BFS GOTChAs, April 2010: Difference between revisions
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This page contains some [[GOTChA Chart|GOTChA charts]] for possible rotation projects in the lab this summer. __NOTOC__ | This page contains some [[GOTChA Chart|GOTChA charts]] for possible rotation projects in the lab this summer. __NOTOC__ | ||
= Active = | |||
=== Consistent Gene Expression Level (ES and JTM) === | |||
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==== Goals ==== | |||
* Design, synthesize and characterize an inducible gene circuit that will express a constant level of a protein regardless of inducer concentration | |||
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==== Technical Challenges ==== | |||
* Might have issues designing an ACR circuit synthetically | |||
* Getting an inducible circuit might be difficult, may start with the simpler problem of just expressing a protein at a constant level | |||
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==== Objectives ==== | |||
* Design a circuit that exhibits a constant concentration of gene of interest (probably an xFP at steady state) we might be able to use ACR theory [http://www.sciencemag.org/cgi/content/abstract/327/5971/1389?ijkey=c777f236d838b71911625aae954a625090cf51ca&keytype2=tf_ipsecsha] | |||
* Construct and characterize designed circuit | |||
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==== Approach ==== | |||
* Incorporate feedback into current inducer systems, possibly tie into a gene that is known to be tightly controlled | |||
* Design theoretical circuit, then use canonical examples of reactions | |||
* Try the a fusion protein with the circuit that is tightly regulated in paper as a crutch | |||
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=== State Transition Modeling in Chemical Reaction Networks (JTM and ES) === | |||
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==== Goals ==== | |||
* Develop an enumeration algorithm to find distinct "states" for a chemical reaction network | |||
* Look at transition criteria between states | |||
* Test analysis on simple circuits and biological networks | |||
* Use transition criteria to develop robustness metrics | |||
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==== Technical Challenges ==== | |||
* Not immediately clear how to classify/cluster output | |||
* Not sure how to deal with continuous relationships vs. more discrete relationships (thresholding?) | |||
* May be useful to use analytical techniques () in addition to blind sampling | |||
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==== Objectives ==== | |||
* Program a library of well-characterized reaction circuits (bi-stable flipflops, oscillators, etc) | |||
* Demonstrate proper time-evolution of circuits via numerical analysis | |||
* Run each circuit with a variety of initial conditions and mid-time-course perturbations | |||
* Cluster end states, evaluate quality of clustering, and match to known circuit behavior | |||
* Measure transition criteria between states | |||
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==== Approach ==== | |||
* Attempt naive exhausive approach to evaluation - sweep through all plausible initial conditions and cluster results (fuzzy c-means?) | |||
* Attempt theorem/network solver approach to evaluation - sweep through initial conditions and use Bayesian network analysis and/or theorem postulators (eureqa) to enumerate states | |||
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= Archive == | |||
== Device Projects == | == Device Projects == | ||
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==== Approach ==== | ==== Approach ==== | ||
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Revision as of 17:38, 1 May 2010
This page contains some GOTChA charts for possible rotation projects in the lab this summer.
Active
Consistent Gene Expression Level (ES and JTM)
Goals
|
Technical Challenges
|
Objectives
|
Approach
|
State Transition Modeling in Chemical Reaction Networks (JTM and ES)
Goals
|
Technical Challenges
|
Objectives
|
Approach
|
Archive =
Device Projects
The following GOTChAs are for projects that involve building new device technologies that can be used to push biological circuit design forward.
Integrated Load and Context Compensation (RMM)
Goals
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Technical Challenges |
Objectives
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Approach |
Fast Mechanisms for Biomolecular Feedback (RMM)
Goals
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Technical Challenges |
Objectives
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Approach |
Cell Division Tracker (ES)
Goals
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Technical Challenges
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Objectives
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Approach
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Stoichiometric Protein Expression (JTM)
Goals
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Technical Challenges
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Objectives
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Approach
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Use of photoactive proteins to access multiple time-scale control (JTM)
Goals
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Technical Challenges
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Objectives
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Approach
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Manipulation of the integral controller in photo/chemotaxis (JTM)
Goals
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Technical Challenges
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Objectives
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Approach
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Robustness Projects
CAGEN (RMM)
Goals
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Technical Challenges |
Objectives |
Approach |