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 |