A brief history of networking in the U.S.

Journal of Chemical Information and Computer Sciences

Volumn 38, Issue 6, 1998, Pages 951-955

  Meyer, Edgar ^a   Funkhouser, Norma Field ^a  

^a TEXAS A AND M UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0343180902     PISSN: 00952338     EISSN: None     Source Type: Journal    
DOI: 10.1021/ci9801264     Document Type: Review

References (52)

1. Ophir, D.; Shepherd. B. J.; Spinrad, R. J. Three-Dimensional Computer Display, Comm. A. C. M. 1969, 16, 6. 309-318.
2. Bernstein. F. C; Koetzle, T. F.; Williams, G. J. B.; Meyer, E. F.: Brice. M. D.; Rodgers, J. R.; Kennard, O.; Shimanouchi, T.; Tasumi, M. The Protein Data Bank. J. Mol. Biol. 1977,112, 535-542; Ear. J. Biochem. 1977, 80, 319-324; Arch. Biochem. Biophys. 1978. 185, 584-591.
3. Bernstein. F. C; Koetzle, T. F.; Williams, G. J. B.; Meyer, E. F.: Brice. M. D.; Rodgers, J. R.; Kennard, O.; Shimanouchi, T.; Tasumi, M. The Protein Data Bank. J. Mol. Biol. 1977,112, 535-542; Ear. J. Biochem. 1977, 80, 319-324; Arch. Biochem. Biophys. 1978. 185, 584-591.
4. Bernstein. F. C; Koetzle, T. F.; Williams, G. J. B.; Meyer, E. F.: Brice. M. D.; Rodgers, J. R.; Kennard, O.; Shimanouchi, T.; Tasumi, M. The Protein Data Bank. J. Mol. Biol. 1977,112, 535-542; Ear. J. Biochem. 1977, 80, 319-324; Arch. Biochem. Biophys. 1978. 185, 584-591.
5. Meyer, E. F. The Storage and Retrieval of Macromolecular Structural Data. Biopolymers 1974, 13, 419-421.
6. Meyer, E. F.; Morimoto, C. N.; Villarreal, J.; Berman, H. M.; Carrell, H. L.; Stodola, R. F.: Koetzle, T. F.; Andrews, L. C.; Bernstein. F. C; Bernstein, H. L. CRYSNET, A Crystallographic Computing Network with Interactive Graphics Display. Federation Proceedings 1974, 33, 2399-2402.
7. Koetzle, T. F.; Andrews, L. C.; Bernstein, F. C.; Bernstein, H. L. CRYSNET: A Network for Crystallographic Computing. In Computer Networking and Chemistry; Lykos, P., Ed.; ACS Symposium 1975; Vol. 19, pp 1-8.
8. Baker, S. Naming names. UNIX Rev. Oct 1997. 15, 15-22.
9. Annonymous, Father of invention: Vint Cerf. Data Comnunications Oct 21, 1997, 26, 44.
10. Gilder, G. Inventing the Internet again. Forbes June 2, 1997, 159. s106.
11. Hafner. K.: Lyons, M. Where Wizards Stay Up Late; The Origns of the INTERNET. Simon & Schuster, New York, 1996.
12. Fano, R. M.; Corbato. F. J. Time Sharing on Computers. Sci. Am. 1966, 215, 129-140.
13. Tracey, L. V. 30 years; a brief history of the communications industry. Telecommunications June, 1997, 31, 2410.
14. Senia, A.; Clancy, H. Fifteen turnina points. Computer Reseller News June, 1997, 738, 121-124.
15. Bush, V. As We May Think. The Atlantic Monthly; July 1945, pp 101 -111. cf. http://www.isg.sfu.ca/∼duchier/misc/vbush.
16. Evans, G. T. On-line Library Networking: A Bibliographic Essay. Bull. Am. Soc. Inf. Sci. 1979, 5, 11-14.
17. Bourne, C. P. On-line Systems: History, Technology, and Economics. J. Am. Soc. Inf. Sci. 1980, 980, 155-160.
18. Doszkocs, T. E.; Rapp. B. A.; Schoolman, H. M. Automated information Retrieval in Science and Technology. Science 1980. 208, 25-30.
19. Pizer, I. H. Looking Backwards, 1984-1959: Twenty-five Years of Library Automation - A Personal View. Bull. Med. Libr. Assoc. 1984, 72, 335-348.
20. Williams, M. E. Electronic Databases. Science 1985. 228. 445-456.
21. Neufeld, M. L.; Cornog, M. Database History: From Dinosaurs to Compact Discs. J. Am. Soc. Inf. Sci. 1986, 37. 183-190.
22. Meadow, C. T. Back to the Future: Making and Interpreting the Database Industry Timeline and Online Database Industry Timeline. Database 1988. 11, 14-22, 23-31.
23. Hayes, B. The Infrastructure of the Information Infrastructure. Amr. Sci. 85. 214-218
24. Pizer (ref 17), p 343.
25. Evans (ref 14), p 12.
26. Buchanan, B. G.; Smith, D. H.; White, W. C.; Gritter, R. J.; Feigenbaum, E. A.; Lederberg. J.; Djerassi, C. Automatic Rule Formation in Mass Spectrometry by Means of the Meta-DENDRAL Program. J. Am. Chem. Soc. 1976, 98, 8, 6168.
27. MacFarlane, R. D.; Torgerson, D. F. 252 Californium Plasma Desorption Mass Spectroscopy of nonvolatile Biomolecules. Science 1976. 191, 920-926.
28. Heller, S. R. A Conversational Mass Spectral Retrieval System and Its Use as an Aid in Structure Determination. Anal. Chem. 1972, 44, 1951-1961.
29. Meyer, E. F. The Storage and Retrieval of Macromolecular Structural Data. Biopolymers 1974, 13, 419-421.
30. Structure and function of proteins at the three-dimensional level. Cold Spring Harbor Symposia on Quantitative Biology 1972, XXXVI.
31. Meyer, E. F. How the Protein Data Bank Began. Protein Sci. 1997, 6, 1591-1597.
32. Collins, D. M.; Cotton, F. A.; Hazen, E. E., Jr.; Meyer, E. F., Jr.; Morimoto, C. N. Protein Crystal Structures: Quicker, Cheaper Approaches. Science 1975, 190. 1047-1053.
33. Morimoto, C. N.; Meyer, E. F., Jr. Information Retrieval, Computer Graphics and Remote Computing. In Crystallographic Computing Techniques; Ahmed, F. R., Ed.; Munksgaard, Copenhagen, 1976; pp 488-496.
34. The Cuckoo's Egg: Tracking a Spy through a Maze of Computer Espionage; Clifford Stoll, Doubleday: New York, 1989.
35. Meyer, E. F. Three-dimensional Graphical Models of Molecules and a Time-slicing Computer. J. Appl. Crystallogr. 1970, 3, 392-395. Cf. also the Annual Report of Brookhaven National Laboratory; 1968, pp 55 and 81.
36. Meyer, E. F. Three-dimensional Graphical Models of Molecules and a Time-slicing Computer. J. Appl. Crystallogr. 1970, 3, 392-395. Cf. also the Annual Report of Brookhaven National Laboratory; 1968, pp 55 and 81.
37. Richards F. M. 1968, The Matching of Physical Models to Three-dimensional Electron-density Maps: A Simple Optical Device, J. Mol. Biol. 37, 225-230.
38. "TCP (Transmission-Control Protocol) would be responsible for breaking up messages into datagrams, reassembling them at the other end, detecting errors, resending anything that got lost, and putting packets back in the right order. The Internet Protocol, or IP, would be responsible for routing individual datagrams" cf. p 236 of ref 9, a lively description of the early days of networking.
39. A network is implied but cannot be verified on the basis of available information.
40. The Advanced Research Projects Administration needed a robust communication network; the result, ARPAnet, has been compellingly described (cf. ref 9).
41. Development and progress with networks linking libraries is documented in numerous proceedings and annual reviews of the American Society for Information Science.
42. In the 1970s, mass spectroscopy was limited to the analysis of fragmentation patterns (mass, intensity) of volatile small molecules bombarded by a beam of electrons in a vacuum. In 1976 here at Texas A&M, Ronald MacFarlane (ref 25) described for the first time in a paper in Science a method to create a molecular ion for the mass analysis of biological macromolecules - now a powerful and common method in the arsenal of the biochemist.
43. "An interactive conversational mass spectral retrieval system, available over ordinary telephone lines using a teletype-writer terminal from a central computer in the Division of Computer Research and Technology at the National Institutes of Health (NIH) has been used extensively by many researchers since September, 1971". Cf. Heller, S. R.; Fales, H. M.; Milne, G. W. A. An Interactive Mass Spectral Search System. Anal. Chem. 1972, 44, 4, 725.
44. At this writing, the PDB (http://www.pdb.bnl.gov/) contains 8295 coordinate entries: 93% (7682) proteins, 7% (601) nucleic acids, and <1% (12) carbohydrates.
45. Contrary to other databases, for the first years, the PDB had no budget, no committee. Its relationship to the Crystallographic community was discussed at a meeting of the American Crystallographic Association in 1971. Fortunately, a decision was implicitly made and kept that access would remain free (excepting cost of distribution media). Free access to information is a crucial aspect of education and academic research. The implications of the failure of some industrial laboratories to publish atomic coordinates deserves serious discussion in another forum.
46. In 1970 the structures of only eight proteins were available in the PDB. The proceedings of the Cold Spring Harbor Symposium (ref 28) in 1971 provides an historical record of what had been done and what was yet to come in protein crystallography. Notable in the proceedings of this symposium was the contribution of Prof. Tony North and his group at the University of Leeds. Though one of the pioneers in creating molecular graphics hardware and software, especially the two-color 3-D illustrations in the proceedings. Prof. North subsequently was denied proper recognition for his pioneering accomplishments in computer graphics. A reviewer of one of numerous unfunded research proposals over the last 20 years remarked how a pioneer on the frontier had to be more concerned about "arrows in the back".
47. Myopic advice initially caused a switch to monochromatic CRT displays for the CRYSNET system but color raster graphics ultimately prevailed: lower cost, greater availability, and the anti-aliasing algorithm were contributing factors to its superiority. Initial computer memory limitations permitted use of only two of the three primary color output of television technology. Likewise, the size of the displayed model was limited-but the technology introduced by the BRAD system ultimately proved superior to then-prevalent monochromatic displays and set the standard now fully developed in the graphics workstation and lap top computers.
48. 31) for modeling structure into electron density in the protein (S. nuclease) here at Texas A&M. The following year. Jim Hogle accomplished the Herculean task of using program FIT to model two molecules into the asymmetric unit of monoclinic lysozyme, in a month's time, working all night, every night, on a single-user PDP-11 system with monochromatic graphics. This break-through for protein crystallography was just the opposite of "pedestrian". Also, the untimely death of Dr. Walter Hamilton in 1972 at age 41 surely deprived this novel effort of his leadership. More complex was the lack of enthusiasm within the Crystallographic community. Successful crystallographers in the 1970s had made workable arrangements with their institutional computing centers and had little incentive to change.
49. Cf. http://www.pdb.bnl.gov/pdb-bin/pdbmain, http://expasy.hcuge.ch/ sprot/sprot-top.html, and http://biology.ncsa.uiuc.edu/.
50. Productive academic and research scientists in the 1970s and 1980s generally resisted networking; they tended to look on computers as a necessary tool and were generally reluctant to make the transition from a batch processing central computer to the laboratory minicomputer (e.g., VAX) and saw little need to network. Without sustaining funding, networks could not survive. ARPAnet is the significant exception, as one traces its trajectory to Internet, the worldwide-Web, JAVA, and future supersystems.
51. Molecular graphics was and is a small component of the workstation market. We should not forget the sustaining interest of Dr. David Evans (†1998) and the technically superior graphics hardware of Evans & Sutherland. Likewise, the introduction of low-end graphics workstations within the budget of a larger number of investigators helped expand the technology to the user community. Currently, the emergence of facile graphics capabilities of Macintosh and PC platforms makes quality graphics more affordable to those fated to live on monthly incomes. What impact will the advent of digital television have? Do we march in front of the elephant or behind?
52. This has both figurative and literal significance. While visual input is essential, our spatial perceptions are sometimes better served by manipulating hand-held molecular models.