GcatWiki - User contributions [en]

Missouri Western/Davidson iGEM2010

2010-06-09T16:27:14Z

Sholle:

This space will be used starting January, 2010 for brainstorming and a shared whiteboard space.

[http://gcat.davidson.edu/GcatWiki/index.php/Davidson_Missouri_W/Davidson_Protocols Davidson Lab Protocols] 
[http://gcat.davidson.edu/GcatWiki/index.php/Davidson_Missouri_W/MWSU_protocols MWSU Lab Protocols] 
[http://gcat.davidson.edu/sybr-u/bmc.html BioMath Connections Page] 
[http://gcat.davidson.edu/GCATalog GCAT-alog Freezer Stocks] 
[[Laboratory_Notebooks]] 
[[Data Folder 2010]]

[[Bio-Math Connections January - May 2010]]

"random number" generators

2010-04-16T05:39:48Z

Sholle:

[http://www.random.org/ Random dot Org]

== Pseudo Random Number Generators ==
Algorithms which create a series of numbers having the qualities of randomness, but are deterministic. Not truely random, but maybe could be used in combination with true random numbers as seed values to increase the generation rate.

[http://www1.i2r.a-star.edu.sg/~knandakumar/nrg/Tms/Probability/Probgenerator.htm Linear Congruential RNG]

[http://random.mat.sbg.ac.at/generators/wsc95/inversive/node2.html Inversive RNG]

Linear feedback shift register (usually hardware implemented, can't find a decent link)

== Cellular Automata ==
The repeated application of simple rules to array cells containing values from a finite set can result in emerged behavior over time. Cellular Automata demonstrates this and provides interesting possibilities for randomness from complexity.

[http://mathworld.wolfram.com/CellularAutomaton.html General Summary of Cellular Automata from Wolfram]

[http://mathworld.wolfram.com/ElementaryCellularAutomaton.html Elementary Rulesets from Wolfram]

[http://www.stephenwolfram.com/publications/articles/ca/86-random/ Wolframs 1986 Publication on Random Sequences with CA]

[http://www.tcm.phy.cam.ac.uk/~tmf20/PUBLICATIONS/epl_08b.pdf When are cellular automata random?]

[http://home.southernct.edu/~pasqualonia1/ca/report.html A 256 state CA Random Number Generator]

Previous iGEM projects

2010-04-15T04:11:47Z

Sholle:

[http://2008.igem.org/Team:HKUSTers Hong Kong HKUST 2008]

This team tried to create a randomizer that chooses between two overlapping promoters that are mutually exclusive. One produces RFP while the other produces GFP. The team has a simulation and submitted parts to the registry but we were unable to find any conclusive results.

[http://parts.mit.edu/igem07/index.php/Davidson_Missouri_W Davidson & MWSU 2007] Hin/Hix random flipping

Found a small snippet from the iGEM Idea Exchange in which the MIT Synthetic Biology Working Group listed desired parts that weren't in the registry as of 2008. [http://openwetware.org/wiki/IGEM:Idea_exchange Idea Exchange]

" Random Number Generator

* FimE inverts a specific stretch of DNA, defined by a pair of sequence elements (IRR and IRL), forming a DNA loop between the two elements[3]. If we add multiple copies of one
of these elements (one IRR, two IRL), would FimE randomly choose one of the sites (one IRL out of the pair) to invert between? Either choose one of several promoters to attach
to a given gene, or one of several genes to attach to a given promoter.
* Then, can we tune the probability (from, say, 60:40 to 80:20 to 20:80)? Ideally do this dynamically (based on some small molecule) - use proteins that bend DNA to affect the
probability of loop formation. "

Bio-Math Connections January - May 2010

2010-03-28T17:32:11Z

Sholle: /* Idea #3 */

Write in which project you will present, your name, and which campus you represent. For example:

* MOWestern/Davidson 2009 project:: Malcolm Campbell:: Davidson
* Cambridge 2009 project:: Michael Rydberg, Nitya Rao, Erin Feeney:: Davidson
* U.C. Berkeley 2009 project:: Anvi Raina, Steph Meador, Linda Kleist:: Davidson
* S.J.T.U. Shanghai 2009 project:: Yihharn Hwang, Stephen Streb, Shashank Suresh:: Davidson
* Stanford 2009 project:: Kris Hendershot, Garrett Smith, Tom Shuman:: Davidson
* NCTU Formosa/WetLab 2009 project:: Clif Davis:: Missouri Western
* Paris 2009 project:: Michel Conn:: Missouri Western
* UCSF 2009 project:: Stacey Holle:: Missouri Western
* [http://2009.igem.org/Team:EPF-Lausanne Lausanne Switzerland]:: Erin Feeney:: Davidson

== Summer 2010 Brain Storming ==
MWSU will populate the odd numbered ideas and DC will populate the even numbered ideas. Only work on your idea number page and not the entire page to facilitate multiple people working at a given time.

== Idea #1 ==

Solving the Knapsack Problem - The problem is to figure out how many (integer) of each of several kinds of items to put into a knapsack when each item weighs a certain amount (real number) and the knapsack can only hold a certain amount of weight. Take three different genes (different kinds of items) with different degrees of toxicity (different weights). How can they be combined to get the closest to 100% toxicity, ie. death?

== Idea #2 ==

-testing for pollutants
[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TF4-4RC6R98-2&_user=2665120&_coverDate=02%2F04%2F2008&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_searchStrId=1269769960&_rerunOrigin=google&_acct=C000058476&_version=1&_urlVersion=0&_userid=2665120&md5=ae9a90f529694c35367e1b25b9e67818]
-cleaning up oil spills
[http://www.wired.com/science/discoveries/news/2004/12/66017]
[http://www.treehugger.com/files/2005/05/oileating_bacte_1.php]
-clean pollutants from air (carbon-capture technology, air scrubbers)
[http://www.gizmag.com/ionic-liquid-co2-emissions-control/11105/]
-bio-batteries
[http://www.sciencedaily.com/releases/2009/09/090907013811.htm]
[http://www.sciencedaily.com/releases/2008/03/080303190535.htm]

== Idea #3 ==
Let's Make a Deal! Our idea is to make E. coli play game shows based on decision making and probability. Playing the game means that E. coli makes a decision that produces a selective response. That response determines the ranking (score) of the E. coli and generates an output from the score. Some of the games we thought of include Deal or No Deal, Let's Make a Deal, Card Sharks, Blackjack, or other casino/mathematical based games.

Another game application for this would be to use E. coli to play Conway's Game of Life. It would be interesting if we could get them to function as oscillator's by having them flouresce in certain patterns. [http://www.math.com/students/wonders/life/life.html/link Wonder's of Math - Conway's Game of Life]

== Idea #4 ==
Our idea is to engineer heat producing E.coli and use them in wetsuits for rescue divers and hyperthermia victims. We need to find an inhibitor for the calcium to prevent them from closing. This would produce a non-stop cycle that would produce heat. This is present in some humans with malignant hyperthermia and blue fin tuna. We could study the tuna to find a possible protein or enzyme that enables this cycle. Another alernative is to de-flaggelate E. coli and have continious chemotaxis. This would produce heat as ATP would be constantly consumed.
Keeping the e. coli alive:
The challange would be to find a way to keep these E. coli alive. A possibility is haivng pockets of agar that could provide nutrients to E. coli.

== Idea #5 ==
Pascals triangle pattern solving bacteria idea. This idea is not fully developed but we are interested in the idea of bacteria "solving" whether they are divisible by prime factors. i.e divisible by 1= all bacteria, divisible by 2=red, divisible by 3=green, divisible by 5=blue. The colors would allow to us to see when the bacteria solved a particular problem.

== Idea #6 ==
Bio-sensors can be used to detect toxins in the air, water and on surfaces. Our idea is to use E. coli to monitor toxin levels in the air. The possible applications of this include counter-bioterrorism, pollution monitoring, and general detection of the chemical content of the air we breathe. This could also provide insight into the relationship between pollution and global warming.

We would need to pick either a specific toxin or multiple toxins that would trigger a reaction by our E. coli. Detectors could be hand-held objects with functional ends coated with E. coli that respond (perhaps by glowing a certain color) to detect the undesirable toxins. Different toxins could produce different color responses.

Other sensors could be smoke-detector-like rather than hand held, but work in the same way.

I realize that there are already tons of sensors for different chemicals that don't use E. coli. However, using E. coli would allow us to produce one sensor that reacts to a host of different toxins, producing different responses for each toxin.

== Idea #7 ==

== Idea #8 ==
This idea is based on some work by Olivia Ho-Shing (iGEM2009). She has been exploring the possibility of using biological noise to our advantage rather than fighting it.

Olivia is taking an independent study on biological noise and she has collected her resources on a wiki page.

One of her ideas was to produce a device that utilizes a positive feedback to amplify biological noise and kill cells that contain a device that is noisy. For example, imagine some one designs and builds cells that produce the smell of bananas when they reach stationary phase. However, each cell produces a different level of the necessary enzyme and what you want is a uniform population of cells all producing an output at about the same non-zero level.

The Olivilator would be a modular device that could be added to any existing device that utilizes the Lux quorum sensing mechanism. If a particular cells stays inside a band pass filter range of acceptable outputs, the cells live. If they under produce or over produce, then they are killed by the Olivilator.

== Idea #9 ==

== Idea #10 ==

<hr>