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

From: A survey of enabling technologies in synthetic biology

Tool, Reagent or Method Description (URL or reference) N
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