Mudpie

M U D P I E

n o. i 7

Museum and University Data, Program and Information Exchange

THIRD CRAM-COURSE IN TIME-SHARED COMPUTER PROCRAMMING

The third annual cram-cour se in programming the time-shared
computer using the language BASIC will be given on July 5, 1971.

The entire day will be devoted to ins truction in the language,
and July 6 will be used for al lowing those who attended the course
to use the teletypes in the Museum of Natural History to submi t
and test programs they have written. The course is aimed at the
complete neophyte in computer work ; no background or experience
of any sort is necessary. Individuals with some knowledge of
programming or previous work with time-shared computers are wel¬
come to attend, of course , but it might be a bit boring.

The course will be given in the National Museum of Natural
History, Washington, D. C ., probably in the divisional library
for Reptiles and Amphibians, unless the group gets too large for
that room. The library is in Room 207 , West Wing. The session
will start at 9:00 A.M. It would help if anyone planning to
attend would notify J. A. Peters, Division of Reptiles and
Amphibians, National Museum of Natural History, Wash., D.C.,

20560, as soon as possible, so we can know how many people to
expect.--JAP.

NOTE CONCERNING ENCLOSED REPRINT

You will find enclosed with this issue of MUDPIE another
paper on a computer topic, written by a Smithsonian staff member,
Thomas Waller, of the Division of Invertebrate Pal eontology.

The compartmentalized mailing lists of the Museum of Natural
History are such that papers on computer use cannot be distrib¬
uted to interested people. The lists are structured to accomo¬
date our divisions, so all people on the invertebrate paleon¬
tology list got this paper, whether interested in computer
applications or not, but people in other areas and on other
lists will not get it unless they request it. Since MUDPIE
is sent to people who have either expressed an interest in
its purposes, or requested a reprint of a computer paper,
it seemed appropriate to suggest that a supply be made avail¬
able to cover the MUDPIE mailing list. The press agreed,
and you have a copy of Waller's paper as a result. If you
have no use for it please pass it on to someone who does
(and suggest that they write in for MUDPIE, as well), or
send it back to me.—JAP.

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PETARD HOISTING, No. I

The following excerpt from a letter to a colleague here at
the Smithsonian is self-explanatory:

"Enclosed is a copy of MUDPIE no. 15, which describes Dr. Wilsons
Monograph on the use of GIPSY in Palynology. If you read the last
paragraph, you will note that the author of the newsletter happily
pointed out the misspelling of Permian in the Monograph. I think
it somewhat ironic (perhaps a touch of poetic justice) that, ex¬
cept where quoted from the Monograph, the word GIPSY is spelled
incorrectly. The spelling chosen in the newsletter may be indic¬
ative of how the system is used in some cases, however, with all
respect to Dr. Wilson, I believe the 'I' spelling would be more
closely associated with his use of the system." /s./ Robert W.
Shields (U. Okla. Med. Comp. Center).

My old boss, Norman Hartweg, used to say that if you do
everything right all the time no one will ever notice, but do
something stupid, and it will immediately be brought to your
attention. At leas t I now know that some one out there is
reading this stuff!—JAP.

COMMITTEE ON DATA FOR SCIENCE AND TECHNOLOGY

This committee is a subordinate arm of the International
Council of Scientific Unions (ICSU), and is called CODATA for
short. It is primarily concerned with the compilation of criti¬
cally selected numerical and other quantitative scientific data,
as, for example, "standard heats of formation of water and
carbon dioxide, (or) standard entropies at 25 degrees C of
selected elements," (from Newsletter no. 1). The feeling of the

committee that there was not much data like this in biology is
reflected in their first bulletin, which documents "Automated
Information Handling in Data Centers," and has no biological
centers listed at all. In Newsletter no. 5, however, a paper

is included entitled "Critically evaluated data in the biolog¬
ical sciences," by R. L. Zwemer and P. L. Altman, who have
worked with the Biological Handbooks Series. This apparently
reminded the committee that they had sort of forgotten about
biology, and at their meeting in Naples in November, 1970,

P. Altman was appointed the representative of the International
Union of Biological Sciences on CODATA.

The committee publishes both a newsletter and irregularly
issued bulletins. The former deals with miscellaneous infor¬
mation ; the latter is usually a vehicle for a single subject,
often a report of a "task group" of the committee. CODATA has
also published the "International Compendium of Numerical Data
Projects," 1969, xxiii + 295 pp., which sells for $13.20. I
have not seen this volume, and cannot comment on it.

The newsletter is available on request and free of charge
from: CODATA Central Office, Westendstrasse 19, 6 Frankfurt/Main,

Federal Republic of Germany.—JAP.

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"THE ROCHESTER ULTIMATE WEAPON”

That is what W. Simon calls a new high speed real-time inter¬
pretive language developed for use by biologists, and built for
operation in a PDP-8 with 4K of memory, requiring DEC tapes. The
language is currently available through the Division of Biomath¬
ematics, University of Rochester School of Medicine, 260 Critten¬

den Blvd, Rochester, NY 14620. Although currently only adapted
to the PDP-8, it is expected to be functional on the PDP-12 in the
near future. The purpose of Dr. Simon in developing the new
language was two-fold:

1) To increase the use of small computers by biologists
by making it easy for them to learn the fundamentals
of computing,

2) To circumvent the problems of machine language use,
which was all that had been avai1able on the PDP series
previously.

The technique used in the new language is explained in a short
note in "Medical and Biological Engineering," vo1. 8, 1970, pp.

203-205. A bench mark program took 22 seconds to run in FOCAL,

7 secs in DEC FORTRAN, 6 secs in SNAP (another Simon language),

and only 2 secs in the "Rochester Ultimate Weapon." —JAP.

COMPUTERS IN BIOLOGY AND MEDICINE

Volume 1, number 1, of a new journal with the title above
appeared in August of 1970. As usual, when people talk about
" biology and medicine," they are thinking of biology i_n medicine.
There clearly isn't going to be too much here to interest the
ecologist or systematist, although the editor writes, on p. 1,
that "the purpose of this journal is to establish an international
forum for the exchange of knowledge in the rapidly developing
field of computer use in medicine and the biosciences." In a
long list of possible subj ect matter to be covered, including
such things as Application of Quantum Chemistry to Molecular
Configurations or Functional-force Analysis Applied to Dental
Prostheses and other Dental Problems (or maybe you prefer
"Computer Aids to Morality," whatever that means), we also find
the following MUDPIE possibilities: Taxonomy and Classification
Methods; Information Exchange among Research Workers; Applications
of Computers to Data Processing in the Biomedical Sciences;

Special Purpose Computers for Data Processing; and Computer
Programming of Pattern-recognition Analysis. I miss any refer¬
ence to the possibilities of inter-institution time-shared
networks, establishment of common data banks or mutual access
storage, and so on. A couple of papers from this first issue
are listed below in the "Literature" section.—JAP.

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DATA-COLLECTIN G IN THE SMITHSONIAN

C. A. Bull and R. Shank have completed a survey of the Smith
sonian's activities in data collecting, and have summarized their
results in an unpublished report entitled "Non-conventional File
Structure Data-collecting Projects in the Smithsonian Institution
A Survey, Winter 1960 - Spring 1969." The "non-conventional"
designation is for techniques other than simple alphabetical cat¬
alogues or lists which will facilitate rapid handling of data,
from key-sort to computer. Interest was in proj ects furthering
research or educational functions as opposed to housekeeping.

A total of 49 projects were identified, and each is described.

Some of the findings are:

Twenty-three proj ects are using or anticipate using some
sort of machine assistance in storage and retrieval.

More pro j ects in biology are using automatic means to store
and retrieve data than are proj ects in the physical
sciences, history and technology.

In every case, the highest level of satisfaction with new
systems and methodology can be found where the curator
and researcher was heavily involved in system design
and output control.

The most critical factor is the validity of the data entered
and the positive relationship of the degree of expertise
of the person making the entry with the reliability of
the entry.

In assessing the requirements for making their systems viable
most people who were conducting proj ects felt the need for
manpower with subj ect knowledge more than the need for
electronic muscle.

If anyone would like to know more about the survey, a few
copies of the report are available for distribution. Write
to MUDPIE for a copy.--JAP.

INFORMATION SYSTEMS SURVEY

"RECON"

(NASA Information System)

The NASA Information System, commonly known as RECON, is
a package of programs for creating, maintaining and querying
data files. It consists of two major subsystems. The first
is a batch system which provides for file creation and main¬
tenance, batch query and prepares output for publication. The
second, RECON, is a communication control program, language
analyzer and search program which permits multi-programmed
query from a remote console.

The system operates on variable length data records
composed of fixed header information followed by a variable
number of tagged, variable length fields which may be repeated

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(i.e., the same field type may occur more than once in a record).
Data files are described to the system via Data Description
Tables and hence the system is data independent.

The system provides for maintenance and use of a thesaurus
for query expansion and for data validation and also permits
use of tables for data element conversion to code during file
maintenance.

The system was written under contract for NASA. It is
operational but is being extended and improved. It operates
on the IBM 360/50 under the MFT operating system. The batch
program was written in assembly language. RECON was written
in PL/I except for the mas ter I/O control program which was
also written in assembly language.

FILE ORGANIZATION — The primary file is made up of data
records stored sequentially in accession number order. Each
record is composed of a header containing fixed length fields
of information which are standard for all records in the file.

The header is followed by a series of tagged, variable-length
fields with the possibility of repeating a particular tag
within the record as many times as is necessary. There is,
however, no hierarchy in the sense that a set of fields may be
related to each other and repeated as a set relative to the
header. The record size is unlimited. The file is stored on
a data cell at NASA. It is stored using a specially codecal
variable length ISAM access method.

When a file is first defined to the system through a data
description table, any field, whether in the header or in the
tagged part of the record may be designated for creation of an
inverted index. These inverted indexes are stored on disc.

The system also maintains a thesaurus of legal descriptors
used for validation during file maintenance. This file also
contains "see" and "see also" references and narrower and broader
terms. It can be used to expand a query and is available to the
requestor at a terminal for browsing.

FILE MAINTENANCE — In the file maintenance operation, fields
in existing records can be altered, records can be deleted from
the file and new records can be added to the data base. These
are added at the end of the master file. Inverted indexes are
maintained by the system as changes occur. Data validation
through thesauri and encoding of data via table look-up is also
supported.

RETRIEVAL — The system operates in either of two modes for
retrieval: batch or on-line. In the batch mode, records may be

selected based upon a Boolean combination of any fields in the
record regardless of whether they have been designated as inverted
indexes. In this mode also, the query output can be sorted before
being presented to the requestor.

In the on-line mode only inverted index fields may be used as
terms in the selection logic in order that only qualifying records
be accessed from the data cell. No sorting of data is permitted.

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Data records may be formatted for output on the XX 1403
printer equipped with an upper/lower case chain, for the Linotron
at GPO and for the Photon 713. — Harriet R. Meadow.

AVAILABLE PROGRAMS

CHECKS-—A demonstration program for use with time-shared

computers, in BASIC. Written and available from
Larry Morse, Biological Laboratories, Harvard Univ.,
Cambridge MA 02138. Program lists TOTAL CREDIT,
CHECKS OUT, and ACTUAL BALANCE.

RECENT LITERATURE

Abrams, M. E. Medical Computing. Elsevier, 52 Vanderbilt Ave.,

New York NY 10017, 1970: xi + 396. (A series of short papers

presented at the conference on medical computing held in
Birmingham, Jan., 1969. Re-inforces the notion that medicine
and systematics have a lot in common when it comes to computer
use.--JAP)

Crovello, T. J. Analysis of character variation in ecology and

systematics. Annual Review of Ecology and Systematics, vol.

1, 1970 : 55-99.

Goodall, D. W. Statistical plant ecology. Annual Review of
Ecology and Systematics, vol. 1, 1970: 99-125.

Ohnacker, G. & W. Kalbfleisch. CCBF — A System for the Computer
Processing of Chemical and Biological Facts. Angewandte
Chemie-International Edition in English, vol. 9, 1970:

pp. 605-610. (Primarily a chemical system for storage of

structural formulae. Biological data is that associated
with results of dosage tests.—JAP)

Solow, B. Computers in cephalometric research. Computers in
Biology and Medicine, vol. 1, 1970: 41-51.

Walters, R. F., K. P. Brin, F. Roth, J. T. Morrison & C. Renoud.
Information support systems for experimental investigation.
Computers in Biology and Medicine, vol. 1, 1970: 75-86.

June, 1971

Division of Reptiles and Amphibians
National Museum of Natural History
Washington DC 20560

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