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Shortliffe Ch. 5 Essential Concepts for Biomedical Computing

Shortliffe Ch. 5 Essential Concepts for Biomedical Computing. CIS661 Introduction to Medical and Bioinformatics Sean Fisk 2011-10-03. t opics. s torage and manipulation of medical data c omputer memory and storage a ccurate and efficient data entry i nformation display

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Shortliffe Ch. 5 Essential Concepts for Biomedical Computing

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  1. Shortliffe Ch. 5Essential Concepts for Biomedical Computing CIS661 Introduction to Medical and Bioinformatics Sean Fisk 2011-10-03

  2. topics • storage and manipulation of medical data • computer memory and storage • accurate and efficient data entry • information display • functions of an operating system • advantages of a database management system • local area networks • data confidentiality • the Internet in medical applications

  3. computer architectures • computers are ubiquitous • similarities of most computers • hardware • typical forms of computers • von Neuman architecture

  4. architecture - hardware forms • personal computer (PC) • workstation • servers

  5. forms – personal computer • inexpensive • single user • uses • documents • email • Facebook • forms • desktop • laptop • tablet • handheld • smartphone • example: your laptop

  6. forms – workstations small number of users example: GVSU lab computer next door

  7. forms - server • many users • mainframes • example: the machine hosting GVSU’s website • terminal • only used for accessing a server

  8. von Neuman architecture central processing unit (CPU) short-term memory long-term storage input and output communication data buses

  9. von Neuman – central processing unit • performs computation • parallel processing • hierarchical organization • registers • example: adding two numbers • add R3, R1, R2 • binary digit (bit) – zero or one • electronic switch • base 2 (binary) • represent everything, including decimal, floating point (fractions), characters (letters), CPU instructions, pictures, medical records • fetch and execute cycle • control transfer – branch

  10. von Neuman – short-term memory • store active programs and data • read-only memory (ROM) • fixed • fast access • bootstrap sequence • random-access memory (RAM) • read and write • stores programs, control values, data in use • larger than ROM • word • common size of many things in a computer • 32-bit, 64-bit • volatile

  11. von Neuman – long-term storage • temporal storage • active storage • long-term validity • retrieved quickly • example: record of patient being treated • archival storage • documentary purposes • example: record of discharged patient • storage formats • file system • usually provided by operating system • database • special “table-like” format

  12. long-term storage – technology • magnetic disk • flash memory • memory sticks, flash drives, jump drive • magnetic tape • most reliable, tape backup • optical • compact disc (CD) • digital video/versatile disk (DVD) • network storage

  13. von Neuman – I/O - input • methods • keyboard • pointing (mouse) • touch screen • light pen, track ball, joystick • 3d pointing • tactile feedback – resistance sensitive • cursor • menus • graphical data entry

  14. von Neuman – I/O - output • video (monitor) • technology • cathode-ray tube (CRT) • liquid crystal display (LCD) • picture element (pixel) • color resolution • spatial resolution • sound • print • laser printer • ink-jet printer

  15. von Neuman – communication • connect computers • technology • telephone • dedicated or shared wires • fiber-optic cable • infrared • radio • modulator-demodulator (modem) • digital to analog conversion (DTA) • convert computer signal to those in the vocal range

  16. communication – rates bit rate baud – signals per second assymetric transfer

  17. communication – services & protocols • services • provided by an internet service provider (ISP) • telephone network • Integrated Services Digital Network (ISDN) • Digital Line Subscriber (DSL) • protocols • packet switching vs. circuit switching • small pieces of information versus a stream

  18. communication – media • speed measurement • bandwith • latency • technology • twisted-pair wire • fiber-optic cable • wireless • radio • microwave • infrared • satellite • bands • baseband • broadband

  19. distant networks – wide area network (WAN) • examples: Internet, DoD network • Internet • regional network • example: midwest US • backbone links • standards • transmission control protocol / internet protocol suite (TCP/IP) • IP addresses (v4, v6) • domain name system (DNS) • example: seanfisk.com to 68.62.4.92 • computer.institiution.class– example: mybb.gvsu.edu

  20. distant networks – local area network (LAN) • high-speed communication • file servers • bridges • example: fiber-optic line between GVSU Allendale and Pew campus • routers / switches / gateways • direct packets to different destinations

  21. software • programming languages • machine code • binary instructions • assembly language • text translated directly to machine code • symbolic programming languages • operating systems • data management

  22. common programming languages • Fortran • Lisp • C – all major operating systems • C++ – most application software • Java – platform-independent software • C# – popular language for Windows • Structured Query Language (SQL) • popular database extraction language

  23. software – operating systems • “a program that supervises and controls the execution of all other programs and that directs the operation of the hardware” • resource management • examples • Microsoft Windows • Mac OS X • Debian GNU/Linux • iOS • Android

  24. operating systems – kernel • core of the operating system • examples • Windows NT (Windows) • Darwin (Mac OS X) • GNU/Linux (Debian) • number of users • PC – typically single-user • server – multi-user • multiprogramming • enable use of multiple devices • multiprocessing – utilizing multiple CPUs • memory • pages – sections of memory • application programs • system programs

  25. software – database management systems (DBMS) “integrated set of programs that helps users to store and manipulate data easily and efficiently” schema – metadata front-ends reports views

  26. software – network communication • sharing data • levels • application – HTTP, FTP, SMTP • transport – TCP and UDP • network • data link and physical – Ethernet and wireless • topology for flexible transport • Internet protocols – standards to which Internet-enabled applications must adhere • common Internet services

  27. services – hypertext transfer protocol (HTTP) world wide web (WWW) web browser uniform resource locator (URL) hypertext markup language (HTML) hyper– means linked pages encryption – secure sockets layer (SSL), transport layer security (TLS), HTTPS Java applets extensible markup language (XML)

  28. services – electronic mail (email) send and receive mail, like the postal service protocol – simple mail transfer protocol (SMTP) one of the first protocols mailing list / list server spamming

  29. services – telnet remotely control another machine more common form – secure shell (ssh) on Linux/Mac fantastic system administration tool

  30. data acquisition and signal processing • analog signal = continuous variation • digital signal = discrete values • sampling and rounding • precision • sampling rate – how often measurements are taken • noise • applications – speech recognition

  31. data and system security – concepts privacy confidentiality security

  32. security – key functions of a health care information system availability accountability perimeter role-limited access comprehensibility and control

  33. security • backups are vital • malware • spread • collect and misuse data • escape detection • accountability • authentication • authorization

  34. security • firewall • limit external access • virtual private network • cryptography • secret-key cryptography • public-key cryptography • escrow • more on encryption http://cis.gvsu.edu/~fiskse/classes/cs654/wireless-encryption/

  35. questions, answered • how are medical data stored and manipulated in a computer? • through databases and the operating system’s file system • why does a computer system have both memory and storage? • short-term and persistent storage • how can data be entered into a computer system accurately and efficiently? • by leveraging keyboard, mouse, touch, and menus • how can information be displayed clearly? • high resolution, organized views • what are the functions of a computer's operating system? • manage hardware resources, provide commonly needed tasks

  36. questions, answered • what advantages does using a database management system provide over storing and manipulating your own data directly? • stored in a structured way, easily integrated into backup schemes, industry-standard • how do local area networks facilitate data sharing and communication within health care institutions? • high-speed transfer, firewall security • how can the confidentiality of data stored in distributed computer system be protected? • firewalls, proper authentication techniques, limit unnecessary access • how is the Internet used for medical applications? • long-distance data transfer, browsing of medical records

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