20.20/Biocomputing: Difference between revisions
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==Vision== | ==Vision== | ||
To develop novel models of computation appropriate to the biological world. | To develop novel models of computation appropriate to the biological world. | ||
==Project Idea== | |||
* '''Current: Invertase chain as cell-cycle counter''' | |||
[[20.20/Biocomputing/Specs|Here is where final technical information goes!]] | |||
* <font COLOR="#808080">Write to DNA: transmit bits of information from outside cell to inside cell & have cell rewrite DNA as appropriate</font> | |||
* <font COLOR="#808080">RNA aptamer that recognizes an arbitrary RNA sequence & lights up GFP, or triggers kinase cascade, or alters expression of some related gene, or...</font> | |||
* <font COLOR="#808080">DNA Turing machine (poorly specified)</font> | |||
* <font COLOR="#808080">Implement Game of Life using actual cells; design bacterium that can obey an arbitrary version of Life rules</font> | |||
==Action Items== | |||
* Figure out invertase inhibition! | |||
* Address other actionable questions on the [[20.20/Biocomputing/Specs|specs page]] and the [[20.20/Biocomputing/Brainstorms|brainstorms page]]. | |||
* Our [[20.020: Final presentations|final presentation]] is Weds 7 May -- next week! | |||
* [[20.020: Final presentations|Technical documentation]] is due Weds 14 May, which is in two weeks. | |||
==Team Members== | ==Team Members== | ||
Line 27: | Line 41: | ||
...was a great success. See contents on [[Brainstorms|the brainstorming page]]. | ...was a great success. See contents on [[Brainstorms|the brainstorming page]]. | ||
Idea 1: Intercellular communication (Game of Life) | * Idea 1: Intercellular communication (Game of Life) | ||
Idea 2: DNA Turing Machine | * Idea 2: DNA Turing Machine | ||
Idea 3: Signaling (Ribozymes) | * Idea 3: Signaling (Ribozymes) | ||
Here is the feedback we received from the class poll at the end: | Here is the feedback we received from the class poll at the end: | ||
Line 40: | Line 54: | ||
==Directory of Interesting Things== | ==Directory of Interesting Things== | ||
===Literature and Similar=== | |||
[http://www.pdb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb15_1.html tRNA on the RCSB Protein Data Bank]. | |||
[http://www.pdb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb16_1.html Aminoacyl-tRNA Synthetases on the RCSB Protein Data Bank]. | |||
[http://www.mun.ca/biochem/courses/3107/Lectures/Topics/tRNA.html tRNA, the Adaptor Hypothesis and the Wobble Hypothesis]: lots of good information about tRNA. Nonstandard bases / base pairings; lack of neurotic specificity in the last base of the anticodon; genes coding for tRNAs in E. coli; the works. As well as some good textbook references. | |||
[http://coblitz.codeen.org:3125/citeseer.ist.psu.edu/cache/papers/cs/8322/http:zSzzSzwww.ugcs.caltech.eduzSz~pwkrzSzoettzSzdimacszSzdimacs.pdf/a-dna-and-restriction.pdf A DNA and Restriction Enzyme Implementation of Turing Machines] | [http://coblitz.codeen.org:3125/citeseer.ist.psu.edu/cache/papers/cs/8322/http:zSzzSzwww.ugcs.caltech.eduzSz~pwkrzSzoettzSzdimacszSzdimacs.pdf/a-dna-and-restriction.pdf A DNA and Restriction Enzyme Implementation of Turing Machines] | ||
Line 45: | Line 67: | ||
[http://www.springerlink.com/content/q66xx3672x4n532p/ The Neurally Controlled Animat: Biological Brains Acting with Simulated Bodies] | [http://www.springerlink.com/content/q66xx3672x4n532p/ The Neurally Controlled Animat: Biological Brains Acting with Simulated Bodies] | ||
[http://www.nature.com/embor/journal/v4/n1/full/embor719.html Computing with DNA]. Shortish review in Nature by Jack Parker, describing Adleman's traveling-salesman solver and Shapiro's Turing-machine-oid. | |||
===People=== | |||
[http://www.princeton.edu/~rweiss/ Ron Weiss's web page]. He also wrote a really interesting review paper a few years back on the subject. I can't remember where it is... | [http://www.princeton.edu/~rweiss/ Ron Weiss's web page]. He also wrote a really interesting review paper a few years back on the subject. I can't remember where it is... | ||
[http://www.che.caltech.edu/groups/cds/index.htm Christina Smolke's web page] | [http://www.che.caltech.edu/groups/cds/index.htm Christina Smolke's web page]. Seems to be doing interesting RNA things potentially related to our ribozyme idea. | ||
[http://swiss.csail.mit.edu/projects/amorphous/ Amorphous Computing Home Page]. | |||
[http://web.mit.edu/jakebeal/www/ Jake Beal's web page]. | |||
[http://www.wisdom.weizmann.ac.il/~udi/ Ehud Shapiro @ the Weizmann Institute in Israel], working on DNA Turing machines using restriction enzymes (among other things). | |||
[http://knight.openwetware.org/ Tom Knight's lab]; see also [http://web.archive.org/web/20040202103232/http://www.ai.mit.edu/people/tk/tk.html here]. | |||
===Miscellaneous=== | |||
[http://parts.mit.edu/registry/index.php/Main_Page Registry of Standard Biological Parts] | |||
[http:// | [http://bbf.openwetware.org/ BioBricks Foundation] |
Latest revision as of 20:04, 30 April 2008
Vision
To develop novel models of computation appropriate to the biological world.
Project Idea
- Current: Invertase chain as cell-cycle counter
Here is where final technical information goes!
- Write to DNA: transmit bits of information from outside cell to inside cell & have cell rewrite DNA as appropriate
- RNA aptamer that recognizes an arbitrary RNA sequence & lights up GFP, or triggers kinase cascade, or alters expression of some related gene, or...
- DNA Turing machine (poorly specified)
- Implement Game of Life using actual cells; design bacterium that can obey an arbitrary version of Life rules
Action Items
- Figure out invertase inhibition!
- Address other actionable questions on the specs page and the brainstorms page.
- Our final presentation is Weds 7 May -- next week!
- Technical documentation is due Weds 14 May, which is in two weeks.
Team Members
20.20 Students
- Kelly Drinkwater (Foo)
- Raphael Rush (Bar)
- Star Simpson (Baz)
20.902 Students
- Kay Aull
- Stephanie Nix
Brainstorming
- Biological neural nets
- DNA-encoded Turing machine
- Adder circuit
- PCR readout for genetic switches
- Addressable DNA modification based on RNA input
- Fix scaling issues
- RNA binding screens
- Circuit elements of protein cascades
- Ontology for standard biological parts
3 Ideas Presentation
...was a great success. See contents on the brainstorming page.
- Idea 1: Intercellular communication (Game of Life)
- Idea 2: DNA Turing Machine
- Idea 3: Signaling (Ribozymes)
Here is the feedback we received from the class poll at the end:
- Which idea addresses the most important challenge or opportunity? #3 52%, #2 33%, #1 15%
- Which idea would have the greatest impact if fully successful? #3 61%, #2 29%, #1 11%
- Which idea is most competitive with alternative technologies? #3 59%, #2 30%, #1 11%
- Which idea has the greatest certainty and fewest unknowables? #3 48%, #1 28%, #2 24%
The class seems to agree with us that the ribozyme idea is pretty cool and actually viable as a project.
Directory of Interesting Things
Literature and Similar
tRNA on the RCSB Protein Data Bank.
Aminoacyl-tRNA Synthetases on the RCSB Protein Data Bank.
tRNA, the Adaptor Hypothesis and the Wobble Hypothesis: lots of good information about tRNA. Nonstandard bases / base pairings; lack of neurotic specificity in the last base of the anticodon; genes coding for tRNAs in E. coli; the works. As well as some good textbook references.
A DNA and Restriction Enzyme Implementation of Turing Machines
The Neurally Controlled Animat: Biological Brains Acting with Simulated Bodies
Computing with DNA. Shortish review in Nature by Jack Parker, describing Adleman's traveling-salesman solver and Shapiro's Turing-machine-oid.
People
Ron Weiss's web page. He also wrote a really interesting review paper a few years back on the subject. I can't remember where it is...
Christina Smolke's web page. Seems to be doing interesting RNA things potentially related to our ribozyme idea.
Amorphous Computing Home Page.
Ehud Shapiro @ the Weizmann Institute in Israel, working on DNA Turing machines using restriction enzymes (among other things).
Tom Knight's lab; see also here.