Notes - Life Out of Sequence - page 237

17. Friedhoff and Benzon, Visualization .
18. Sulston et al., “Software for Genome Mapping.”
19. Durbin and Thierry-Mieg, “ACEDB.”
20. Durbin and Thierry-Mieg, “ACEDB.”
21. Durbin and Thierry-Mieg, “ACEDB.”
22. Indeed, object-oriented programming languages were invented for the
purpose of physical modeling. On the need for a general theory of ontology
when using an object-oriented programming language, see Smith, On the
Origin of Objects . Smith argues that “computer scientists wrestle not just with
notions of computation itself, but with deeper questions of how to understand
the ontology of worlds in which their systems are embedded. This is so not
for the elementary (if signifi cant) reason that anyone building a functioning
system must understand the context in which it will be deployed, but for the
additional one that computational systems in general, being intentional, will
represent at least some aspects of those contexts. The representational nature
of computation implies something very strong: that it is not just the ontology
of computation that is at stake; it is the nature of ontology itself ” (42, Smith's
emphasis).
23. Dahl and Nygaard, Simula , 1-2.
24. Dahl and Nygaard, Simula , 4.
25. AceDB, “Introduction to AceDB.”
26. Interview with Ewan Birney, November 12, 2008, Hinxton, UK.
27. Hubbard et al., “Ensembl Genome Database Project,” 38. For more
on Birney's career, see Hopkin, “Bring Me Your Genomes,” and Birney, “An
interview.”
28. Stabenau et al., “Ensembl Core.”
29. Stabenau et al., “Ensembl Core,” 930.
30. Stabenau et al., “Ensembl Core,” 931.
31. Stabenau et al., “Ensembl Core,” 931.
32. Hubbard et al., “Ensembl Genome Database Project,” 39.
33. For more on the internal workings of the Ensembl website, see Stalker
et al., “Ensembl Web Site.”
34. The website can be seen at http://www.ensembl.org.
35. Kent et al., “Human Genome Browser,” 996.
36. Kent et al., “Human Genome Browser,” 1004.
37. For more on autoSql, see Kent and Brumbaugh, “autoSql and
autoXml.”
38. Smith, On the Origin of Objects , 49. Smith's emphasis.
39. Kent et al., “Human Genome Browser,” 996.
40. For a detailed description of using the UCSC Genome Browser, see
Harte and Diekhans, “Fishing for Genes.”
41. Harte and Diekhans, “Fishing for Genes,” 3.
42. Maps of various sorts have played an important role in genetics
and genomics. See the signifi cant work on mapping cultures in Rheinberger
and Gaudillière, From Molecular Genetics to Genomics , and Gaudillière and
Rheinberger, Classical Genetic Research .
43. Burge and Karlin, “Prediction of Complete Gene Structures.”