User:Lance Martin: Difference between revisions
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== | ==Projects== | ||
=== | ===Electronic counter review=== | ||
[http://openwetware.org/wiki/Endy:Notebook/Electronic_counters Electronic counter notebook] | |||
=== | ===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:// | [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]] | ||
===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.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] | |||
===Biological computation=== | ===Biological computation=== | ||
*[http://www.citeulike.org/user/dylan77/article/1281370 Arkin: computation in biochemical networks] | *[http://www.citeulike.org/user/dylan77/article/1281370 Arkin: computation in biochemical networks] | ||
*[http://www.pnas.org/content/89/1/383.abstract Chemical implementation of finite state machine] | *[http://www.pnas.org/content/89/1/383.abstract Chemical implementation of finite state machine] | ||
*[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] | ||
[[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 | ||
[[Media: Principles.ppt]] | [[Media: Principles.ppt]] | ||
Line 86: | Line 54: | ||
[[Media:Modeling.ppt]] | [[Media:Modeling.ppt]] | ||
[[Image:PriorWork.jpg|thumb|right|Some engineered biological memory & logic systems]] | [[Image:PriorWork.jpg|thumb|right|Some engineered biological memory & logic systems]] | ||
=== | ===Prior work: implementing recombinase switches=== | ||
*Ham & Arkin inversion switch | *Ham & Arkin inversion switch | ||
**[[Media:Ham&Arkin.ppt]] | **[[Media:Ham&Arkin.ppt]] | ||
Line 95: | Line 62: | ||
**Their final presentation | **Their final presentation | ||
***[[Media:iGem.ppt]] | ***[[Media:iGem.ppt]] | ||
** | **Notes on this work | ||
***[[Media:iGemLance.ppt]] | ***[[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 |
Latest revision as of 09:52, 6 April 2009
I am a new member of OpenWetWare!
Projects
Electronic counter review
Gemini
Simulation
Computational modeling notebook
Genetic switches: methylation & feedback regulation
Recombination switches
Assorted items of interest
James Ferrell
- Timekeeping (James Ferrell)
- Feedback loops (James Ferrell)
Biological computation
- Arkin: computation in biochemical networks
- Chemical implementation of finite state machine
- Chemical implementation of Turing machine
Basic construction / design principles
- Summary of reviews by
- Voight, Endy, Arkin
Computational modeling to aid design
- Review of
- Collins toggle switch
- Elowitz repressilator
Prior work: implementing recombinase switches
- Ham & Arkin inversion switch
- Harvard/BU 2004 iGem Int/Xis inversion switch & counter
- Their final presentation
- Notes on this work
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