User:Lance Martin: Difference between revisions
From OpenWetWare
Jump to navigationJump to search
Lance Martin (talk | contribs) |
Lance Martin (talk | contribs) |
||
| Line 9: | Line 9: | ||
===Devices=== | ===Devices=== | ||
*Transistors | *Transistors | ||
**[[ | **[[Transistor Detail.ppt]] | ||
*Logic gates | *Logic gates | ||
*Latches | *Latches | ||
| Line 16: | Line 16: | ||
===Summary presentation=== | ===Summary presentation=== | ||
[[ | [[Electronic_Memory_&_Logic_Devices.ppt]] | ||
==Electronic counters & system architecture== | ==Electronic counters & system architecture== | ||
Revision as of 16:18, 23 March 2009
I am a new member of OpenWetWare!
Electronic memory & logic devices
Devices
- Transistors
- Logic gates
- Latches
- D-type flip-flops
- JK flip-flops
Summary presentation
Electronic_Memory_&_Logic_Devices.ppt
Electronic counters & system architecture
Architectures
- Cascade
- Asynchronous
- Synchronous
Summary presentation
Native biological memory & logic
Basic requirements
- Reliably holds state
- Controllable state change
- Many additional application-specific requirements
Systems
- Recombination
- Types of enzymes
- Kinetic modeling recombinase mechanism
- DNA methylation
- Others?
- Feedback loops
- Bi-stable networks
Design of engineered biological systems
Basic construction / design principles
- Summary of reviews by
- Voight
- Endy
- Arkin
Computational modeling to aid design
- Review of
- Collins toggle switch
- Elowitz repressilator
Past engineered biological memory & logic devices/systems
Of particular interest to us
- Ham & Arkin inversion switch
- Harvard/BU 2004 iGem Int/Xis inversion switch & counter
- Their final presentation
- My notes on this work
- DNA methylation switch
My projects
Gemini
- Summary
- synBERC poster
- Current focus
- What is the unique application for compact (LacZa-GFP) dual reporter?
- What is the dynamic range (transfer function) for the LacZa-GFP fusion construct?
- Sequence: understand what we have.
- Determine method to modulate PoPS input (use the existing, different promoters or build with inducible promoter).
- Set up assays (plate reader for GFP and beta-gal)
- How does this compare to full length LacZ-GFP fusion, GFP, and LacZ?
- With information from the above in hand, determine additional work necessary to make genetically identical constructs (same promoter, RBS, reporters – from Meagan)
Modeling recombinase-driven genetic counters
- What are the key questions that we want a model to help us answer?
- What is counter's dynamic behavior across a range of parameter settings within both asynchronous and synchronous system architectures?
- Which architecture is more reliable (exhibits "robust" counting) across the range of parameters?
- What do we need to know in order to build a model that answers our questions?
- Desired dynamic behavior of our system (e.g. counting within cell division timescale, etc)
- How much do we need to know about flipee performance (e.g latency, transfer function, etc)?
- Defined state variables (e.g. recombinase mRNA/protein, excisionase mRNA/protein, the bits, etc)
- Defined parameters that describe dynamic behavior of the state variable
- (e.g. gene expression rate, recombinase-DNA association and dissociation rates, etc)
- Lay out model architecture and build it
- parameters from mathematical model for recombinase kinetics provide foundation
- iGem 2004 model serves as an example and provides additional foundation
