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Chem 498C: Computer Interfacing in Chemistry, Fall, 1994
T. C. O'Haver, University of Maryland, revised Spring 1996.
Detailed Course Outline
I. Introduction: Why interface?
II. Computer basics
III. Interfacing computers to laboratory equipment
1. CPU chips; bus width and clock speed
2. ROM and RAM
3. Mass storage: floppy, hard, and optical disks; tape
4. Monitors, printers, sound I/O, RS-232, IEEE-488, SCSI ports
5. Communications and network hardware, modems, Ethernet, etc.
6. Common bus types: XT (8-bit), AT, (16-bit), EISA, Microchannel, NuBus, etc.
7. The main laboratory computer hardware platforms
1. Operating systems, network extensions, applications, programming languages
2. Basic operation of IBM-PC and Macintosh desktop systems
3. Files and documents
A. Analog Data Acquisition.
IV. Interfacing Computers to Other Computers
1. Types: Character-oriented vs Bit/byte oriented; External vs add-in boards.
B. Digital Output (on-off control)
2. Characteristics of and use of analog-to-digital converters
a. Strobe (begin conversion)
3. Characteristics of and use of digital-to-analog converters
b. End of conversion (EOC) bit
d. Front-end electronics: External voltage dividers and amplifiers
e. Input multiplexer: Number of input channel: channel selection.
f. Gain (volts full-scale); hardware jumpers or switches; software programmable
monopolar (+ only)
h. Control of sampling rate
bipolar (±), two possibilities
How to read 12-bit ADC with 8-bit PEEK or INP instructions
Selecting the sample rate: How fast is fast enough?
Limiting factors: Data acquisition hardware, computer hardware, or software?
Software loops vs real-time clock.
Sampling rate requirement for peak-type and periodic signals.
Use of TIMER function and ON TIMER(n) GOSUB in QuickBasic.
1. TTL compatible signals (0 - 5 volts)
C. RS-232 serial interfacing.
2. Transistor switches (DC voltages up to 50 volts)
3. electromechanical relays
4. solid-state power controllers (AC power).
5. How to convert binary to decimal to binary by program.
6. Digital input: how to sense contact closure with TTL input.
Connectors: DB-25, male or female; (DB-9, DIN).
2. The ASCII code.
Cable (Pin 7 = ground, pin 2, 3 : transmit or receive, other pins: handshake)
Null modem cable or adaptor; breakout boxes, sex changers.
3. Communication parameter settings
a. The parameters and what they mean: Baud (bit rate); data bits: 7 or 8
stop bits: usually 1 or 2; Parity; Duplex: half or full; Send LF with CR
or not; strip or add LF from incoming text or not; Pacing with ASCII
characters: XON / XOFF.
4. RS-232 diagnostics with an oscilloscope
b. Parameter diagnostics: how to tell what's wrong (and it will be wrong).
5. Communications Software Services
a. Setting communication parameters
6. Programming the serial port .
b. Capturing incoming text to disk and sending text files from disk.
c. Using the character translation table to solve format problems.
A. Telephone-based communications
V. Interfacing Computers to Humans: the User Interface
B. Local Area Networks (LANs)
a. Types of modems; Internal vs external; CCITT "V." standard
2. On-line systems and services
Modes: Command mode (off-line) vs. on-line (connected)
b. Terminal programs
Hayes "AT" command set
How to connect with U of M host computers via phone lines.
Typical features, advantages over dumb terminal
c. Communication parameters and terminal types
Where to get PD terminal programs: Procomm, Zterm, and Kermit
Baud rate, data bits, parity, and stop bits, duplex, CR/LF conversion
Terminal emulation, vt100 "full-screen", etc.
a. Commercial on-line services:
Chemical Abstracts, STN International, ACS, Dialog
3. Front-end software vs text terminal programs:
STN Express, Chemtalk, ChemConnection; America Online.
b. General-purpose information services:
Compuserve, GEnie, America Online; Features of interest to scientists
c. Bulletin board systems
d. Downloading and uploading files
Error-correction protocols: xmodem, ymodem, zmodem, kermit.
File compression and expansion
Where to find free science and math software
4. Connecting two microcomputers
5. Connecting to organizational host systems
1. Types of networks: asynchronous vs true multi-drop
C. The store-and-forward wide-area networks
2. Local area vs wide area networks
3. Popular network hardware and their transmission speeds:
Token Ring, ArcNet, Ethernet, LocalTalk
4. Network protocols: Netware, AppleTalk. TCP/IP
5. Network services: Net-modem, FAX, file, print, mail, and license servers
6. Accessing network services
a. Asynchronous connection to networked host
b. Direct network connection; network adaptors for PCs
1. BITNET, Internet, UseNet, Fidonet
D. Data transfer and conversions
2. The Domain Name System: Common DNS domains
3. How to address electronic mail:
4. Mail-accessible network services
a. Automatic-distribution mail lists: Listserv
Chemistry and science-related lists; Subscribing and signing off lists.
5. Network Resources accessible by Telnet
b. Mail-accessible file servers
6. FTP: Interactive file transfer:
Anonymous FTP sites; FTP front-ends for PCs; FTP by mail
7. How to find software: using Archie
8. Network News; sci.chem and other news groups; News front ends for PCs
9. Gopher and related network information services
1. Ways to connect "incompatible" hardware:
RS-232, network, disk exchange, OS emulation, add-in processor card.
2. Problems in MAC/DOS file transfer.
a. Text file conversion: line breaks (CR vs CR/LF); formatted text;
difference between tab character and tab stops on display;
Tabs vs spaces: a PC is not a Typewriter.
3. Graphics: input, output, and conversion
b. How to import numeric data tables into spreadsheets
c. File name conventions
d. Binary files: UUencode/UUdecode
a. Vector vs. raster graphics
b. Graphic file types
c. Compression schemes
d. Importing graphics
f. Photographic image capture
g. Making slides and transparencies from computer output
h. Dynamic animated and interactive graphics
VI. Digital data and signal processing
A. Unit operations in signal processing
1. signal arithmetic
B. Software approaches to signal processing
2. signal-to-noise improvement
6. resolution enhancement
7. peak area measurement
8. background correction
9. curve fitting
10. Fourier transformation and Fourier filtering
11. Convolution and deconvolution
1. Numeric Recipes and Libraries
2. Commercial software: spreadsheets; MatLab, SPECTRUM, etc.
This page is maintained by Tom O'Haver , Department of Chemistry and
Biochemistry, The University of Maryland at College Park.
Comments, suggestions and questions should be directed to
Prof. O'Haver at firstname.lastname@example.org.