1. Computing Environments CSC8304 Marcus Kaiser http://www.biological-networks.org http://www.biological-networks.org

2. About this module Module Leader: Dr Marcus Kaiser Today’s lecture – Introduction to Computing Environments Lectures for the next 4 weeks cover the need for database systems, statistical packages, security and poll-based/event-driven software Reading Week then follows – no lecture Remaining lectures cover programming languages, scripting and Perl Lectures are on Tuesdays, 9:30-11am, CLT.602 Lecture notes can be found on http://www.biological-networks.org/http://www.biological-networks.org/ (Training > Computing Environments for Bioinformatics ) Practical classes start in DAYSH.821 and are on Wednesdays 11-12am

3. Assessment Coursework Databases/SQL5 Nov deadline15% of final mark Scripting/Perl10 Dec deadline15% of final mark Exam ExamJanuary70% of final mark

4. A computing environment Requirements Services Enabling presentation of services to users and interaction with such services by users Mobile devices (e.g., mobile phones) Video game consoles Printers Tactile feedback devices Monitors A world of supporting services Robots

5. A heterogeneous environment A modern day computing environment is made up from many different types of enabling technologies. An enabling technology refers to the mechanism that is used to implement a service. Many technologies share the same ultimate goal (e.g., sending a message from one computer to another). However, such technologies may attempt to achieve the same goal in different ways (e.g., Microsoft and Linux operating systems).

6. Standards There are instances when vendors must adhere to some standard to ensure integration (the Internet protocols exemplify this). Standards play a crucial role in computer system development. There are two types of standard: Provided by an organisation that is recognised by the community as assuming the role of identifying standards (members of such an organisation are usually drawn from different vendors). Provided by a vendor (or group of vendors) and deployed without international recognition (however, such recognition may occur at a later date).

7. Computer technology evolution 1945: ENIAC http://en.wikipedia.org/wiki/Eniac http://en.wikipedia.org/wiki/Eniac 2004:Pentium Complexity18,000 ValvesX 10 3 42 M transistors Size200 m 3 X 10 -8 6 cm 3 Speed150 ops/sX 10 6 1.6 x 10 9 ops/s Consumption10 kWX 10 -3 68W Cost$10 000 000X 10 -4 <£1000 ReliabilityHoursX 1000Years

8. What if cars improved in a similar fashion?!! Speed70 mphX 10 6 11000km/s Fuel50 mpgX 10 -3 50,000 mpg Cost£10,000X 10 -4 £1 Reliability1 YearX 10001000 Years Weight1 tonX 10 -8 10 mg

9. Conceptual Levels of Computers A digital computer is capable of computation, communication and storage. Computation is performed by carrying out instructions, a sequence of instructions to solve a problem is called a program Instructions are recognised and executed by the electronic circuits in the computer Instructions can only permit simple operations, typically, they can: Add two numbers Check if a number is zero Move data around in Memory This set of instructions is called the machine language Different types of computers usually have different machine languages The machine language is said to be the interface between the software and the hardware.

10. Conceptual Levels of Computers contd. Most users do not use machine language Use high level language e.g. Java The high level language is translated to machine language by a compiler Computers can be thought of as having different levels, each with its own language. Each level carries out tasks on behalf of the level above it. Helps to cope with understanding the complexity of computing systems Software and/or Hardware Assembly Language Level (Assembly programmer) Conventional machine level (hardware designer) Integrated circuit level (VLSI designer) Transistor level (Physical designer) Silicon + electronics level Chemical engineer Application Software (anybody) High Level Language (Java programmer) Operating System Level (programmer)

11. Data Representation (1) Humans count in base 10, using 10 digits Difficult to represent electronically Machines count in base 2 Two-state devices are easy to make (transistors) Only two digits used (0 and 1) called binary digits or bits Electrically represented by 0 volts and 5 volts Each bit occupies one memory cell or wire The basic working unit consists usually of 8 bits, called a byte The basic memory unit is a multiple number of bytes e.g. 2 bytes = 16 bits 4 bytes = 32 bits 8 bytes = 64 bits The basic memory unit is called the word length

12. Data Representation (2) All bytes in the memory are numbered, or addressable The first byte is numbered 0, the second 1, and so on Memory size is usually expressed in terms of (Mega)bytes It is common practice to: Write the least significant bit (LSB) on the right Write the most significant bit (MSB) on the left Start counting from zero All data held within the computer is represented by a number of bits or bytes All high level objects, such as a Java or C++ class must be translated into bits

13. Data Representation (3) Data comes in many forms Booleans Characters (i.e. text) Integers, both positive and negative; e.g. -230, -1, 0, 45319 Real numbers, also called floating point numbers, e.g. 3.0, log (13), sin(π/4), 22/7 Structured data types defined by programming languages e.g. Arrays Strings Classes Each type is represented by one or more bits

14. Bits, Bytes, and Buzzwords Byte Kilobyte (KB) Megabytes (MB) Gigabytes (GB) Terabytes (TB) = 8 bits = 1024 (2 10 ) Bytes = 2 20 Bytes = 2 30, or about a billion, Bytes = 2 40, or about a trillion, Bytes Terms used to describe file size or memory size:

15. Integer data Integer numbers don’t allow fractions Humans use the decimal number system. There are 10 digits, 0 – 9. Each place within a decimal number represents a power of 10. For example 236 = 2 * 10 2 + 3 * 10 1 + 6 * 10 0 + 10 is not a ‘natural’ base (it is an anatomical incident!) Computers work more naturally with base 2 because transistors have two states In base 2, only digits 0 and 1 are used. Greatly simplifies the arithmetic and makes it much faster

16. Binary Numbers Each place within a binary number represents a power of 2. e.g binary 101 = 1 x 2 2 + 0 x 2 1 + 1 x 2 0 (equals five in decimal) Electrical representation: three wires ONOFFON (5V)(0V)(5V)

17. Binary Arithmetic Humans perform decimal addition by: Memorising all single-digit additions Writing the numbers to be added down right-aligned, one above the other Starting at the right and working towards the left Adding the digits, writing down the result and propagating any carry to the next column Subtraction works much the same way except that you must borrow from the next column Multiplication with a single-digit number works much the same way too Multiplication with a multi-digit number is treated as a series of separate single digit multiplications, the results of which are added together Binary addition, subtraction and multiplication can treated exactly the same except that only the digits 0 and 1 are used.

18. Basic Binary Arithmetic - examples 1001010 0011101+ ------- 1100111 0011010 0001001- ------- 0010001

19. Hexadecimal Numbers Problem with binary arithmetic – Long strings are fine for machines but awkward for humans e.g. What is the binary number 0100101011100011 ?? Guess then work it out! We (humans) therefore often use hexadecimal numbers (or hex for short). This uses base 16. There are 16 “digits” (0 1 2 3 4 5 6 7 8 9 A B C D E F) Each place represents a power of 16: e.g. 29F = 2 * 16 2 + 9 * 16 1 + F * 16 0 (=671 in decimal)

20. Integer Representation For the sake of economy, different hardware representations are used to implement different integer ranges The following are commonly found: NameBitsRange signedRange unsigned Byte8-128 … 1270.. 255 Word16-32768.. 327670.. 65535 Long32-2 31.. 2 31 -10.. 2 32 -1 Quad64-2 63.. 2 63 -10.. 2 64 -1

21. Integer overflow It is possible that the result of an integer calculation is bigger than the allowed maximum (both positive and negative) Look at the following 8-bit addition 11001000200 -56 10010110150 -106 ------------------------- (1)01011110 (256+) 94 (-256+) 94 The final carry “disappears” because there is no hardware provision for it. The problem is called overflow (or underflow) Is this serious? Would you like this to happen to your bank account? Overflow is a serious problem. It indicates the presence of a bug in your program. The hardware can detect overflow and will cause your program to crash Overflow occurred in the European Space Agency’s Ariane 5 rocket when the on-board software attempted to fit a 64 bit number into 16 bits. This did indeed cause the program to crash...

22. Floating Point data The range of possible values using 32 bits to represent a number, positive or negative, is large However, bigger number representations are needed. e.g. numbers to allow fractions and powers as required by many scientific applications To represent fractions using integers, you would need two of them One for the numerator and one for the denominator Would be a major nuisance – not computationally amenable The way to do this is to use floating point numbers. Floating point data types allow a much greater range of possible values They are represented in floating point notation

23. Floating Point Notation Details of how floating point values are represented vary from one machine to another. The IEEE standard is one of the standard floating point representations More info at http://www.cs.uaf.edu/~cs301/notes/Chapter4/node13. html

24. Character Data Used for textual data, but can represent small integers Usually held in a byte although commonly only 7 bits are needed There are two major character sets: EBSIDIC (on IBM mainframe machines) ASCII (on all other machines) We concentrate on ASCII (American Standard Code for Information Interchange) It has been standardised by ISO (International Standardisation Organisation) ASCII was actually designed for use with teletypes and so the descriptions are somewhat obscure Often ‘text’ documents are referred to as in ‘ASCII’ format – easier for document interchange

25. ASCII The characters are classed as Graphic characters (printable or displayable symbols) Control characters (intended to be used for various control functions, such as vertical motion and data communications. The basic ASCII set uses 7 bits for each character, giving it a total of 128 unique symbols. The extended ASCII character set uses 8 bits, which gives it an additional 128 characters. The extra characters represent characters from foreign languages and special symbols for drawing pictures. More info @ http://www.jimprice.com/jim-asc.htm

26. Unicode Unicode is a new system to standardise character representation Unicode provides a unique number for every character, independent of platform, program, or language Adopted by such industry leaders as Apple, HP, IBM, JustSystem, Microsoft, Oracle, SAP, Sun, Sybase, Unisys. Required by modern standards such as XML, Java, ECMAScript (JavaScript), LDAP, CORBA 3.0, WML An implementation of the ISO/IEC 10646 standard Enables Internationalization

27. Unicode How Unicode Works It defines a large (and steadily growing) number of characters (> 110,000). Each character gets a name and a number, e.g. LATIN CAPITAL LETTER A is 65 and TIBETAN SYLLABLE OM is 3840. Includes a table of useful character properties such as "this is lower case" or "this is a number" or "this is a punctuation mark". The Unicode standard also includes a large volume of helpful rules and explanations about how to display these characters properly, do line-breaking and hyphenation and sorting Unicode is important – do some extra reading! – try a Google search

28. Summary A modern day computing environment is made up from many different types of enabling technologies Standards are used to permit interoperability Computers can be thought of as a number of different levels, ranging from the application software that we all use, right through to the electronic circuits within the computer Computers count in binary Various ways of representing numeric and character data