Ham&Arkin.ppt]]
**[[Media:Ham&Arkin.ppt]]
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**Their final presentation
**Their final presentation
***[[Media:iGem.ppt]]
***[[Media:iGem.ppt]]
**My notes on this work
**Notes on this work
***[[Media:iGemLance.ppt]]
***[[Media:iGemLance.ppt]]
*DNA methylation switch
==My projects==
[[Image:Gemini.jpg|thumb|right|LacZ alpha-GFP fusion]]
===Gemini===
*Summary
**[[Media:Gemini.ppt]]
*synBERC poster
**[[Media:GeminiPoster.pdf]]
*Current focus
**What is the unique application for compact (LacZa-GFP) dual reporter?
**What is the dynamic range (transfer function) for the LacZa-GFP fusion construct?
***Sequence: understand what we have.
***Determine method to modulate PoPS input (use the existing, different promoters or build with inducible promoter).
***Set up assays (plate reader for GFP and beta-gal)
**How does this compare to full length LacZ-GFP fusion, GFP, and LacZ?
***With information from the above in hand, determine additional work necessary to make genetically identical constructs (same promoter, RBS, reporters – from Meagan)
===Modeling recombinase-driven genetic counters===
*What are the key questions that we want a model to help us answer?
**What is counter's dynamic behavior across a range of parameter settings within both asynchronous and synchronous system architectures?
**Which architecture is more reliable (exhibits "robust" counting) across the range of parameters?
*What do we need to know in order to build a model that answers our questions?
**Desired dynamic behavior of our system (e.g. counting within cell division timescale, etc)
**How much do we need to know about flipee performance (e.g latency, transfer function, etc)?
**Defined state variables (e.g. recombinase mRNA/protein, excisionase mRNA/protein, the bits, etc)
**Defined parameters that describe dynamic behavior of the state variable
**(e.g. gene expression rate, recombinase-DNA association and dissociation rates, etc)


*Lay out model architecture and build it
===Challenges===
**parameters from mathematical model for recombinase kinetics provide foundation
*No spatial addressing of signals in biological systems
**iGem 2004 model serves as an example and provides additional foundation
*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

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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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