User:Jarle Pahr/Synthetic biology

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

Synthetic biology The influence of a host: http://www.nature.com/nmeth/journal/v10/n9/full/nmeth.2624.html

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

www.synthetic-bestiary.com

http://www.synbioproject.org/

http://www.synbiont.org/

Competitions and challenges:

http://igem.org

http://genocon.org/

http://www.ia-sb.eu/go/synthetic-biology/

LabGenius: www.labgeni.us

http://synbio.org.uk/

Synthetic Biology timeline: http://www.labgeni.us/synbiotimeline/

Invitrogen synthetic biology webinars: http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/synthetic-biology/Synthetic-Biology-Webinars.html

TASBE: A Tool-Chain to Accelerate Synthetic Biological Engineering: http://synthetic-biology.bbn.com/tasbe.html

Raytheon BBN Synthetic biology publications: http://synthetic-biology.bbn.com/pubs.html'

BBN Synthetic biology tools: https://synbiotools.bbn.com/

http://www.synberc.org/

http://www.teselagen.com/

Organizations and websites

http://syntheticbiology.org/

http://synberc.org

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

http://www.synbioproject.org/

http://synbiosoc.org/

http://www.arsbiotechnica.org/

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

What's hot in synthetic biology? http://peccoud.vbi.vt.edu/whats-hot-in-synthetic-biology/

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/

Synthetic biology thoughts: http://synth-bio-thoughts.blogspot.no/

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/

http://genomebiology.com/tags/genomeengineering

http://web.mit.edu/newsoffice/2013/update-editing-the-genome-0721.html

Genome-scale engineering for systems and synthetic biology. http://www.nature.com/msb/journal/v9/n1/pdf/msb201266.pdf

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

http://peccoud.vbi.vt.edu/workshop-on-the-interface-between-synthetic-biology-and-language-engineering/

A Review of CADs, Languages and Data Models for Synthetic Biology: http://www.jurnalteknologi.utm.my/index.php/jurnalteknologi/article/viewFile/1644/1396

GenoCAD

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

SBOL

http://www.sbolstandard.org/

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

Persons/Research labs

Wyss institute: http://wyss.harvard.edu/viewpage/101/synthetic-biology

Synthetic biology labs: http://www.synbio.org.uk/index/labs.html

http://synth-bio.org/

Zhao group: http://www.scs.illinois.edu/~zhaogrp/

Douglas Densmore: http://people.bu.edu/dougd/publications.html

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

Chris Voigt: http://web.mit.edu/voigtlab/

Silver: http://openwetware.org/wiki/Silver_Lab

Endy: http://openwetware.org/wiki/Endy_Lab

Gardner: http://gardnerlab.bu.edu/

Anderson: http://andersonlab.qb3.berkeley.edu/index.html

Knight: http://openwetware.org/wiki/Knight

Weiss: http://web.mit.edu/be/people/weiss.shtml

Ellis: http://openwetware.org/wiki/Ellis_Lab

Bibliography

Precise and reliable gene expression via standard transcription and translation initiation elements: http://www.nature.com/nmeth/journal/v10/n4/pdf/nmeth.2404.pdf

The visualization of evolutionary stability dynamics and competitive fitness of Escherichia coli engineered with randomized multi-gene circuits: http://pubs.acs.org/doi/abs/10.1021/sb400055h

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

Synthetic biological networks: http://iopscience.iop.org/0034-4885/76/9/096602/pdf/0034-4885_76_9_096602.pdf

Article collections

PLOS ONE Synthetic biology papers: http://www.ploscollections.org/article/browse/issue/info%3Adoi%2F10.1371%2Fissue.pcol.v02.i18

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

https://salis.psu.edu/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/SleeplessByte/programming-life

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

PromoterCAD: http://promotercad.org/

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

Rapid construction of insulated genetic circuits via synthetic sequence-guided isothermal assembly: http://nar.oxfordjournals.org/content/early/2013/09/26/nar.gkt860.full.pdf+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