SUMEX STANFORD UNIVERSITY MEDICAL EXPERIMENTAL COMPUTER RESOURCE COMPETING RENEWAL APPLICATION RR - 00785 BOOK | RESEARCH PROPOSAL Submitted to BIOTECHNOLOGY RESOURCES PROGRAM NATIONAL INSTITUTES OF HEALTH — June 1, 1977 DEPARTMENT OF GENETICS STANFORD UNIVERSITY SCHOOL OF MEDICINE Joshua Lederberg, Principal Investigator Table of Contents BOOK I ~ ection Page Table of Contents - BOOK I . . ee ee ee i List of Figures . . ee ee ek iv Table of Contents - BOOK II . . . . - 6 ee Vv 1. BACKGROUND AND PROPOSED WORK . . . . ee ee ee a 1.1 OVERVIEW OF OBJECTIVES AND RATIONALE . . . . - re | 1.2 SIGNIFICANCE rr . . 68 6 - - - & 1.3 BACKGROUND AND PROGRESS . . . 0.0. 1.3.1 PROGRESS SUMMARY se ee 1.3.2 DETAILED PROGRESS REPORT . . . . . , 1.3.2.1 DEFINITION OF TERMS AND CBJECTIVES . . . 1.3.2.2 FACILITY HARDWARE. 2... kk wk 11 1.3.2.3 SYSTEM SOFTWARE eee i a 18 1.3.2.4 NETWORK COMMUNICATION FACILITIES . 2... . ., 20 1.3.2.5 SYSTEM RELIABILITY AND BACKUP . . . . 1.3.2.6 PROGRAMMING LANGUAGES a 1.3.2.7 STANFORD AT HANDBOOK PROJECT 2. 2... uw, 320 1.3.2.8 USER SOFTWARE AND INTRA-COMNUNITY COMMUNICATION - 31 1.3.2.9 DOCUMENTATION AND EDUCATIGN a rn 32 1.3.2.10 SOFTWARE COMPATIBILITY AND SHARING - 8 32 1.3.2.11 RESOURCE MANAGEMENT . 2... : 33 1.3.2.12 SUMMARY OF RESOURCE USAGE . . . . 4Q 1.3.2.13 NETWORK USAGE STATISTICS J. Lederberg i Privileged Communication 1.3.2. 1.3.2. 2. SPECIFIC AIMS 2.1 RESOURCE 2.2 TRAINING TABLE OF CONTENTS BOOK I (continued) 14 PUBLICATIONS 15 RESOURCE STAFFING HISTORY OPERATIONS AIMS . 2. . AND EDUCATION AIMS . . 2.3 CORE RESEARCH AIMS . . 3. METHODS OF PROCEDURE ee ee 3.1 RESOURCE OPERATIONS PLANS 8 ee ee 3.1.1 SYSTEM HARDWARE AND MONITOR PLANS 3.1.2 COMMUNICATION NETWORK PLANS . . . . 3.1.3 SOFTWARE SUPPORT PLANS ee ee 3.1.4 COMMUNITY MANAGEMENT PLANS . . . wl 3.2 TRATNING 3.3 CORE RESEARCH PLANS a AND EDUCATION PLANS ee ee 3.3.1 GENERALIZATION OF AI TECHNIQUES 3.3.1.1 DESIGN OF KNOWLEDGE-BASED CONSULTATION 3.3.1.2 ATTEMPT TO GENERALIZE (AGE) PACKAGE 3.3.1.3 PLAN PACKAGE - ee : 3.3.1.4 HEURISTIC KNOWLEDGE ACQUISITION : 3.3.1.5 GENERAL EXPLANATION SYSTEM . . 3.3.2 SOPTWARE EXPORT ALTERNATIVS eee 3.3.2.1 NETWORK ACCESS .. 3.3.2. 3.3.2 SYSTEMS 2 MACHIN#-INDEPENDENT LANGUAGE IMPLEMENTATION 3 EXPORTABLE (PDP-10) SYSTEM . 3.3.3 EXPORTABLE MACHINE PLANS . . Privileged Communication Li 56 - 57 - - 58 : 58 59 39 61 - 62 62 - « 64 . 64 ~ 65 - -« 56 - 67 - . 67 : 57 - 69 : 71 2 + 73 * 75 - + 78 - 79 79 80 . 31 Lederberg TABLE OF CONTENTS BOOK I (continued) 3.3.4 MAINSAIL DEVELOPMENT PLANS . . 2. 3.3.4.1 DEVELOPMENT MANAGEMENT . . . wl 3.3.4.2 LANGUAGE DEVELOPMENT . . . 2. . 3.3.4.3 COMPILER DEVELOPMENT . . . 2. . 3.3.4.4 RUNTIME DEVELOPMENT . . . . . . 3.3.4.5 DEBUGGING SYSTEM DEVELOPMENT . . . 3.3.4.6 DOCUMENTATION PLANS . . . . . 3.3.4.7 MAINTENANCE AND DISTRIBUTION PLANS . 3.3.4.8 PLANS FOR ADDITIONAL IMPLEMENTATIONS 3.3.4.9 MAINSALL OPERATING SYSTEM PLANS . . 3.3-4.10 MICROCODED MAIWSAIL MACHINE PLANS : 3.3.-4.11 DEVELOPMENT OF PORTABLE SOFTWARE . . q, AVATLABLE FACILITIES oe J. Lederberg 83 83 83 84 85 85 86 87 87 88 89 90 92 iii. Privileged Communication 10. 11. 12. 13. 14. J. Lederberg TABLE OF CONTENTS BOOK I (continued) List of Figures SUMEX-AIM Computer Configuration . . . . Cost-effectiveness of SUMEX Augmentations - * « . « * Capacity and Loading Increase with Dual Processor Augmentation TYMNET Network Map 2 ARPANET Geographical Network Map . . . . . .«. .- ARPANET Logical Network Map. . . . trionthly CPU Time Consumed ee eel ~ 6 6 ‘CPU Usage by Community 8 ee . File Space Usage by Community . . . . : . Average Diurnal Loading (3/77): Total Number of Jobs . .. . Average Diurnal Loading (3/77): Percent Time Used . . . . Average Diurnal Loading (3/77): Percent Overhead . Average Diurnal Loading (3/77): Balance Set - Joos in Core Average Diurnal Loading (3/77): Runnable Jobs . . . . TYMNET and ARPANET Usage Data. . . . . . . . iv 13 15 17 25 40 42 50 59 51 51 52 54 Privileged Communication Table of Contents BOOK II Section 5. BIOGRAPHICAL SKETCHES : - . 6. COLLABORATIVE PROJECT PROGRESS AND OBJECTIVES 6.1 STANFORD PROJECTS . . . . « . 6.1.1 DENDRAL PROJECT . . . . 6.1.2 HYDROID PROJECT . . . . . 6.1.3 MOLGEN PROJECT . ©. 2. .« « se 6.1.4 MYCIN PROJECT oe ee 6.1.5 PROTEIN STRUCTURE PROJEC . 6.2 NATIONAL AIM PROJECTS . . 6.2.1 ACQUISITION OF COGNITIVE PROCEDURES (ACT) 6.2.2 CHEMICAL SYNTHESIS PROJECT (SECS) . 6.2.3 HIGHER ciENTAL FUNCTIONS PROJECT - 6.2.4 INTERNIST PROJECT . . . . 6.2.5 MEDICAL INFORHATION SYSTEMS LABORATORY 6.2.6 RUTGERS COMPUTERS IN BIOMEDICINE 6.3 PILOT STANFORD PROJ#CTS . . . 6.3.1 GENETICS APPLICATIONS PROJSCT . . 6.3.2 BAYLOR-METHODIST CEREBROVASCULAR PROJECT 6.3.3 COMPUTER ANALYSIS OF CORONARY ARTERIOGRAMS 6.3.4 QUANTUM CHEMICAL INVESTIGATIONS . Privileged Communication . Page 2 ee eT - ee AY - 6 eA ~ « . 42 7 + «6 75 ~ . . 81 ~~ . 6 84 - « « 108 * «© « 112 «= 2 6 113 - 6 « 118 ee 128 - 2 . 132 » 2 2) 138 oe TAY - 2. = 158 7 - « 159 - « «. 161 2 - -) 165 2 ee) 169 J. Lederberg TABLE OF CONTENTS BOOX II (continued) 6.4 PILOT AIM PROJECTS . 2. 2... hehe 6.4.1 COMMUNICATION ENHANCEMENT PROJECT. . 6.4.2 AY IN PSYCHOPHARMACOLOGY . . . 6.4.3 ORGAN CULTURE PROJECT . . . . «. . 6.4.4 NEUROPROSTHESES PROJECT . . . 6.4.5 MATHEMATICAL MODELING OF PHYSIOLOGICAL 6.4.6 PUFF/VM PROJECT . 2. 2. . ee Appendix I OVERVIEW OF ARTIFICIAL INTELLIGENCE RESEARCH Appendix II AI HANDBOOK OUTLINE a Appendix III SUMMARY OF MAINSAIL LANGUAGE FEATURES . . . . Appendix IV MICROPROGRAMMED MAINSATL PLANS . . . Appendix V AIM MANAGEMENT COMMITTEE MEMBERSHIP - ee Appendix VI USER INFORMATION ~ GENERAL BROCHURE ee Appendix VII GUIDELINES FOR PROSPECTIVE USERS 8 eee Privileged Communication vi- . . SYSTEMS 6 -) 191 . 194 - + + 197 235 + 2 « 239 2 ee ONG J. Lederberg