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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
A. Hardware
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
B. Software
1. Operating systems, network extensions, applications, programming languages
2. Basic operation of IBM-PC and Macintosh desktop systems
3. Files and documents
III. Interfacing computers to laboratory equipment
A. Analog Data Acquisition.
1. Types: Character-oriented vs Bit/byte oriented; External vs add-in boards.
2. Characteristics of and use of analog-to-digital converters
a. Strobe (begin conversion)
b. End of conversion (EOC) bit
c. resolution
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
g. Coding
monopolar (+ only)
bipolar (±), two possibilities
How to read 12-bit ADC with 8-bit PEEK or INP instructions
h. Control of sampling rate
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.
3. Characteristics of and use of digital-to-analog converters
B. Digital Output (on-off control)
1. TTL compatible signals (0 - 5 volts)
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.
C. RS-232 serial interfacing.
1. Hardware
Connectors: DB-25, male or female; (DB-9, DIN).
Cable (Pin 7 = ground, pin 2, 3 : transmit or receive, other pins: handshake)
Null modem cable or adaptor; breakout boxes, sex changers.
2. The ASCII code.
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.
b. Parameter diagnostics: how to tell what's wrong (and it will be wrong).
4. RS-232 diagnostics with an oscilloscope
5. Communications Software Services
a. Setting communication parameters
b. Capturing incoming text to disk and sending text files from disk.
c. Using the character translation table to solve format problems.
6. Programming the serial port .
IV. Interfacing Computers to Other Computers
A. Telephone-based communications
1. Modems
a. Types of modems; Internal vs external; CCITT "V." standard
Modes: Command mode (off-line) vs. on-line (connected)
Hayes "AT" command set
How to connect with U of M host computers via phone lines.
b. Terminal programs
Typical features, advantages over dumb terminal
Where to get PD terminal programs: Procomm, Zterm, and Kermit
c. Communication parameters and terminal types
Baud rate, data bits, parity, and stop bits, duplex, CR/LF conversion
Terminal emulation, vt100 "full-screen", etc.
2. On-line systems and services
a. Commercial on-line services:
Chemical Abstracts, STN International, ACS, Dialog
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
3. Front-end software vs text terminal programs:
STN Express, Chemtalk, ChemConnection; America Online.
4. Connecting two microcomputers
5. Connecting to organizational host systems
B. Local Area Networks (LANs)
1. Types of networks: asynchronous vs true multi-drop
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
C. The store-and-forward wide-area networks
1. BITNET, Internet, UseNet, Fidonet
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.
b. Mail-accessible file servers
5. Network Resources accessible by Telnet
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
D. Data transfer and conversions
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.
b. How to import numeric data tables into spreadsheets
c. File name conventions
d. Binary files: UUencode/UUdecode
3. Graphics: input, output, and conversion
a. Vector vs. raster graphics
b. Graphic file types
c. Compression schemes
d. Importing graphics
e. Printers
f. Photographic image capture
g. Making slides and transparencies from computer output
h. Dynamic animated and interactive graphics
V. Interfacing Computers to Humans: the User Interface
VI. Digital data and signal processing
A. Unit operations in signal processing
1. signal arithmetic
2. signal-to-noise improvement
3. smoothing
4. differentiation
5. integration
6. resolution enhancement
7. peak area measurement
8. background correction
9. curve fitting
10. Fourier transformation and Fourier filtering
11. Convolution and deconvolution
B. Software approaches to signal processing
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 to2@umail.umd.edu.