1 st. MB Medical Informatics1 st. MB Medical InformaticsIntroductory courseIntroductory course

05-10-2000/06-10-200005-10-2000/06-10-2000Week1Week1

Clinical Science InstituteNational University of Ireland

Galway

Why you should follow this Why you should follow this course ?course ?

Medicine is a profession as well as an academic discipline.

A professional is a knowledge worker who uses his/her knowledge to make decisions, decisions that of great importance to patients.

A good doctor needs to hold a great deal of information in his/her head.

Dramatic change with in a few Dramatic change with in a few generations generations

The 18th or 19th century doctor learned his/her profession by apprenticeship- knowledge was limited and changed little over a professional career. There were few effective treatments.

The doctor todayThe doctor today

The doctor today trains in a demanding academic and professional environment. He/she faces huge amounts of information which is undergoing constant change.

Knowlegde is increasingly based on critical assessment and research. The doctor is responsible for assessing the quality of the information and for having the most recent and best available information for his/her patients.

Evidence based medicineEvidence based medicineClinical practice is constantly changing, the rate of changing is accelerating and consequently it may even take years before the results of clinical research will be incorporated in day-to-day practice. So there is a large gap between what the biomedical literature contains and the care that most patients receive. The gap is widened by the extensive processing that the results of clinical research require before they can be used. Evidence-based medicine is a new approach to health care promoting the collection, interpretation and integration of valid, important and applicable research-derived evidence. The best available evidence, moderated by patient circumstances and preferences, is applied to improve the quality of clinical judgements.

Evidence based medicineEvidence based medicineThere are many information tools that facilitate the practice of evidence based medicine. These include users’ guides to the medical literature, strategies to improve the yield of MEDLINE searches, meta-analyses, resources on-line and software tools bringing high quality information to the point of clinical decision making.The doctor today has effective and potent therapeutic agents to treat disease; these agents often carry major undesirable side effects and toxicities. The doctor must function as a judicious decision maker in managing his patient’s illness

The use of IT supportThe use of IT supportBecause the doctor is dealing with complex biologicl systems, often he/she is required to make decisions under conditions of uncertainty and involving large amounts of data.The use of IT support will often result in better decisions.

In assessing the medical literature and in carrying out research, the doctor requires competence in statistical methods. This is facilitated by the use of appropriate computer programs.

ConclusionConclusionComputer aided data management has the potential of resolving the problems of legibility, completeness, retrievability and organization, all of which are so difficult to accomplish by hand.

IT and the use of computers are essential component of the skills required by the competent doctor.An integral part of medicine.

Next section shows the basic parts of a Computer. Read the presentation and answer the questions given on the sheet.

Department of Medical Informatics and

Medical Education

Monitor

System unit

KeyboardMouse

A General Computer System

What is a Computer?A Computer is a tool that people use to achieve a goal, just like any other tool that we use for example a hammer to knock in nails. A Computer in its simplest form is a box full of switches. These switches can have two possible states, On or Off. That is why a Computer is known as a ‘Two State Electronic Device’. Most people assume that Computers are intelligent, but this is not true. Computers are really thick, they can’t do anything without being told to do so, and when a Computer does something wrong, it is not usually the Computer that is wrong but either the person using the Computer, or the person who programmed the software.

What are the parts of a Computer?A Computer has three main parts:

                                      The Input devices

Usually a keyboard and a mouseOutput devicesUsually a Monitor (sometimes known as a VDU, Visual Display Unit) or a Printer.Processing unit. The Processing Unit contains other devices that make the Computer work. There are three main parts of the Processing Unit these are:

Central Processing Unit The brains of the Computer, also known as just a CPU. There are various types of CPU, the most common one people will know is the Intel Pentium Processor (as seen on TV). The speed of a CPU is measured in Megahertz or MHz for short. The faster the MHz the faster you can run things on your Computer.

MemoryThe Memory inside a Computer is what the CPU uses as a work area. The more memory the Computer has, the more it can do in a shorter time. When the Computer uses up all its memory, sometimes it can not do the task asked of it. In other cases if it runs out of memory, it will start to use the space on the Hard Disk. This area on the Hard Disk is called a ‘swapfile’, the Computer copies data onto the disk that it is not using at that time.

This makes room for more data that it requires, then it copies it to and from the Computer memory and the disk drive, and this has the effect of virtually giving the Computer more memory that it really has. This is why it gets the name ‘swapfile’. Unfortunately if the Computer uses the swapfile a lot, it can severely reduce the speed in which the task could be achieved, because real memory is much faster than using the swapfile. You may notice while you are using your Computer, that the disk drive suddenly starts to come on and off, what is happening is the Computer is either writing data to the swapfile, or it is cleaning up data from the swapfile it no longer needs.

Memory

Disk Drives,

                         There are three main types of disk

drives on most modern Computers. They are as follows:3.5in Floppy Disk A 3.5 in Floppy Disk is known as ‘removable media’. This is because the disk can be removed easily, and transported to another Computer, the downside to a Floppy Disk is that the storage space is quite limited, usually 1.44 megabytes.

The Hard DiskThe Hard Disk is known as ‘permanent media’. The Hard Drive lives inside your Computer and you are not meant to remove it and place it in another Computer. The Hard Drive has many advantages over its Floppy counterpart, these are in the speed it can save and read data, and on the size of storage space, the average Hard Disk today is around 1.2 Gigabytes, almost 1000 times greater than a Floppy.

CD ROM

A CD-ROM is known as ‘removable media’ just like the Floppy Disk. However, the CD-ROM Disc can store up to 650 megabytes on one CD as opposed to 1.44 on a single Floppy Disk. The CD-ROM is much faster to use than a Floppy Disk, and it has many more uses. Today you can get whole encyclopaedias, interactive games and videos on CD-ROM. The only downside to a CD-ROM is that on standard Computer systems, the CD-ROM is known as ‘read only’.

This means that you can not store files on the CD-ROM, but you can use the files on it, or copy the files to another type of media such as your Hard Disk. However it is now possible to purchase as an extra, a CD-ROM Drive that can write to the disc, these are known as ‘CD-ROM Writers’. Depending on the type of drive you buy, you may only write to the CD-ROM once, or if you were to buy the newer ‘CD-ROM Re-Writer’ you could write to it in excess of 1000 times.

What does my Computer dowhen I switch it on?When you switch your Computer on, the Computer does a check of all the components that are connected to it, to see if they are all working correctly. As we said before, Computers are thick, and don’t do anything until they are told to. So how does the Computer know when to check itself? Well the Computer has a microchip that lives inside the Computer that tells it how to talk to the devices connected to it, this microchip also tells the Computer to check all the devices when it is first started up. This microchip is called the BIOS. BIOS stands for Basic Input Output System.

The BIOS checks the following components when it is first started up:MemoryThe BIOS checks to see if all the memory in the Computer is working correctly. On some systems you can visually see this on the monitor. It looks like the Computer is counting, and that is exactly what it is doing, it is counting the number of bytes (the smallest measurable part of a Computers memory) to see if it all adds up correctly.

KeyboardThe BIOS then checks to see if you have a keyboard connected and working. On some systems you may see the ‘NUM Lock’ light come one.

Disk DrivesThe BIOS then checks to see if you have a Floppy and a Hard Disk drive connected.If they are working it then checks the Floppy Disk to see if there is a disk inserted in it. If there is then in some systems the Computer then tries to ‘Boot’ from your floppy disk drive. If the Computer does try to boot from the Floppy Disk, it expects to find a disk that has system files on it (files that tell the Computer how to load the operating system). If it does not find these files on the disk, it will give an error message like ‘Non System Disk Inserted, Replace and Strike a Key’.

What this tells you to do is to either replace the disk with a disk that has the system files on it or just remove the disk and press a key. If you remove the disk and press a key, the Computer then checks your Hard Disk for the system files. If it can not find them on the Hard Disk, the only option left is to try and find a Floppy Disk with the files on it, so you can put them back onto your Hard Disk. In most cases, unless something seriously went wrong, your Hard Disk will always have the system files on it. Once the Computer has found these files, it will load the Operating System. Most people will use the Microsoft Windows 95, 98 Operating System.

A functional PC is made up of two distinct elements. A functional PC is made up of two distinct elements. These are:These are:

The Hardware, the physical instruments consisting of the electronic and other constituents that together make up the device that sits on the desk.The Software, in the form of electronic or magnetic pulses that provides the programs that instruct the computer what to do and the data to be processed by these programs.

HARDWARE.HARDWARE. The hardware constituents of a PC are represented

in Figure 1.It consists of Systems Unit which executes the operations on the data. & peripherals for sending programs and data into and out of the System Unit

CentralProcessing unit

Clock RAM ROM

KeyboardInput

CD-ROMInput

FaxI & O

ScannerInput

Modem

I & O

Monitor

Output

PortsI & O

MouseInput

FloppydiscStorage

Hard discStorage

Fig 1.

Printer

Output

The Systems UnitThe Systems Unit..

The heart of the System Unit is the Mother Board.This carries the central processing unit,(CPU) an integrated circuit chip which performs the logical operations of the computer. The CPU is part of the microprocessor, a group of chips controlling all major instructions performed by the PC.

      System Unit       Video card: It controls signals that let you see things on the computer monitor.       SCSI: Pronounced "scuzzy," this controller lets you hook up additional hardware to your personal computer, including CD-ROM drives, printers, scanners, hard disks and backup storage drives. It stands for Small Computer System Interface.       System bus: This is like a traffic system that connects components to each other.       RAM chips: They add memory (Random Access Memory) to the personal computer.       Motherboard: This is the main circuit board of the computer. It has many slots for other circuit boards.       Microprocessor: This is the brain and the messenger. It also is known as the CPU, or the central processing unit.       Clock: It keeps the CPU or microprocessor on time.       CD-ROM drive.       Floppy disk drive

                                                         

                             

Monitor       Magnetic deflection yoke: It's a fancy term of the focus and aiming of the electron guns.       Electron guns: Red, blue and yellow guns fire streams of electrons toward your screen       Shadow mask: Keeps the electrons from the guns aligned as they stream toward your screen.       Screen: Displays text and images.

                                                         

                              

KeyboardWhen you press a key, the electronic flow is altered and a signal is sent to the power supply box in the system unit.

                                                         

   Mouse

      Buttons: They send electronic signals to your PC.       Ball: When the mouse moves, the rubber-coated, steel ball moves rollers.       Rollers: They correspond to vertical and horizontal movements the cursor makes across the monitor screen.       Encoder: Wheels turned by rollers initiate electronic signals.       Cable: Signals are sent to your system unit through this cable.

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Functions of a General Computer System: An Analogy

A General Computer System

                                                                                                                  

Intel Microprocessors, used in IBM and clone PCs, in Intel Microprocessors, used in IBM and clone PCs, in ascending levels of power,ascending levels of power,

8086, 8088 Early PCs, mid 1980s. 80286 AT PC 80386 (Dx 32 wire bus,Sx 16 wire bus) 80486 (Dx has maths co-processor) Pentium 100 to 200 . Powerful than old 486s. Pentium 2 (233 to 400 Mhz.) Pentium 3 ( 450 Mhz)

Components of a Processor•Control unit -- responsible for supervising the operation of the entire computer system. •Arithmetic/logic unit (ALU) -- provides the computer with logical and computational capabilities. •Register -- a storage location inside the processor.

Comparing MicroprocessorsPerformance Ratings of Intel  Processors

                                                                                                                 

                 

Microprocessor speed. Microprocessor speed. An eassential component of the micro processor is the Clock

which drives every operation of the PC. A given class of microprocessors may operate at different speeds, e.g an 80486 at 25 Megahertz (MHz), 50 MHz, 66 MHz.(MHz = millions of cycles per second). A later microprocessor (80486) operating at a lower clock speed may be more powerful than an earlier chip (80386) at a higher speed.. Pentium 2 and 3 operates at a clock speed of 400 Mhz and above.

• Computer speed is also measured in millions of instructions Computer speed is also measured in millions of instructions per second, (MIPs) which is a less commonly used but per second, (MIPs) which is a less commonly used but perhaps more useful index.perhaps more useful index.

Number of Unique Binary Symbols as Bit Strings•1 Bit: 0 1 •2 Bits: 00 01 10 11 •3 Bits: 000 001 010 011 100 101 110 111 •4 Bits: 0000 0001 0010 0011 0100 0101 0110 0111 1000 1001 1010 1011 1100 1101 1110 1111

In general, for a string of length n, there are 2n power possible, unique binary symbols.

Binary Digit (Bit) Facts•The bit is the basic unit of information in all electronic computers. •The bit is capable of storing the same amount of information regardless of its physical size. •The bit's hardware counterpart -- the switch, the transistor, the semiconductor -- is the physical embodiment of electronic information in bits.

Memory chips

Memory chips are present on the mother board. These are of two major categories, Random Access Memory(RAM) and Read Only Memory (ROM).

Measurement of Computer Memory 1 Bit (Binary Digit) Value of 0 ,1 8 Bits 1 Byte (one alphanumeric chr) 1024 Bytes 1 Kilobyte ( 1K) a page of text 1024 Kilobyte 1 Megabyte( 1M) 1024 Megabyte 1 Ggabyte( 1G).

Primary StoragePrimary Storage

ROM (read-only memory) -- the processor can read information from ROM (read-only memory) -- the processor can read information from ROM, but it can neither erase information from it nor write to it -- thus ROM, but it can neither erase information from it nor write to it -- thus the name, read-only memory. the name, read-only memory. RAM (random-access memory) -- the processor can load programs and RAM (random-access memory) -- the processor can load programs and data into RAM and read from and write to RAM. RAM can store any data into RAM and read from and write to RAM. RAM can store any kind of information that the processor is capable of handling. In kind of information that the processor is capable of handling. In random-access memory, it takes the same amount of time to access any random-access memory, it takes the same amount of time to access any one piece of information as it does another, no matter where it is stored one piece of information as it does another, no matter where it is stored in RAM. in RAM.

                                                                                                                                                   

                                                                      

     

Primary StorageRandom-Access Memory

Secondary Storage

Disskettes-- made from thin sheets of flexible plastic, inexpensive and portable, usually 800 K - 1.44 MB.

Diskettes

                                                                                                                                                                     

               

Secondary StorageHard Disk

                                                                  

           

•Hard disks -- made from rigid platters of aluminium, faster and with much more capacity than diskettes, from 200 MB to 10 gigabytes.

                                                                            

              

Tracks on a Disk

•Portable hard drive alternatives -- portable like large diskettes but store large quantities of data like hard drives

ZIP Drives

Secondary Storage

•massive portable ROM storage in CD format readable by a laser beam, about 600 MB.

Secondary StorageCD-ROMs and CD-ROM Drive

                                                                                            

          

Hard/Soft Copy Output

•Hard Copy -- recording letters, graphics, or pictures on a permanent medium, such as paper or film. Examples include printing, drawing lines with a plotter, or photographically recording an impression on film or microfilm.

•Soft Copy -- using electronic signals to display a temporary image on a surface such as a video CRT screen. Although this may seem to be a limitation, the image can quickly be changed, as in the case of graphic animation, to create movement.

Desktop Printers

Some Printer Facts

Type Category Quality Speed Cost

Impact Dot-matrix Serial Draft to near letter quality

30-500 cps $100-300

Non impact

Ink-jet Serial Near letter quality

35-400 cps $300-1500

Laser Page Letter 8-28 ppm $500-10,000

(cps=characters per second)

(ppm=pages per minute 48 cps=1ppm)

Fax.Fax.

Faxes and fax modems may be incorporated into PCs. There is the disadvantage that only data in the computer (not printed documents) may be sent. .

ModemsModems

Modems are devices which facilitate the sending of data from one computer to another via telephone lines. There must be a modem on the sending and on the receiving PCs. Additional software is needed. The speed of transmission is measured in Bauds- pbs or bits/second. The speed of modems ranges from 300 to 14.4K pbs. There are a number of recognised classes of modems.

Scanners.Scanners.

Scanners read paper documents and graphics and transmit the resulting data in electronic form to the computer. Software programs are required; for text, this is optical character recognition(OCR). The scanner may be a hand held instrument or a larger flatbed device resembling a photocopier.

Internet.Internet.

The Internet is not a company,or a service,or a branch of any government. Rather, it is the name given to the interconnection of computers worldwide. It was created in 1969 for the defense establishment as a means by which vital computer operations could continue in the event of a nuclear attack and the destruction of computer infrastructure.The network was designed to be seamless and “self healing”,where any computer on the network could function fully and communicate with other surviving systems. Since its birth,the Internet has grown--today’s estimates of individualusers run as high as 35 million .

Networks.Networks. The early computers were huge in size and very costly;they were

scheduled for use 24 hours a day. PCs were developed to be personal computers. They were inexpensive and so an individual might have one for his occasional personal use.In time,it became apperent in certain circumstances that there were advantages in connecting PCs together in a network. For example, communication was improved and data,programs, printers and hard disks could be shared. Networks may be local area networks (LAN) or wide area networks (WAN). There are a number of configurations, token ring, star and bus. In some networks the PCs are connected to a more powerful computer with advanced facilities, the file server. Security may be a concern.

Example of a hardware specificationAdvertisements often display the specifications of computers. When considering the purchase of a computer it is important that these specifications are understood. An example is given below, followed by an explanation of each term.

Hardware specification:Pentium 90 MHz CPU--- clock speed of the CPU

16 Mb RAM---16million bytes of information can be contained in the RAM of the PC. This memory is used by the operating system and the application software. Larger the RAM the better.

850 Mb hard disk---850 million bytes can be stored on the hard disk

CD-ROM drive----special drive used to read compact disks

3.5” floppy disk drive---this drive can use 3.3” floppy disks.

SVGA VDU---Super Video Graphic Adaptor Visual Display Unit. This is a higher resolution screen and will display graphics very clearly.

Windows---is operating software, developed by Microsoft, which uses menus and icons for command options.

Some Computer companies Web addressesCompaq http://www.compaq.com

Hewlett-Packard http://www.hp.com

Dell http://www.us.dell.com

Gateway- 2000 http://www.gw2k.com

Access these sites on the Internet