PROPOSAL FOR
STANFORD UNIVERSITY
MEDICAL EXPERIMENTAL COMPUTING FACILITY

(SUMEX)

Submitted to the
Biotechnology Resources Branch
of the

National Institutes of Health

June 1, 1972

School of Medicine
Stanford University
TABLE OF CONTENTS

INTRODUCTION

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1. Objectives and Long-Term GoalSerecrneeseee Peer ee w es wenens eee ervceve 1
2. Background: ACME Computer Facility Experience.......ccceceeceseseed

SUMMARY 1... cece ccc s cece nce cere rtenesecvncace teen e ee eens sce e rev eaee 4
JUSTIFICATION ..... ce eee ete e cece cece nees pees et ee ees sees ssueaes 00028
1. Demonstration of need. or sec cesvercccccccvccercrcesuves Cece ene aceee .6
2. SUMEX Relationship to Institutional Plans ...+..ceeeeeeceeseceee osaol
RESOURCE OPERATIONS -- ees esc c secs cc scr cere enter eccrescecsseeeesttsnsves 29
1. Adminstrative Structure ---+-++-+-cces Cee ec cee eee ee eer e coer er sreereted
2. Operating Procedures and Policies --+---++-see. a ras 11
COMPUTER CONFIGURATION RATIONALE----- Cotte eee e neces ccons sence aeee coe el
1. IMtroduction «+--+ cece cece cece ec re www ee ee eet et nese nee rec enscaceaees 13
2. Computing Environment --+-++-.+++eeseoee tree ee eee etter eters er eevee ole
3. Technical Requirements -..-..... Ferenc ener owner eae receseeeresesseedly
4. Configuration Topologies .+-.. eee c cece cece ce cence cnn c eee eevanerenaes l7
5. Hardware Selection .-- ec ecc cee crccccvccrascccccseccacsccssvseseseces 20
a. Mainframe --.--scececevesrcee Ce i a a rr i rrr decease 22020
b. Peripherals, Data Channels, and Satellite Computers............ 23
6. Implementation Plan ..-- cece cece ccc a rent ceca esses secnrectetcvces 26
RESOURCE PERSONNEL «+--+ eececevecsecssceces ogee ese baeaeeseeeesesucse 222-28
RESOURCE ACTIVITIES «--cceccvccccevccvcucsscesses eect wenee cece nance 22 30
1. Services to be provided..... i i a rr 30
2. Research «e+e secre scceae ene eres coseee eee rr ews rae veesoe ee err ws eae eee JL
a. Core Research «cr-ccerccecccescesscouee seam e ee nweee seen teens eee DL
(1) Satellite Machine Support..-..... Pe i re teem ae veee 31
(a) Problem Statement--..--. Cer m erm e mere rnc ener sree eree 31
(1) Limitations of standalone small computers.-.....31
(2) Attributes of large host systems........... veeee DL
(3) Anticipated direction of some technological
innovations. ,............. ee beet e ec eceee 32

(b) Background and Rationale ..... cece cence cere cee r eens DD
(1) Current environment for satellites in

S.U. Medical Center <«-+-cessecereee eee er rar cesr ove 35

(2) Initial Approach in Software.....cscceeceeseceee DO

(3) Incorporation of new hardware techniques........ 36

(4) Resolution of specific goals with collaborators. 3/

(c) Methods and Procedures.-..-..ecessscccceccucse seve ences 38
(1) Satellite System Software Support

(a) Assemblers... ..- ccc sec e cer cece rs veesreeces 38

(b) High level language support.........-.++.4.. 38

(c) Realtime applications module library....... 39

(d) Extensions to manufacturers supplied
operating SysteMS ..----- ee ee cece reece ecees 10
(2) Computer to computer communications .........41

(4) Data transfers .......... ccc cece cuee Al

(b) Controlled interactions ................ Al

(3) Data manipulation ....... cc. ccc eee c cece ence ne 42

(a) Data collection .......... ccc cece eee eee 42

(b) Data analysis ........ cc ccc eee ce eee nee 43

(4) Satellite performance, measurement and

evaluation 1... cee cee ec eee cee eee enna 44

(d) Significance of satellite machine Support......... 46

(2) Extended Realtime Computing ...........cceceecceeceeees 47
(a) Problem Statement and Objectives ............0000. 47

(b) Background ..... 0... ccc eect c ne ce cece eeees 49

(c) Rationale ...... ccc ccc eect ee enc eceenane 51

(d) Methods and Procedures ........ccccccececacceccecs 53

(e) Significance ... ccc cece eee cece ce cee eee eens 58

(f) Collaborative Arrangement............. cee eceeeeues 58

(3) PL/ACME on a PDP-10 ......euues ee rr 62
b. Collaborative Research and Development...............0ee000- 65

(1) Predictive Modeling of Cardiovascular Function Utilizing
X-Ray and Ultrasonic Imaging Techniques.............6-. 65

(a) Problem Statement........... Cee mer wt nw ene ete 65

(b) Background ....... cc ccc cece cece ete c eee eececteeans 66

(c) Rationale ...... ccc ccc cece cece cece eee ees ee ae eens 67

(d) Methods and Procedures ..... sence ec eneseenes 210 68

l. X-ray Image Processing ..--- sss cece cece eacese 68

2. Ultrasonic Image Processing ............ee.00. 69

3. Small Computer Integration -.+..+.. ee seeeeeeee 70

(e) Significance -.- sce c cece c cence cece eee tater eee neee 70

(£) Relationships Cem ene eee eae eee reece anen ewe suss 71

(2) Digital Computer «-- eee c eee eee ccc ee ene eee tence tees 74

Processing of Cineurographic Images of the Urinary Tract

(a) Problem Statement --- +--+ cece cece ccc nce cn cusnscceevee 74

(b) Background Pee meer mmm mmr weer err ene nen ners ernvrseene 75

(c) Rationale «see e cere crn cccnsvvacrvvence Pew wn were ee ene 75

(d) Methods and Procedures «+--+ eccesserecnenccuscecae 76

(e) Collaborative Affiliations .--......e.. cesses eee 77

(£) Significance Hee ee meme ree ner emer ene creer nenesneezens 77
(3) Automated Gas Chromatography/Mass Spectrometry Analysis 78
(a) Tntroduction «cece cere rece cece erence nes a seen ceean 78

(b) Problem Statement-.---.. ccc cece cence nce ncevvcteuce 78

(c) Background Ca 80

(d) Rationale «----.. Cee ee eee cere ee ee te ete e eee eas 81

(e) Methods and Procedure «-.+-- eee wee e rece a rece neces 85

(£) Significan€e tee eee eee eee eee cece eee eee eect ees 87

(g) Facilities Available -+-- ese cece cece cece eee enaee 87

(h) Collaborative Arrangements ---++-+ eee eee eee eee ees 87

(4) Cell Separator Proj CCE cree ner e enc w errr evar nerves esccas 90
(a) Background «+--+ sees cece cee eee eee ete eee eee eeee 2

(b) Rationale Ca 93

(c) Methods and Procedures + ec c rece ren rene never cucve 94

(d) Significance «+++ eee e cece eee cece cee teen enaes 94

(e) Computer Tnteractions sss escent ener wenn ane ane vrece 94
(5) Average Evoked Potentials and Perception ...... cee eee IT
(a) Problem Statement........0. 0... ccc cece cece ecu ceues 97
(b) Background and Rationale.......... ccc cece ce ccc uee 97
(c) Methods and Procedures ...... seeeae see ncee swe nes 98
(d) Significance co.cc ccc cece nce ccc cece ence eenens 99
(e) Relationship to other work.........ccccceccccccses 100
H. BUDGET 2... ccc ccc ec cece nee e eee ceneeeeeeteeueeneueeeuans 101
1. Detailed Budget for First 12-month Period,,.... cece ne eeeee sees 102
2. Budget Estimates for all years of Support.........ccccecececeees 103
3. Explanation ........ seen eee eee eee ne anace Sasa ee eseenesensecsece 105
I. FUTURE PLANS 1... cece ccc ce ccc nce tence c ences euneteaternees 109
J. APPENDICES...... seme e rence scenes rr eee wer eee ee reat aee 110
1. ACME User Publications..... Bee eee eee eee eee ee eee eee wuss eseesaeun 111
2. Biographical Sketches .......... 0... cece ccc cece cece eee cceecaees 120
FIGURES
E-l ACME Configuration: May 1972 ....... cc cee ee eee sete cece eee 16
E-2 General Characteristics of the Proposed System ,................ 19
E~3 Tentative Initial Machine Configuration for SUMEX............... 22
E-4 Implementation Scheme for Remote Data Channels..... sce w ence eee 25
E-5 Implementation Phasing Plan ..... 0... ccc cece cc cece ccc ncnccrceuce 27
G-1 Elements of Laboratory Instrumentation Data Systems............. 52
G-2 Proposed topology for Central Processor and Peripherals........ 254
G-3 Tentative Initial Machine Configuration for SUMEX............... 56
G-4 Software..... Poe eee mene etme tee eee eet te eee ete e es eneneantesee 57
DENDRAL~1 Realtime Mass Spectrum Interpretation System... . ccc eee 83
DENDRAL-2 Processing Time Interdependence ...........cccccecccerceceaes 84

Cell Separator-1 Simplified Blcok Diagram of Cell Separator.....ees oe IL