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Conference on BIOLOGICAL INFORMATICS 6-8 July 1998 Australian Academy of Science, Canberra, Australia.

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Presentation on theme: "Conference on BIOLOGICAL INFORMATICS 6-8 July 1998 Australian Academy of Science, Canberra, Australia."— Presentation transcript:

1 Conference on BIOLOGICAL INFORMATICS 6-8 July 1998 Australian Academy of Science, Canberra, Australia

2 What is Bioinformatics? ( ) Robert J. Robbins Fred Hutchinson Cancer Research Center 1100 Fairview Avenue North, LV-101 Seattle, Washington (206)

3 Abstract In the last 25 years, Moore's Law has transformed society, delivering exponentially better computers at exponentially lower prices. Bioinformatics is the application of powerful, affordable information technology to the problems of biology. With $2500 desktop PCs now delivering more raw computing power than the first Cray, bioinformatics is rapidly becoming the critical technology for 21st Century biology. DNA is legitimately seen as a biological mass-storage device, making bioinformatics a sine qua non for genomic research. Others areas of biological investigation are equally information rich –– an exhaustive tabulation of the Earth's biodiversity would involve a cross–index of the millions of known species against the approximately 500,000,000,000,000 square meters of the Earth's surface. Bioinformatics is also becoming a scholarly discipline in its own right, melding information science with computer science, seasoning it with engineering methods, and applying it to the most information rich component of the known universe –– the Biosphere.

4 4 What is Bioinformatics? Bioinformatics is: the use of computers in pursuit of biological research. an emerging new discipline, with its own goals, research program, and practitioners. the sine qua non for 21st Century biology. all of the above. Bioinformatics is: the use of computers in pursuit of biological research. an emerging new discipline, with its own goals, research program, and practitioners. the sine qua non for 21st Century biology. all of the above.

5 5 Topics Biotechnology and information technology will be the magic technologies of the 21st Century.

6 6 Topics Biotechnology and information technology will be the magic technologies of the 21st Century. Moores Law constantly transforms IT (and everything else). Biotechnology and information technology will be the magic technologies of the 21st Century. Moores Law constantly transforms IT (and everything else).

7 7 Topics Biotechnology and information technology will be the magic technologies of the 21st Century. Moores Law constantly transforms IT (and everything else). Information Technology (IT) has a special relationship with biology. Biotechnology and information technology will be the magic technologies of the 21st Century. Moores Law constantly transforms IT (and everything else). Information Technology (IT) has a special relationship with biology.

8 8 Topics Biotechnology and information technology will be the magic technologies of the 21st Century. Moores Law constantly transforms IT (and everything else). Information Technology (IT) has a special relationship with biology. 21st-Century biology will be based on bioinformatics. Biotechnology and information technology will be the magic technologies of the 21st Century. Moores Law constantly transforms IT (and everything else). Information Technology (IT) has a special relationship with biology. 21st-Century biology will be based on bioinformatics.

9 9 Topics Biotechnology and information technology will be the magic technologies of the 21st Century. Moores Law constantly transforms IT (and everything else). Information Technology (IT) has a special relationship with biology. 21st-Century biology will be based on bioinformatics. Bioinformatics is emerging as an independent discipline. Biotechnology and information technology will be the magic technologies of the 21st Century. Moores Law constantly transforms IT (and everything else). Information Technology (IT) has a special relationship with biology. 21st-Century biology will be based on bioinformatics. Bioinformatics is emerging as an independent discipline.

10 10 Topics Biotechnology and information technology will be the magic technologies of the 21st Century. Moores Law constantly transforms IT (and everything else). Information Technology (IT) has a special relationship with biology. 21st-Century biology will be based on bioinformatics. Bioinformatics is emerging as an independent discipline. A connected, federated information infrastructure for biology is needed. Biotechnology and information technology will be the magic technologies of the 21st Century. Moores Law constantly transforms IT (and everything else). Information Technology (IT) has a special relationship with biology. 21st-Century biology will be based on bioinformatics. Bioinformatics is emerging as an independent discipline. A connected, federated information infrastructure for biology is needed.

11 11 Topics Biotechnology and information technology will be the magic technologies of the 21st Century. Moores Law constantly transforms IT (and everything else). Information Technology (IT) has a special relationship with biology. 21st-Century biology will be based on bioinformatics. Bioinformatics is emerging as an independent discipline. A connected, federated information infrastructure for biology is needed. Current support for public bio-information infrastructure seems inadequate. Biotechnology and information technology will be the magic technologies of the 21st Century. Moores Law constantly transforms IT (and everything else). Information Technology (IT) has a special relationship with biology. 21st-Century biology will be based on bioinformatics. Bioinformatics is emerging as an independent discipline. A connected, federated information infrastructure for biology is needed. Current support for public bio-information infrastructure seems inadequate.

12 Introduction Magical Technology

13 13 Magic To a person from 1897, much current technology would seem like magic.

14 14 Magic To a person from 1897, much current technology would seem like magic. What technology of 2097 would seem magical to a person from 1997?

15 15 Magic To a person from 1897, much current technology would seem like magic. What technology of 2097 would seem magical to a person from 1997? Candidate:Biotechnology so advanced that the distinction between living and non-living is blurred. Information technology so advanced that access to information is immediate and universal. Candidate:Biotechnology so advanced that the distinction between living and non-living is blurred. Information technology so advanced that access to information is immediate and universal.

16 16 Magic To a person from 1897, much current technology would seem like magic. What technology of 2097 would seem magical to a person from 1997? Candidate:Biotechnology so advanced that the distinction between living and non-living is blurred. Information technology so advanced that access to information is immediate and universal. Candidate:Biotechnology so advanced that the distinction between living and non-living is blurred. Information technology so advanced that access to information is immediate and universal.

17 Moores Law Transforms InfoTech (and everything else)

18 18 Moores Law: The Statement Every eighteen months, the number of transistors that can be placed on a chip doubles. Gordon Moore, co-founder of Intel...

19 19 Moores Law: The Effect Performance (constant cost) Time 100,000 10,000 1,

20 20 Moores Law: The Effect Performance (constant cost) Cost (constant performance) Time 100,000 10,000 1, ,000 1,

21 21 Moores Law: The Effect Three Phases of Novel IT Applications Its Impossible Three Phases of Novel IT Applications Its Impossible

22 22 Moores Law: The Effect Three Phases of Novel IT Applications Its Impossible Its Impractical Three Phases of Novel IT Applications Its Impossible Its Impractical

23 23 Moores Law: The Effect Three Phases of Novel IT Applications Its Impossible Its Impractical Its Overdue Three Phases of Novel IT Applications Its Impossible Its Impractical Its Overdue

24 24 Moores Law: The Effect Performance (constant cost) Cost (constant performance) Time 100,000 10,000 1, ,000 1, D P

25 25 Moores Law: The Effect Performance (constant cost) Cost (constant performance) Time 100,000 10,000 1, ,000 1, D P

26 26 Moores Law: The Effect Performance (constant cost) Cost (constant performance) Time 100,000 10,000 1, ,000 1, D P

27 27 Moores Law: The Effect Performance (constant cost) Cost (constant performance) Time 100,000 10,000 1, ,000 1, D P

28 28 Moores Law: The Effect Performance (constant cost) Cost (constant performance) Time 100,000 10,000 1, ,000 1, D P C

29 29 Moores Law: The Effect Performance (constant cost) Cost (constant performance) Time 100,000 10,000 1, ,000 1, D P C

30 30 Moores Law: The Effect Performance (constant cost) Cost (constant performance) Time 100,000 10,000 1, ,000 1, D P AA C

31 31 Moores Law: The Effect Performance (constant cost) Cost (constant performance) Time 100,000 10,000 1, ,000 1, D P A C

32 32 Moores Law: The Effect Performance (constant cost) Cost (constant performance) Time 100,000 10,000 1, ,000 1, D P A C Relevance for biology?

33 33 Cost (constant performance) ,000 10, ,000 1,000,000 10,000,000 University Purchase

34 34 Cost (constant performance) ,000 10, ,000 1,000,000 10,000,000 University Purchase Department Purchase

35 35 Cost (constant performance) ,000 10, ,000 1,000,000 10,000,000 RO1 Grant Purchase University Purchase Department Purchase

36 36 Cost (constant performance) ,000 10, ,000 1,000,000 10,000,000 Personal Purchase RO1 Grant Purchase University Purchase Department Purchase

37 37 Cost (constant performance) ,000 10, ,000 1,000,000 10,000,000 Personal Purchase RO1 Grant Purchase University Purchase Department Purchase Unplanned Purchases

38 IT-Biology Synergism IT-Biology Synergism

39 39 IT is Special Information Technology: affects the performance and the management of tasks Information Technology: affects the performance and the management of tasks

40 40 IT is Special Information Technology: affects the performance and the management of tasks allows the manipulation of huge amounts of highly complex data Information Technology: affects the performance and the management of tasks allows the manipulation of huge amounts of highly complex data

41 41 IT is Special Information Technology: affects the performance and the management of tasks allows the manipulation of huge amounts of highly complex data is incredibly plastic Information Technology: affects the performance and the management of tasks allows the manipulation of huge amounts of highly complex data is incredibly plastic (programming and poetry are both exercises in pure thought)

42 42 IT is Special Information Technology: affects the performance and the management of tasks allows the manipulation of huge amounts of highly complex data is incredibly plastic Information Technology: affects the performance and the management of tasks allows the manipulation of huge amounts of highly complex data is incredibly plastic (programming and poetry are both exercises in pure thought) improves exponentially (Moores Law)

43 43 Biology is Special Life is Characterized by: individuality Life is Characterized by: individuality

44 44 Biology is Special Life is Characterized by: individuality historicity Life is Characterized by: individuality historicity

45 45 Biology is Special Life is Characterized by: individuality historicity contingency Life is Characterized by: individuality historicity contingency

46 46 Biology is Special Life is Characterized by: individuality historicity contingency high (digital) information content Life is Characterized by: individuality historicity contingency high (digital) information content

47 47 Biology is Special Life is Characterized by: individuality historicity contingency high (digital) information content Life is Characterized by: individuality historicity contingency high (digital) information content No law of large numbers...

48 48 Biology is Special Life is Characterized by: individuality historicity contingency high (digital) information content Life is Characterized by: individuality historicity contingency high (digital) information content No law of large numbers, since every living thing is genuinely unique.

49 49 IT-Biology Synergism Physics needs calculus, the method for manipulating information about statistically large numbers of vanishingly small, independent, equivalent things.

50 50 IT-Biology Synergism Physics needs calculus, the method for manipulating information about statistically large numbers of vanishingly small, independent, equivalent things. Biology needs information technology, the method for manipulating information about large numbers of dependent, historically contingent, individual things. Physics needs calculus, the method for manipulating information about statistically large numbers of vanishingly small, independent, equivalent things. Biology needs information technology, the method for manipulating information about large numbers of dependent, historically contingent, individual things.

51 51 Biology is Special For it is in relation to the statistical point of view that the structure of the vital parts of living organisms differs so entirely from that of any piece of matter that we physicists and chemists have ever handled in our laboratories or mentally at our writing desks. Erwin Schrödinger What is Life.

52 52 Genetics as Code [The] chromosomes... contain in some kind of code- script the entire pattern of the individual's future development and of its functioning in the mature state.... [By] code-script we mean that the all-penetrating mind, once conceived by Laplace, to which every causal connection lay immediately open, could tell from their structure whether [an egg carrying them] would develop, under suitable conditions, into a black cock or into a speckled hen, into a fly or a maize plant, a rhodo-dendron, a beetle, a mouse, or a woman. Erwin Schrödinger What is Life.

53 53 One Human Sequence We now know that Schrödingers mysterious human code-script consists of 3.3 billion base pairs of DNA.

54 54 One Human Sequence Typed in 10-pitch font, one human sequence would stretch for more than 5,000 miles. Digitally formatted, it could be stored on one CD- ROM. Biologically encoded, it fits easily within a single cell. We now know that Schrödingers mysterious human code-script consists of 3.3 billion base pairs of DNA.

55 55 One Human Sequence For details on Ripleys interest in DNA, see A variant of this factoid actually made it into Ripleys Believe It or Not, but thats another story...

56 56 Bio-digital Information DNA is a highly efficient digital storage device: There is more mass-storage capacity in the DNA of a side of beef than in all the hard drives of all the worlds computers. DNA is a highly efficient digital storage device: There is more mass-storage capacity in the DNA of a side of beef than in all the hard drives of all the worlds computers.

57 57 Bio-digital Information DNA is a highly efficient digital storage device: There is more mass-storage capacity in the DNA of a side of beef than in all the hard drives of all the worlds computers. Storing all of the (redundant) information in all of the worlds DNA on computer hard disks would require that the entire surface of the Earth be covered to a depth of three miles in Conner 1.0 gB drives. DNA is a highly efficient digital storage device: There is more mass-storage capacity in the DNA of a side of beef than in all the hard drives of all the worlds computers. Storing all of the (redundant) information in all of the worlds DNA on computer hard disks would require that the entire surface of the Earth be covered to a depth of three miles in Conner 1.0 gB drives.

58 Genomics: An Example Genomics: An Example

59 59 Human Genome Project - Goals –construction of a high-resolution genetic map of the human genome; USDOE Understanding Our Genetic Inheritance. The U.S. Human Genome Project: The First Five Years.

60 60 Human Genome Project - Goals –construction of a high-resolution genetic map of the human genome; –production of a variety of physical maps of all human chromosomes and of the DNA of selected model organisms; –construction of a high-resolution genetic map of the human genome; –production of a variety of physical maps of all human chromosomes and of the DNA of selected model organisms; USDOE Understanding Our Genetic Inheritance. The U.S. Human Genome Project: The First Five Years.

61 61 Human Genome Project - Goals –construction of a high-resolution genetic map of the human genome; –production of a variety of physical maps of all human chromosomes and of the DNA of selected model organisms; –determination of the complete sequence of human DNA and of the DNA of selected model organisms; –construction of a high-resolution genetic map of the human genome; –production of a variety of physical maps of all human chromosomes and of the DNA of selected model organisms; –determination of the complete sequence of human DNA and of the DNA of selected model organisms; USDOE Understanding Our Genetic Inheritance. The U.S. Human Genome Project: The First Five Years.

62 62 Human Genome Project - Goals –construction of a high-resolution genetic map of the human genome; –production of a variety of physical maps of all human chromosomes and of the DNA of selected model organisms; –determination of the complete sequence of human DNA and of the DNA of selected model organisms; –development of capabilities for collecting, storing, distributing, and analyzing the data produced; –construction of a high-resolution genetic map of the human genome; –production of a variety of physical maps of all human chromosomes and of the DNA of selected model organisms; –determination of the complete sequence of human DNA and of the DNA of selected model organisms; –development of capabilities for collecting, storing, distributing, and analyzing the data produced; USDOE Understanding Our Genetic Inheritance. The U.S. Human Genome Project: The First Five Years.

63 63 Human Genome Project - Goals –construction of a high-resolution genetic map of the human genome; –production of a variety of physical maps of all human chromosomes and of the DNA of selected model organisms; –determination of the complete sequence of human DNA and of the DNA of selected model organisms; –development of capabilities for collecting, storing, distributing, and analyzing the data produced; –creation of appropriate technologies necessary to achieve these objectives. –construction of a high-resolution genetic map of the human genome; –production of a variety of physical maps of all human chromosomes and of the DNA of selected model organisms; –determination of the complete sequence of human DNA and of the DNA of selected model organisms; –development of capabilities for collecting, storing, distributing, and analyzing the data produced; –creation of appropriate technologies necessary to achieve these objectives. USDOE Understanding Our Genetic Inheritance. The U.S. Human Genome Project: The First Five Years.

64 64 Infrastructure and the HGP Progress towards all of the [Genome Project] goals will require the establishment of well- funded centralized facilities, including a stock center for the cloned DNA fragments generated in the mapping and sequencing effort and a data center for the computer-based collection and distribution of large amounts of DNA sequence information. National Research Council Mapping and Sequencing the Human Genome. Washington, DC: National Academy Press. p. 3

65 65 GenBank Totals (Release 103) DIVISION Phage Sequences (PHG) Viral Sequences (VRL) Bacteria (BCT) Plant, Fungal, and Algal Sequences (PLN) Invertebrate Sequences (INV) Rodent Sequences (ROD) Primate Sequences (PRI1–2) Other Mammals (MAM) Other Vertebrate Sequences (VRT) High-Throughput Genome Sequences (HTG) Genome Survey Sequences (GSS) Structural RNA Sequences (RNA) Sequence Tagged Sites Sequences (STS) Patent Sequences (PAT) Synthetic Sequences (SYN) Unannotated Sequences (UNA) EST1-17 TOTALS Entries 1,313 45,355 38,023 44,553 29,657 36,967 75,587 12,744 17,713 1,120 42,628 4,802 52,824 87,767 2,577 2,480 1,269,737 1,765,847 Base Pairs 2,138,810 44,484,848 88,576,641 92,259, ,703,550 45,437, ,944,314 12,358,310 17,040,159 72,064,395 22,783,326 2,487,397 18,161,532 27,593,724 5,698,945 1,933, ,634,317 1,160,300,687 Per Cent 0.184% 3.834% 7.634% 7.951% 9.110% 3.916% % 1.065% 1.469% 6.211% 1.964% 0.214% 1.565% 2.378% 0.491% 0.167% % % Per Cent 0.074% 2.568% 2.153% 2.523% 1.679% 2.093% 4.280% 0.722% 1.003% 0.063% 2.414% 0.272% 2.991% 4.970% 0.146% 0.140% % %

66 66 Base Pairs in GenBank GenBank Release Numbers

67 67 Base Pairs in GenBank GenBank Release Numbers Growth in GenBank is exponential. More data were added in the last ten weeks than were added in the first ten years of the project.

68 68 Base Pairs in GenBank GenBank Release Numbers Growth in GenBank is exponential. More data were added in the last ten weeks than were added in the first ten years of the project. At this rate, whats next...

69 69 ABI Bass-o-Matic Sequencer In with the sample, out with the sequence... TGCGCATCGCGTATCGATAG speed gB/sec EnterEnter Defrost

70 70 Whats Really Next The post-genome era in biological research will take for granted ready access to huge amounts of genomic data. The challenge will be understanding those data and using the understanding to solve real-world problems...

71 71 Base Pairs in GenBank GenBank Release Numbers Net Changes

72 72 Base Pairs in GenBank (Percent Increase) Year Percent Increase average = 56% Percent Increase average = 56%

73 73 Projected Base Pairs Year Assumed annual growth rate: 50% (less than current rate)

74 74 Projected Base Pairs Year Assumed annual growth rate: 50% (less than current rate) Is this crazy? One trillion bp by trillion by 2025 Is this crazy? One trillion bp by trillion by 2025

75 75 Projected Base Pairs Year Is this crazy? One trillion bp by trillion by 2025 Is this crazy? One trillion bp by trillion by ,000 50,000 5,000 Maybe not... Projected database size, indicated as the number of base pairs per individual medical record in the US.

76 21st Century Biology Post-Genome Era

77 77 The Post-Genome Era Post-genome research involves: applying genomic tools and knowledge to more general problems asking new questions, tractable only to genomic or post-genomic analysis moving beyond the structural genomics of the human genome project and into the functional genomics of the post-genome era Post-genome research involves: applying genomic tools and knowledge to more general problems asking new questions, tractable only to genomic or post-genomic analysis moving beyond the structural genomics of the human genome project and into the functional genomics of the post-genome era

78 78 The Post-Genome Era Suggested definition: functional genomics = biology Suggested definition: functional genomics = biology

79 79 The Post-Genome Era An early analysis: Walter Gilbert Towards a paradigm shift in biology. Nature, 349:99.

80 80 Paradigm Shift in Biology To use [the] flood of knowledge, which will pour across the computer networks of the world, biologists not only must become computer literate, but also change their approach to the problem of understanding life. Walter Gilbert Towards a paradigm shift in biology. Nature, 349:99.

81 81 Paradigm Shift in Biology The new paradigm, now emerging, is that all the genes will be known (in the sense of being resident in databases available electronically), and that the starting point of a biological investigation will be theoretical. An individual scientist will begin with a theoretical conjecture, only then turning to experiment to follow or test that hypothesis. Walter Gilbert Towards a paradigm shift in biology. Nature, 349:99.

82 82 Paradigm Shift in Biology Case of Microbiology < 5,000known and described bacteria 5,000,000base pairs per genome 25,000,000,000TOTAL base pairs If a full, annotated sequence were available for all known bacteria, the practice of microbiology would match Gilberts prediction.

83 21st Century Biology The Science

84 84 Fundamental Dogma The fundamental dogma of molecular biology is that genes act to create phenotypes through a flow of information from DNA to RNA to proteins, to interactions among proteins (regulatory circuits and metabolic pathways), and ultimately to phenotypes. Collections of individual phenotypes, of course, constitute a population. DNA RNA Proteins Circuits Phenotypes Populations

85 85 Fundamental Dogma DNA RNA Proteins Circuits Phenotypes Populations GenBank EMBL DDBJ Map Databases SwissPROT PIR PDB Although a few databases already exist to distribute molecular information,

86 86 Fundamental Dogma DNA RNA Proteins Circuits Phenotypes Populations GenBank EMBL DDBJ Map Databases SwissPROT PIR PDB Gene Expression? Clinical Data ? Regulatory Pathways? Metabolism? Biodiversity? Neuroanatomy? Development ? Molecular Epidemiology? Comparative Genomics? the post-genomic era will need many more to collect, manage, and publish the coming flood of new findings. Although a few databases already exist to distribute molecular information,

87 21st Century Biology The Literature

88 88 P I R -- Beta Hemoglobin DEFINITION [HBHU] Hemoglobin beta chain - Human, chimpanzee, pygmy chimpanzee, and gorilla SUMMARY [SUM] #Type Protein #Molecular-weight #Length 146 #Checksum 1242 SEQUENCE V H L T P E E K S A V T A L W G K V N V D E V G G E A L G R L L V V Y P W T Q R F F E S F G D L S T P D A V M G N P K V K A H G K K V L G A F S D G L A H L D N L K G T F A T L S E L H C D K L H V D P E N F R L L G N V L V C G D B -- Beta Hemoglobin ** Locus Detail View ** Symbol: HBB Name: hemoglobin, beta MIM Num: Location: 11p15.5 Created: 01 Jan 86 00: ** Polymorphism Table ** Probe Enzyme ================================= beta-globin cDNA RsaI beta-globin cDNA,JW10+ AvaII Pstbeta,JW102,BD23,pB+ BamHI pRK29,Unknown HindII beta-IVS2 probe HphI IVS-2 normal HphI Unknown AvrII beta-IVS2 probe AsuI Electronic Data Publishing O M I M -- Beta Hemoglobin Title * HEMOGLOBIN--BETA LOCUS [HBB; SICKLE CELL ANEMIA, INCLUDED; BETA-THALASSEMIAS, INCLUDED; HEINZ BODY ANEMIAS, BETA-GLOBIN TYPE,...] The alpha and beta loci determine the structure of the 2 types of polypeptide chains in adult hemoglobin, Hb A. By autoradiography using heavy-labeled hemoglobin-specific messenger RNA, Price et al. (1972) found labeling of a chromosome 2 and a group B chromo- some. They concluded, incorrectly as it turned out, that the beta-gamma-delta linkage group was on a group B chromosome since the zone of labeling was longer on that chromosome than on chromosome 2 (which by this reasoning GenBank -- Beta Hemoglobin DEFINITION [DEF] [HUMHBB] Human beta globin region LOCUS [LOC] HUMHBB ACCESSION NO. [ACC] J00179 J00093 J00094 J00096 J00158 J00159 J00160 J00161 KEYWORDS [KEY] Alu repetitive element; HPFH; KpnI repetitive sequence; RNA polymerase III; allelic variation; alternate cap site; SEQUENCE gaattctaatctccctctcactactgtctagtatccctcaaggag tggtggctcatgtcttgagctcaagagtttgatataaaaaaaa attagccaggcaaatgggaggatcccttgagcgcactcca

89 89 Electronic Scholarly Publishing The ESP site is dedicated to the electronic publishing of scientific and other scholarly materials. Of particular interest are the history of science, genetics, computational biology, and genome research.

90 90 Electronic Scholarly Publishing The Classical Genetics: Foundations series provides ready access to typeset-quality, electronic editions of important publications that can otherwise be very difficult to find.

91 91 Electronic Scholarly Publishing Hardy (of Hardy- Weinberg) is a name well known to most students of biology.

92 92 Electronic Scholarly Publishing But how many have read, or even seen, all of Hardys biological writings? This is it: A single, one-page letter to the editor of Science.

93 93 Electronic Scholarly Publishing Entire monographs can be made instantly available to readers world-wide..

94 94 Electronic Scholarly Publishing Todays computer technology was nearly unimaginable just ten years ago. The technol- ogy of ten years from now will also bring many surprises. How is it that IT can maintain such an amazing rate of sustained change? And what, if any, are the implications of that rate of change for biology?

95 95 Traditional Publishing Scientific Literature Researcher Print publication seems straightforward,...

96 96 Traditional Publishing Scientific Literature Researcher... with an infrastructure that is largely invisible,... Creation and Publication Infrastructure Distribution and Management Infrastructure

97 97 Traditional Publishing Management Classify Acquire Order Catalog Shelve Circulate Research Bench Work Analyze Acquire Literature Interpret Data Synthesis Write Distribution Pick Process Orders Store Package Address Ship & Invoice Research Draft Scientific Literature Collections & Libraries Publishing Edit Revise Review Typeset Print Bind Researcher... yet essential.

98 98 Electronic Publishing Management ??? Research Bench Work Analyze Acquire Literature Interpret Data Synthesis Write Distribution Edit Review Database Operation User Assistance Distribute Output Access Date Submission Scientific Database Federations & Libraries Publishing Revise Review Submit Accession Edit Release Researcher Some of the needed infrastructure is undefined.

99 21st Century Biology The People

100 100 Human Resources Issues Reduction in need for non-IT staff

101 101 Human Resources Issues Reduction in need for non-IT staff Increase in need for IT staff, especially information engineers Reduction in need for non-IT staff Increase in need for IT staff, especially information engineers

102 102 Human Resources Issues Reduction in need for non-IT staff Increase in need for IT staff, especially information engineers Reduction in need for non-IT staff Increase in need for IT staff, especially information engineers In modern biology, a general trend is to convert expert work into staff work and finally into computation. New expertise is required to design, carry out, and interpret continuing work.

103 103 Human Resources Issues Elbert Branscomb: You must recognize that some day you may need as many computer scientists as biologists in your labs.

104 104 Human Resources Issues Elbert Branscomb: You must recognize that some day you may need as many computer scientists as biologists in your labs. Craig Venter: At TIGR, we already have twice as many computer scientists on our staff. Elbert Branscomb: You must recognize that some day you may need as many computer scientists as biologists in your labs. Craig Venter: At TIGR, we already have twice as many computer scientists on our staff. Exchange at DOE workshop on high- throughput sequencing.

105 New Discipline of Informatics

106 106 What is Informatics? Informatics Computer Science Research Biological Application Programs

107 107 What is Informatics? Informatics combines expertise from: domain science (e.g., biology) computer science library science management science Informatics combines expertise from: domain science (e.g., biology) computer science library science management science All tempered with an engineering mindset...

108 108 What is Informatics? IS Medical Informatics Medical Informatics Bio Informatics Bio Informatics Other Informatics Other Informatics Library Science Library Science Computer Science Computer Science Mgt Science Mgt Science Domain Knowledge Engineering Principles

109 109 Engineering Mindset Engineering is often defined as the use of scientific knowledge and principles for practical purposes. While the original usage restricted the word to the building of roads, bridges, and objects of military use, today's usage is more general and includes chemical, electronic, and even mathematical engineering. Parnas, David Lorge Computer, 23(1):17-22.

110 110 Engineering Mindset Engineering is often defined as the use of scientific knowledge and principles for practical purposes. While the original usage restricted the word to the building of roads, bridges, and objects of military use, today's usage is more general and includes chemical, electronic, and even mathematical engineering. Parnas, David Lorge Computer, 23(1): or even information engineering.

111 111 Engineering Mindset Engineering education... stresses finding good, as contrasted with workable, designs. Where a scientist may be happy with a device that validates his theory, an engineer is taught to make sure that the device is efficient, reliable, safe, easy to use, and robust. Parnas, David Lorge Computer, 23(1):17-22.

112 112 Engineering Mindset Engineering education... stresses finding good, as contrasted with workable, designs. Where a scientist may be happy with a device that validates his theory, an engineer is taught to make sure that the device is efficient, reliable, safe, easy to use, and robust. Parnas, David Lorge Computer, 23(1): The assembly of working, robust systems, on time and on budget, is the key requirement for a federated information infrastructure for biology.

113 113 Informatics Triangle BS LSCS MS

114 114 Informatics Triangle BS LSCS comp bio info SILS

115 115 Informatics Triangle MS LSCS CIS/ITMIS SILS

116 116 Informatics Triangle BS LSCS MS IS

117 117 What is Informatics? MS IS BS LS CS

118 Federated Information Infrastructure Federated Information Infrastructure

119 119 National Information Infrastructure analog commercial uses non-commercial uses digital Edu LibotherResETC

120 120 ODN Model ODN Bearer Service Layer 1 ATM Network Technology Substrate LANs SMDS Wireless Dial-up Modems Frame Relay Point-to-Point Circuits Direct Broadcast Satellites Middleware Services Layer 3 Service Directories Privacy Electronic Money Storage Repositories Multisite Coordination File Systems Security Name Servers Applications Layer 4 Video Server Fax Audio Server Financial Services Electronic Mail Tele- Conferencing Interactive Education Information Browsing Remote Login Open Bearer Service Interface Transport Services and Representation Standards Layer 2 (fax, video, audio, text, etc.) A recent NRC report, Realizing the Information Future, laid out a vision of an Open Data Network model, in which any information appliance could be operated over generic networking protocols...

121 121 FIIST & NII FIIST (science & technology) FIIE (engineering) FIIS (science) FII (climatology) FII (chemistry) FII (geology) FII (physics) FII (biology) FII (physiology) FII (ecology) FII (structural biology) FII ( ) FII (geography) FII (human) FII (mouse) FII ( ) FII (Arabidopsis) FII (genomics) FII (E. coli) FII (zoology) FII (botany) FII ( ) FII (systematics) FII ( ) analog commercial uses non-commercial uses digital Edu LibotherResETC The research component of the NII contains a Federated Information Infrastructure for Science and Technology..

122 122 FIIST (science & technology) FIIE (engineering) FIIS (science) FII (climatology) FII (chemistry) FII (geology) FII (physics) FII (biology) FII ( ) FII (geography)

123 123 FIIB FII (biology) FII (physiology) FII (ecology) FII (structural biology) FII (human) FII (mouse) FII ( ) FII (Arabidopsis) FII (genomics) FII (E. coli) FII (zoology) FII (botany) FII ( ) FII (systematics) FII ( )

124 124 Public Funding of Databases Stand-alone Criteria: Is there a need? Will this meet the need? Can they do it? Is it worth it?

125 125 Public Funding of Databases Global Criteria: Does it adhere to standards? Will it interoperate? Is there commitment to federation? Is it worth it?

126 126 Information Resources and the GII Guiding Principles: Global value explosion Componentry Anonymous interoperability Technical scalability Social scalability Value additivity

127 Funding for Bio-Information Infrastructure Funding for Bio-Information Infrastructure

128 128 Call for Change Among the many new tools that are or will be needed (for 21st- century biology), some of those having the highest priority are: bioinformatics computational biology functional imaging tools using biosensors and biomarkers transformation and transient expression technologies nanotechnologies Among the many new tools that are or will be needed (for 21st- century biology), some of those having the highest priority are: bioinformatics computational biology functional imaging tools using biosensors and biomarkers transformation and transient expression technologies nanotechnologies Impact of Emerging Technologies on the Biological Sciences: Report of a Workshop. NSF-supported workshop, held June 1995, Washington, DC.

129 129 The Problem IT moves at Internet Speed and responds rapidly to market forces.

130 130 The Problem IT moves at Internet Speed and responds rapidly to market forces. IT will play a central role in 21st Century biology. IT moves at Internet Speed and responds rapidly to market forces. IT will play a central role in 21st Century biology.

131 131 The Problem IT moves at Internet Speed and responds rapidly to market forces. IT will play a central role in 21st Century biology. Current levels of support for public bio- information infrastructure are too low. IT moves at Internet Speed and responds rapidly to market forces. IT will play a central role in 21st Century biology. Current levels of support for public bio- information infrastructure are too low.

132 132 The Problem IT moves at Internet Speed and responds rapidly to market forces. IT will play a central role in 21st Century biology. Current levels of support for public bio- information infrastructure are too low. Reallocation of federal funding is difficult, and subject to political pressures. IT moves at Internet Speed and responds rapidly to market forces. IT will play a central role in 21st Century biology. Current levels of support for public bio- information infrastructure are too low. Reallocation of federal funding is difficult, and subject to political pressures.

133 133 The Problem IT moves at Internet Speed and responds rapidly to market forces. IT will play a central role in 21st Century biology. Current levels of support for public bio- information infrastructure are too low. Reallocation of federal funding is difficult, and subject to political pressures. Federal-funding decision processes are ponderously slow and inefficient. IT moves at Internet Speed and responds rapidly to market forces. IT will play a central role in 21st Century biology. Current levels of support for public bio- information infrastructure are too low. Reallocation of federal funding is difficult, and subject to political pressures. Federal-funding decision processes are ponderously slow and inefficient.

134 134 Federal Funding of Bio-Databases The challenges:

135 135 Federal Funding of Bio-Databases The challenges: providing adequate funding levels The challenges: providing adequate funding levels

136 136 Federal Funding of Bio-Databases The challenges: providing adequate funding levels making timely, efficient decisions The challenges: providing adequate funding levels making timely, efficient decisions

137 IT Budgets A Reality Check

138 138 Rhetorical Question Which is likely to be more complex: identifying, documenting, and tracking the whereabouts of all parcels in transit in the US at one time identifying, documenting, and analyzing the structure and function of all individual genes in all economically significant organisms; then analyzing all significant gene-gene and gene- environment interactions in those organisms and their environments Which is likely to be more complex: identifying, documenting, and tracking the whereabouts of all parcels in transit in the US at one time identifying, documenting, and analyzing the structure and function of all individual genes in all economically significant organisms; then analyzing all significant gene-gene and gene- environment interactions in those organisms and their environments

139 139 Business Factoids United Parcel Service: uses two redundant 3 Terabyte (yes, 3000 GB) databases to track all packages in transit. has 4,000 full-time employees dedicated to IT spends one billion dollars per year on IT has an income of 1.1 billion dollars, against revenues of 22.4 billion dollars United Parcel Service: uses two redundant 3 Terabyte (yes, 3000 GB) databases to track all packages in transit. has 4,000 full-time employees dedicated to IT spends one billion dollars per year on IT has an income of 1.1 billion dollars, against revenues of 22.4 billion dollars

140 140 Business Comparisons CompanyRevenuesIT BudgetPct Bristol-Myers Squibb15,065,000,000440,000, %Pfizer11,306,000,000300,000, %Pacific Gas & Electric10,000,000,000250,000, %K-Mart31,437,000,000130,000, %Wal-Mart104,859,000,000550,000, %Sprint14,235,000,000873,000, %MCI18,500,000,0001,000,000, %United Parcel22,400,000,0001,000,000, %AMR Corporation17,753,000,0001,368,000, %IBM75,947,000,0004,400,000, %Microsoft11,360,000,000510,000, %Chase-Manhattan16,431,000,0001,800,000, %Nations Bank17,509,000,0001,130,000, %

141 141 Federal Funding of Biomedical-IT Appropriate funding level: approx. 5-10% of research funding i.e., billion dollars per year Appropriate funding level: approx. 5-10% of research funding i.e., billion dollars per year Source of estimate: - Experience of IT-transformed industries. - Current support for IT-rich biological research. Source of estimate: - Experience of IT-transformed industries. - Current support for IT-rich biological research.

142 Conference on BIOLOGICAL INFORMATICS 6-8 July 1998 Australian Academy of Science, Canberra, Australia

143 Conference on Biological Informatics Conference Sessions Overview of Biological Informatics Biodiversity Informatics Environmental Informatics Molecular Informatics Medical / Neuroinformatics Teaching and Training in Informatics Conference Sessions Overview of Biological Informatics Biodiversity Informatics Environmental Informatics Molecular Informatics Medical / Neuroinformatics Teaching and Training in Informatics

144 Extras

145 145 Slides:

146 Extras

147 Basics Business 101

148 148 Market Forces Vendors products services Buyers $ purchases In a simple market economy, vendors try to anticipate the needs of buyers and offer products and services to meet those needs. Real users decide whether or not to buy a product or service, depending upon whether or not it meets a real need at a reasonable price. In a simple market economy, vendors try to anticipate the needs of buyers and offer products and services to meet those needs. Real users decide whether or not to buy a product or service, depending upon whether or not it meets a real need at a reasonable price. Business 101 Insight: Successful vendors target a niche and excel at meeting the needs of that niche. Business 101 Insight: Successful vendors target a niche and excel at meeting the needs of that niche.

149 149 Market Forces Venture Capital Vendors $ Buyers $ Stock Offerings Funding to initiate the development of products and services come from investors, not from buyers. Investors decide whether or not to provide start-up funding based upon the estimated ability of the vendor to create products and services that will meet real needs at competitive prices. Funding to initiate the development of products and services come from investors, not from buyers. Investors decide whether or not to provide start-up funding based upon the estimated ability of the vendor to create products and services that will meet real needs at competitive prices. $ Vendor Investment products services $ purchases

150 150 Federal Funding Investors Database $ Users products services $ purchases If biological databases were driven by market forces, individual users would choose what services they need and individual database providers would choose what services to make available. Investors would provide start-up money on the likelihood of successful products and services being developed. Ultimate success would depend on meeting the needs of real users. Decisions could be made rapidly, in response to changing needs and emerging opportunities. If biological databases were driven by market forces, individual users would choose what services they need and individual database providers would choose what services to make available. Investors would provide start-up money on the likelihood of successful products and services being developed. Ultimate success would depend on meeting the needs of real users. Decisions could be made rapidly, in response to changing needs and emerging opportunities.

151 151 Federal Funding Agency Database Reviewers Other Agencies Agency Advisors Congress products services OMB $ $ Database Advisors Users Instead, funding decisions for grant- supported biological databases can follow a ponderously slow course, with almost no opportunity for real- time input from real users. Even with the best of intentions at all levels, this process is slow, inefficient, risk-averse, and non- responsive to the real and changing needs of users. Instead, funding decisions for grant- supported biological databases can follow a ponderously slow course, with almost no opportunity for real- time input from real users. Even with the best of intentions at all levels, this process is slow, inefficient, risk-averse, and non- responsive to the real and changing needs of users.

152 152 Federal Funding of Bio-Databases Possible solutions: increase the direct support of federal service organizations providing information infrastructure (e.g., NCBI). reduce support for investigator-initiated, grant- funded public database projects. create market forces, initially through subsidization, later simply through direct support for affected science (e.g., NSFnet into internet). Possible solutions: increase the direct support of federal service organizations providing information infrastructure (e.g., NCBI). reduce support for investigator-initiated, grant- funded public database projects. create market forces, initially through subsidization, later simply through direct support for affected science (e.g., NSFnet into internet).

153 153 Federal Funding of Bio-Databases Creating market forces: stop supporting the supply side of biodatabases through slow, inefficient processes. Creating market forces: stop supporting the supply side of biodatabases through slow, inefficient processes.

154 154 Federal Funding of Bio-Databases Creating market forces: stop supporting the supply side of biodatabases through slow, inefficient processes. start supporting the demand side through fast, efficient processes. Creating market forces: stop supporting the supply side of biodatabases through slow, inefficient processes. start supporting the demand side through fast, efficient processes.

155 155 Federal Funding of Bio-Databases Creating market forces: stop supporting the supply side of biodatabases through slow, inefficient processes. start supporting the demand side through fast, efficient processes. provide guaranteed supplementary funding, redeemable only for access to bio-databases. Creating market forces: stop supporting the supply side of biodatabases through slow, inefficient processes. start supporting the demand side through fast, efficient processes. provide guaranteed supplementary funding, redeemable only for access to bio-databases.

156 156 Federal Funding of Bio-Databases Creating market forces: stop supporting the supply side of biodatabases through slow, inefficient processes. start supporting the demand side through fast, efficient processes. provide guaranteed supplementary funding, redeemable only for access to bio-databases. data stamps Creating market forces: stop supporting the supply side of biodatabases through slow, inefficient processes. start supporting the demand side through fast, efficient processes. provide guaranteed supplementary funding, redeemable only for access to bio-databases. data stamps

157 157 Federal Funding of Bio-Databases Creating market forces: stop supporting the supply side of biodatabases through slow, inefficient processes. start supporting the demand side through fast, efficient processes. provide guaranteed supplementary funding, redeemable only for access to bio-databases. data stamps, AKA food (for-thought) stamps ?! Creating market forces: stop supporting the supply side of biodatabases through slow, inefficient processes. start supporting the demand side through fast, efficient processes. provide guaranteed supplementary funding, redeemable only for access to bio-databases. data stamps, AKA food (for-thought) stamps ?!

158 158 Food (for thought) Stamps Funding Agencies could: provide a 10% supplement to every research grant in the form of stamps redeemable only at database providers. allow the stamps to be transferable among scientists, so that a market for them could emerge. provide funding only after the stamps have been redeemed at a database provider. Funding Agencies could: provide a 10% supplement to every research grant in the form of stamps redeemable only at database providers. allow the stamps to be transferable among scientists, so that a market for them could emerge. provide funding only after the stamps have been redeemed at a database provider.

159 159 Food (for thought) Stamps Problems: how to estimate the amount of FFT stamps that would actually be redeemed (and thus the required budget set-aside). how to identify approved database providers. how to initiate the FFT system. etc etc Problems: how to estimate the amount of FFT stamps that would actually be redeemed (and thus the required budget set-aside). how to identify approved database providers. how to initiate the FFT system. etc etc

160 160 Food (for thought) Stamps Alternatives (if no solution emerges): increasingly inefficient research activities (abject failure will occur when it becomes simpler to repeat research than to obtain prior results). loss of access to bio-databases for public-sector research. movement of majority of important biological research into the private sector. loss of American pre-eminence (if other countries solve the problems first). Alternatives (if no solution emerges): increasingly inefficient research activities (abject failure will occur when it becomes simpler to repeat research than to obtain prior results). loss of access to bio-databases for public-sector research. movement of majority of important biological research into the private sector. loss of American pre-eminence (if other countries solve the problems first).


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