20.20/Biocomputing: Difference between revisions
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[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://swiss.csail.mit.edu/projects/amorphous/ Amorphous Computing Home Page]. | ||
[http://web.mit.edu/jakebeal/www/ Jake Beal's web page]. | [http://web.mit.edu/jakebeal/www/ Jake Beal's web page]. |
Revision as of 19:38, 12 March 2008
Vision
To develop novel models of computation appropriate to the biological world.
Action Items
- Hit up Sussman and Knight again -- in particular, clarify exactly why Sussman thought the ribozyme idea was such a useful important thing to do.
- Research RNA folding / 2,3-ary structure
- Research tRNAs (see links below for starters)
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.