User:Jarle Pahr/Synthetic biology

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Genome Consortium for active teaching (GCAT): http://gcat.davidson.edu/
Genome Consortium for active teaching (GCAT): http://gcat.davidson.edu/
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Martin Fussenegger: http://www.bsse.ethz.ch/people/martinf
=Bibliography=
=Bibliography=

Revision as of 14:49, 13 July 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/

http://synbiosoc.org/

See also WikiGenes article - synthetic biology community: http://www.wikigenes.org/e/art/e/189.html

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/

http://gen9bio.com/

Blogs and commentary

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

http://synberc.org/blog

http://88proof.com/synthetic_biology/blog/

Work

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

Concepts

Polymerases per second (POPS):

http://openwetware.org/wiki/PoPS


Genome engineering

See also http://openwetware.org/wiki/User:Jarle_Pahr/Biology for biological systems exploited in genome engineering.

http://geneditors.com/


Genome reduction & minimal genomics

Chemical synthetic biology

Engineering a reduced Escherichia coli genome.: http://www.ncbi.nlm.nih.gov/pubmed/11932248

Clean genome E coli: http://www.scarabgenomics.com/

See also http://openwetware.org/wiki/CHE391L/S13/Genome_Editing

Design languages

GenoCAD

GenoCAD tutorials: http://figshare.com/articles/GenoCAD_Training_Set_I/153827

Eugene

SBOL

http://www.sbolstandard.org/

SBOL visual: http://dspace.mit.edu/handle/1721.1/78249

Persons/Research labs

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

http://openwetware.org/wiki/Forster_Lab

http://www.leukippos.org/Leukippos_Institute/Leukippos_Institute_News.html

Haynes lab: http://openwetware.org/wiki/Haynes_Lab


Genome Consortium for active teaching (GCAT): http://gcat.davidson.edu/


Martin Fussenegger: http://www.bsse.ethz.ch/people/martinf

Bibliography

Tuning the dials of synthetic biology: http://mic.sgmjournals.org/content/early/2013/05/22/mic.0.067975-0.abstract

SynBioSS designer: a web-based tool for the automated generation of kinetic models for synthetic biological constructs. Brief Bioinform, 11 (2010), pp. 394–402

Approaches to chemical synthetic biology.: http://www.ncbi.nlm.nih.gov/pubmed/22265689

Synthetic genomics. Potential and limitations. http://www.sciencedirect.com/science/article/pii/S0958166912000298

FEBS Lett. 2012 Jul 16;586(15):2129-37. doi: 10.1016/j.febslet.2011.12.024. Epub 2012 Jan 2. Scaling up synthetic biology: Do not forget the chassis. http://www.ncbi.nlm.nih.gov/pubmed/22226636


From essential to persistent genes: a functional approach to constructing synthetic life: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3642372/

MoClo Planner: Supporting Innovation in Bio Design through Multi touch Interaction: http://cs.wellesley.edu/~hcilab/publication/2012ITS-MoCloDemo.pdf


Designing Reality Based Interfaces for Experiential Bio Design: http://wiki.bu.edu/wiki/ece-cidar/images/e/ea/EIST_journal_03-29-Final.pdf


RESEARCH PAPER Programming languages for synthetic biology : http://link.springer.com/content/pdf/10.1007%2Fs11693-011-9070-y.pdf

COMMENTARY The ten grand challenges of synthetic life: http://link.springer.com/content/pdf/10.1007%2Fs11693-011-9084-5.pdf


Evolving cell models for systems and synthetic biology Towards a whole-cell modeling approach for synthetic biology: http://covertlab.stanford.edu/publicationpdfs/ChaosJKarr2013.pdf

AutoBioCAD: Full Biodesign Automation of Genetic Circuits: http://pubs.acs.org/doi/abs/10.1021/sb300084h

Research highlight. Complex logic in a single layer: http://www.nature.com/nmeth/journal/v10/n6/full/nmeth.2501.html


Grand challenges in synthetic biology to be accomplished: http://www.frontiersin.org/Synthetic_Biology/10.3389/fbioe.2013.00002/full

Xenobiology: A new form of life as the ultimate biosafety tool: http://www.markusschmidt.eu/pdf/Xenobiology-Schmidt_Bioessays_201004.pdf

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

Survey of enabling technologies in synthetic biology: http://www.jbioleng.org/content/pdf/1754-1611-7-13.pdf


Review - ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering: http://www.sciencedirect.com/science/article/pii/S0167779913000875


Open Source Synthetic Biology: Problems and solutions: http://erepository.law.shu.edu/student_scholarship/47/


Synthetic Biology: It's an analog world: http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12246.html

Reviews

Impact of Synthetic Biology: http://pubs.acs.org/doi/pdf/10.1021/sb400027x

Engineering for the 21st Century: Synthetic Biology: http://pubs.acs.org/stoken/presspac/presspac/full/10.1021/sb400039g

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/

http://syntheticyeast.org/


ST-FLOW: http://www.cnb.csic.es/~stflow-project/ST-Flow/Welcome.html

SYNMOD: http://www.biofaction.com/project/evaluating-novel-antibiotics-synmod/

Software

MoClo planner: http://2012.igem.org/Team:Wellesley_HCI/MoClo_Planner

SBOL designer: http://clarkparsia.github.io/sbol/

https://synbiotools.bbn.com

https://github.com/Derkje-J/programming-life

http://coffeedoc.info/github/Derkje-J/programming-life/feature/undo/refactor/


Oligator: http://gcat.davidson.edu/igem10/


Proto Biocompiler. See An End-to-End Workflow for Engineering of Biological Networks from High-Level Specifications: http://pubs.acs.org/doi/abs/10.1021/sb300030d

GoSynthetic - a synthetic biology workbench: http://gosyn.bioapps.biozentrum.uni-wuerzburg.de./index.php

Plant synthetic biology

GoldenBraid2.0: A comprehensive DNA assembly framework for Plant Synthetic Biology: http://www.plantphysiol.org/content/early/2013/05/13/pp.113.217661.abstract

Parts and sequences

https://www.dna20.com/products/protein-paintbox


Terminators

Characterization of 582 natural and synthetic terminators and quantification of their design constraints: http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.2515.html


Insulators

Ribozyme-based insulator parts buffer synthetic circuits from genetic context: http://www.nature.com/nbt/journal/v30/n11/abs/nbt.2401.html


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

Genetic circuits

See Genetic circuits.

Courses and conferences

http://syntheticbiology.org/Courses.html


http://www.bio.davidson.edu/projects/gcat/GCATSynBio.html#workshops

DNA synthesis

DNA synthesis, assembly and applications in synthetic biology. Current opinion in chemical biology [1367-5931] 2012 vol:16 iss:3-4 pg:260 -7. http://www.sciencedirect.com/science/article/pii/S1367593112000622


Books

Schmidt, Markus (ed.) Synthetic Biology Industrial and Environmental Applications: http://www.wiley-vch.de/publish/en/books/forthcomingTitles/BE00/3-527-33183-2/?sID=70srgh2srq08r1bstktv48f410

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