User:Jarle Pahr/Synthetic biology

From OpenWetWare

Notes on news and articles related to synthetic biology:

RNA-guided editing of bacterial genomes using CRISPR-Cas systems:

Amplifying genetic logic gates:

Synthetic biology The influence of a host:

RNA processing enables predictable programming of gene expression:

Ribozyme-based insulator parts:

Competitions and challenges:


Synthetic Biology timeline:

Invitrogen synthetic biology webinars:

TASBE: A Tool-Chain to Accelerate Synthetic Biological Engineering:

Raytheon BBN Synthetic biology publications:'

BBN Synthetic biology tools:

Organizations and websites

See also WikiGenes article - synthetic biology community:

What's hot in synthetic biology?






Synthetic Genomics


Blogs and commentary

Synthetic biology thoughts:



Polymerases per second (POPS):

Genome engineering

See also for biological systems exploited in genome engineering.

Genome-scale engineering for systems and synthetic biology.

Genome reduction & minimal genomics

Chemical synthetic biology

Engineering a reduced Escherichia coli genome.:

Clean genome E coli:

See also

Design languages

A Review of CADs, Languages and Data Models for Synthetic Biology:


GenoCAD tutorials:



SBOL visual:

Persons/Research labs

Wyss institute:

Synthetic biology labs:

Zhao group:

Douglas Densmore:

Synthetic biology map:

Haynes lab:

Genome Consortium for active teaching (GCAT):

Martin Fussenegger:

Chris Voigt:









Precise and reliable gene expression via standard transcription and translation initiation elements:

The visualization of evolutionary stability dynamics and competitive fitness of Escherichia coli engineered with randomized multi-gene circuits:

Tuning the dials of synthetic biology:

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.:

Synthetic genomics. Potential and limitations.

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.

From essential to persistent genes: a functional approach to constructing synthetic life:

MoClo Planner: Supporting Innovation in Bio Design through Multi touch Interaction:

Designing Reality Based Interfaces for Experiential Bio Design:

RESEARCH PAPER Programming languages for synthetic biology :

COMMENTARY The ten grand challenges of synthetic life:

Evolving cell models for systems and synthetic biology Towards a whole-cell modeling approach for synthetic biology:

AutoBioCAD: Full Biodesign Automation of Genetic Circuits:

Research highlight. Complex logic in a single layer:

Grand challenges in synthetic biology to be accomplished:

Xenobiology: A new form of life as the ultimate biosafety tool:

Stacking nonenzymatic circuits for high signal gain.:

Amplifying Genetic Logic gates:

Targeted Development of Registries of Biological Parts:

Survey of enabling technologies in synthetic biology:

Review - ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering:

Open Source Synthetic Biology: Problems and solutions:

Synthetic Biology: It's an analog world:


Impact of Synthetic Biology:

Engineering for the 21st Century: Synthetic Biology:

Synthetic biological networks:

Article collections

PLOS ONE Synthetic biology papers:


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.





MoClo planner:

SBOL designer:



Proto Biocompiler. See An End-to-End Workflow for Engineering of Biological Networks from High-Level Specifications:

GoSynthetic - a synthetic biology workbench:

Plant synthetic biology

GoldenBraid2.0: A comprehensive DNA assembly framework for Plant Synthetic Biology:

Parts and sequences


Characterization of 582 natural and synthetic terminators and quantification of their design constraints:


Ribozyme-based insulator parts buffer synthetic circuits from genetic context:

RNA processing enables predictable programming of gene expression:

Rapid construction of insulated genetic circuits via synthetic sequence-guided isothermal assembly:

Genetic circuits

See Genetic circuits.

Courses and conferences

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.


Schmidt, Markus (ed.) Synthetic Biology Industrial and Environmental Applications: