Post-archival genomics and the bulk logistics of DNA sequences

BioSocieties

Volumn 11, Issue 1, 2016, Pages 82-105

  Mackenzie, Adrian ^a   McNally, Ruth ^b   Mills, Richard ^c   Sharples, Stuart ^d  

^a LANCASTER UNIVERSITY   (United Kingdom)

^b ANGLIA RUSKIN UNIVERSITY   (United Kingdom)

^c UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^d LANCASTER UNIVERSITY   (United Kingdom)

Author keywords

archive; data infrastructures; DNA sequencing; genomics; scale; value

Indexed keywords

EID: 84959327493     PISSN: 17458552     EISSN: 17458560     Source Type: Journal    
DOI: 10.1057/biosoc.2015.22     Document Type: Review

References (43)

1. Bowker, G.C. (2005) Memory Practices in the Sciences. Cambridge, MA: MIT Press.
2. Busch, L. (2007) Performing the economy, performing science: From neoclassical to supply chain models in the agrifood sector. Economy and Society 36(3): 437-466.
3. Callaway, E. (2011) Unpopular genomic database faces budget axe: Nature News Blog. http://blogs.nature. com/news/2011/02/database-cuts.html, accessed 29 January 2013.
4. Canguilhem, G. (2000) In: Delaporte (ed.) A Vital Rationalist: Selected Writings from Georges Canguilhem. New York: Zone Books.
5. Chow-White, P.A. and Garcia-Sancho, M. (2011) Bidirectional shaping and spaces of convergence: Interactions between biology and computing from the first DNA sequencers to global genome databases, science, technology & human values. http://sth.sagepub.com/content/early/2011/02/26/0162243910397969. abstract , accessed 1 September 2011.
6. Cochrane, G. et al (2009) Petabyte-scale innovations at the European nucleotide archive. Nucleic Acids Research 37(1): D19-D25.
7. Cochrane, G. et al (2013) Facing growth in the European nucleotide archive. Nucleic Acids Research 41(D1): D30-D35.
8. Cochrane, G., Cook, C. E. and Birney, E. (2012) The future of DNA sequence archiving. GigaScience 1(1): 2.
9. Cock, P.J.A. et al (2010) The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Research 38(6): 1767-1771.
10. DDBJ (2013) Introduction of DDBJ | DDBJ. Available at , accessed 25 January 2013.
11. Edwards, P.N., Mayernik, M.S., Batcheller, A.L., Bowker, G.C. and Borgman, C.L. (2011) Science friction: Data, metadata, and collaboration. Social Studies of Science 41(5): 667-690.
12. Encode Consortium (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489 (7414): 57-74, Available at , accessed 10 September 2012.
13. Galperin, M.Y., Rigden, D.J. and Fernandez-Suarez, X.M. (2014) The 2015 nucleic acids research database issue and molecular biology database collection. Nucleic Acids Research 43(D1): D1-D5.
14. Goldman, N. et al (2013) Towards practical, high-capacity, low-maintenance information storage in synthesized DNA. Nature 494(7435): 77.
15. Helmreich, S. (2009) Alien Ocean: Anthropological Voyages in Microbial Seas. Berkeley, CA: University of California Press.
16. Helmreich, S. (2008) Species of biocapital. Science as Culture 17(4): 463-478.
17. Hilgartner, S. (1995) Biomolecular databases new communication regimes for biology? Science Communication 17(2): 240-263.
18. Hilgartner, S. (2013) Constituting large-scale biology: Building a regime of governance in the early years of the Human Genome Project. BioSocieties 8(4): 397-416.
19. Leinonen, R. et al (2010) Improvements to services at the European Nucleotide Archive. Nucleic Acids Research 38(Database issue): D39-D45.
20. Leonelli, S. and Ankeny, R.A. (2011) Re-Thinking organisms: The impact of databases on model organism biology. Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 43(1): 29-36.
21. Leonelli, S. (2013) Global data for local science. BioSocieties 8(4): 449-465.
22. Leonelli, S. (2014) What difference does quantity make? On the epistemology of Big Data in biology. Big Data and Society 1-11.
23. Li, H. et al (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25(16): 2078-2079.
24. Loman, N.J. et al (2012) Performance comparison of benchtop high-Throughput sequencing platforms. Nature Biotechnology 30(5): 434-439.
25. Mackenzie, A. (2015) Machine learning and genomic dimensionality: From features to landscapes. In: H. Stevens and S. Richardson (eds.) Post-genomic Sciences. Durham, NC: Duke University Press.
26. Mardis, E.R. (2011) A decade/s perspective on DNA sequencing technology. Nature 470(7333): 198-203.
27. Nadim, T. (2012) Inside the sequence universe: The amazing life of data and the people who look after them. PhD thesis. http://eprints.gold.ac.uk/8012/, accessed 30 October 2013.
28. NCBI (2011) Status of the NCBI sequence read archive (SRA). http://www.ncbi.nlm.nih.gov/About/news/13Oct2011.html, accessed 29 January 2013.
29. Neilson, B. (2012) Five theses on understanding logistics as power. Distinktion: Scandinavian Journal of Social Theory 13(3): 322-339. http://www.tandfonline.com/doi/abs/10.1080/1600910X.2012.728533, accessed 30 October 2013.
30. Nekrutenko, A. and Taylor, J. (2012) Next-generation sequencing data interpretation: Enhancing reproducibility and accessibility. Nature Reviews Genetics 13(9): 667-672.
31. Rohde, H. et al (2011) Open-source genomic analysis of Shiga-Toxin-producing E. coli O104:H4. New England Journal of Medicine 365(8): 718-724.
32. Rose, N. (2006) The Politics of Life Itself: Biomedicine, Power, and Subjectivity in the Twenty-first Century. Princeton, NJ: Princeton University Press.
33. SEQanswers (2011) Short Read archive canned-SEQanswers. http://seqanswers.com/forums/showthread.php? t=9431, accessed 29 January 2013.
34. Shendure, J. and Aiden, E.L. (2012) The expanding scope of DNA sequencing. Nature Biotechnology 30(11): 1084-1094.
35. Siva, N. (2008) 1000 Genomes project. Nature Biotechnology 26(3): 256-256.
36. Snyder, L.A.S., Loman, N., Pallen, Mark, J and Penn, C.W. (2009) Next-generation sequencing-The promise and perils of charting the great microbial unknown. Microbial Ecology 57(1): 1-3.
37. Star, S.L. and Ruhleder, K (1996) Steps toward an ecology of infrastructure: Design and access for large information spaces. Information Systems Research, 7, 1, 111-134
38. Stevens, H. (2011) Coding sequences: A history of sequence comparison algorithms as a scientific instrument. Perspectives on Science 19(3): 263-299.
39. Stevens, H. (2012) Dr. Sanger, meet Mr. Moore. BioEssays 34(2): 103-105.
40. Sunder Rajan, K. (2006) Biocapital: The Constitution of Postgenomic Life. Durham, NC: Duke University Press.
41. Thacker, E. (2005) The Global Genome: Biotechnology, Politics, and Culture. Cambridge, MA: MIT Press.
42. Tsing, A. (2009) Supply chains and the human condition. Rethinking Marxism 21(2): 148-176.
43. Zhu, Y., Stephens, Robert, M., Meltzer, Paul, S. and Davis, S.R. (2013) SRAdb: Query and use public nextgeneration sequencing data from within R. BMC Bioinformatics 14(1): 19.