Table 3 Additional technologies considered enabling for synthetic biology by survey participants

BioCyc

a collection of 1962 pathway and genome databases (http://biocyc.org)

1

Bioinformatics

the application of computational techniques to analyze the information associated with biomolecules on a large-scale (http://www.ncbi.nlm.nih.gov/About/primer/bioinformatics.html)

1

CAGE: Conjugative Assembly Genome Engineering

a technology that permits the hierarchical consolidation of modified genomic regions [18]

1

High Throughput Computing

the ability to run many copies of software at the same time across many different computers, reviewed in [19]

1

in vitro screens

tests for biological activity such as metal binding screens, electron uptake, and other enzymatic activity

2

IonTorrent

an approach to DNA sequencing that enables a direct connection between chemical and digital information and aims to place DNA sequencing within the reach of any laboratory or clinic [20]

1

EcoCyc

a database for Escherichia coli K-12 MG1655 (http://ecocyc.org)

1

Flow Cytometry

a technology that uses the principles of light scattering, light excitation, and emission of fluorochrome molecules to generate specific multi-parameter data from particles and cells in the size range of 0.5 μm to 40 μm diameter (http://crl.berkeley.edu/flow_cytometry_basic.html)

3

KEGG: Kyoto Encyclopedia of Genes and Genomes

a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from genomic and molecular-level information (http://www.genome.jp/kegg)

1

Mass spectrometry

a technology for targeted protein quantification, reviewed in [21]

2

MetaCyc

a database of nonredundant, experimentally elucidated metabolic pathways (http://metacyc.org)

1

Molecular biology technologies, generally

includes methods and reagents for creating competent cells, nucleic acid transfer, digestion, primer extension, ligation, assembly of DNA molecules, etc.

9

OptForce

an algorithm that identifies all possible metabolic interventions that lead to the overproduction of a biochemical of interest [22]

1

PDB: Protein DataBank

an information portal to biological macromolecular structures (http://www.rcsb.org/pdb/home/home.do)

1

Protein purification technologies

methods for purifying a protein of interest efficiently, reviewed in [23]

1

Recombineering

an in vivo method of genetic engineering applicable to chromosomal and episomal replicons in E. coli[24]

1

Robotic automation

use of robots for repetitive laboratory tasks such as pick and place, liquid and solid additions, heating, cooling, mixing, shaking, etc.

2

Single cell microscopy

a technology that enables visualization of gene expression with exquisite spatial and temporal sensitivity, reviewed in [25]

1

Standards, needed

includes standards for calibrating and sharing data from plate readers, standards for test, measurement and characterization, standards for documentation and sharing of biological modules, for example see Arkin, 2008 [26] and Endy, 2005 [27]

3

SOLiD

a next generation sequencing technology that allows identification of hundreds of millions of short RNAs in a sample in a single run [28]

1

Transcription Activator-Like (TAL) effector technology

a technology that allows proteins to be designed to specifically target and bind to a desired sequence of DNA [29]

1

UniProt: Universal Protein Resource

a collaboration between the European Bioinformatics Institute (EBI), the SIB Swiss Institute of Bioinformatics and the Protein Information Resource (PIR) that aims to provide a comprehensive resource for protein sequence and annotation data (http://www.uniprot.org)

1

Yeast in vivo recombination

methods for assembling large DNA constructs in the yeast Saccharomyces cerevisiae, for example see Gibson et al., 2008 [30] and Jaschke et al., 2012 [31]

1