User:Jarle Pahr/Synthetic biology

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Amplifying Genetic Logic gates: http://www.sciencemag.org/content/340/6132/599.abstract
Amplifying Genetic Logic gates: http://www.sciencemag.org/content/340/6132/599.abstract
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Targeted Development of Registries of Biological Parts: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0002671
=Ideas=
=Ideas=

Revision as of 09:59, 9 May 2013

Notes on news and articles related to synthetic biology:

RNA-guided editing of bacterial genomes using CRISPR-Cas systems: http://www.nature.com/nbt/journal/v31/n3/full/nbt.2508.html

Amplifying genetic logic gates: http://www.sciencemag.org/content/early/2013/03/27/science.1232758.abstract


RNA processing enables predictable programming of gene expression: http://www.nature.com/nbt/journal/v30/n10/full/nbt.2355.html

Ribozyme-based insulator parts: http://www.nature.com/nbt/journal/v30/n11/full/nbt.2401.html?WT.ec_id=NBT-201211

Contents

Organizations and websites

http://syntheticbiology.org/

http://synberc.org

http://www.synbio.org.uk/

http://www.synbioproject.org/

Companies

http://greeneconomypost.com/synthetic-biology-biofuel-biochemical-company-17244.htm

Intrexon: http://www.dna.com/

Amyris

Ls9

Solazyme

Synthetic Genomics

Synthace

http://www.biosergen.no/

Blogs and commentary

http://blogs.scientificamerican.com/oscillator/

http://synberc.org/blog

Work

http://www.indeed.co.uk/Synthetic-Biology-jobs-in-England

Concepts

Polymerases per second (POPS):

http://openwetware.org/wiki/PoPS


Design languages

GenoCAD

Eugene

Persons/Research labs

Synthetic biology map: http://www.synbioproject.org/sbmap/

http://openwetware.org/wiki/Forster_Lab

Bibliography

http://www.nature.com/nbt/journal/v27/n12/full/nbt1209-1109.html


Stacking nonenzymatic circuits for high signal gain.: http://www.ncbi.nlm.nih.gov/pubmed/23509255


Amplifying Genetic Logic gates: http://www.sciencemag.org/content/340/6132/599.abstract


Targeted Development of Registries of Biological Parts: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0002671

Ideas

A biological PID? Input and the objective to be controlled could be levels of a protein or a metabolite. Output would be summed from the activity of three transcription units. Would need a way to create a set-point and convert the difference between the present level and the set-point to serve as input to the PID circuit.

  • Proportional term. Activity is proportional to input (current level).
  • Integrative term. Activity is proportional to the total input over a recent timeframe (how can this be achieved?)
  • Derivative term. Activity is proportional to the change in input over a recent timeframe (how can this be achieved?)

Might be helpful to study mechanical or analog PID circuits.

Projects

http://www.kickstarter.com/projects/antonyevans/glowing-plants-natural-lighting-with-no-electricit

http://glowingplant.com/

Personal tools