Introduction to Bioinformatics

Transcription

1 BMS2062 Introduction to Bioinformatics Use of information technology and telecommunications in bioinformatics Topic 1: Practical uses of Internet services Ros Gibson IT Staff Lecturer: Ros Gibson Demonstrators: IT - Silvia and Natalia Biomed 2 IT module assessment Numerous small practical tasks Multiple Choice questions in exam Web page and PowerPoint Presentation layouts and interface (not content) Attendance: the roll will be marked each practical class 3

2 Module outline Lectures: Practical uses of internet services (22/7) Internet, web and multimedia (28/7) Digitised images and image compression (29/7) Practical: Practical use of internet services (Week 2) Web pages design and use (Week 3) Using PowerPoint (Week 4) Questions? OK, let s start.. 4 Practical uses of Internet services Biologists are one of the largest research communities using the Internet. The internetprovides a simple means to distribute data allows easy access to data sources and analysis services. Overview Communication and information The Internet as a communication means Protocols, Internet and Web services 5 Communication and information Communication is The imparting or interchange of thoughts, opinions or information by speech, writing, or signs The science or process of conveying information especially by electronic or mechanical means ( Purposes - business / social interaction / infotainment / education / research / personal fulfillment Immediacy Distance Power / impact / effectiveness 6

3 Communication Representation Physical objects / actuality Written /spoken words Sound - music, sound effects Pictures - diagrams, photographs, charts, maps, animated pictures, moving pictures Transmission Direct: Face-to-face contact (speech/nonverbal), telephone Indirect: Radio, Printed word/pictures - newspapers/books/magazines/etc, film/tv 7 Issues What method of representation is the most accurate and appropriate for the intended information? What method of transmission is the most effective and efficient? How suitable are the different representation and transmission methods to the needs and capabilities of the sender and receiver - in particular in bioinformatics? 8 Same information - different representations During the LAG PHASE, the bacteria in the original inoculum adapt to their new environment (e.g. synthesise enzymes required for Growth curve of E.coli in batch culture growth). The number of cells Time (h): Viable cells/ml: does not increase during this x10 time. During the x10 EXPONENTIAL or x10 LOGARITHMIC PHASEof x10 growth, the number of x10 bacteria doubles at regular 5 intervals. During the x10 6 STATIONARY PHASE, the x10 7 bacteria have exhausted one x10 7 or more critical requirements x10 9 for growth. Growth slows as x10 wastes accumulate and/or x10 nutrients are depleted x10 8 9

4 Communication and the Internet The Internet is a relatively new form of communication It is perceived as a means of communicating Standards and expectations are still being developed But what is the Internet? 10 What is the Internet? Standard definition: The interconnection of networked computers. A computer network is a group of two or more computers that are connected together and are able to share resources (hardware/software/data) The Internet is the world s largest computer network, connecting thousands of networks and millions of computers all over the world enabling a global sharing of information. 11 A little Internet history ARPANet installed (4 nodes) introduction of , telnet and TCP/IP, (32 servers) first international connections hypertext concept developed by Tim Berners-Lee (CERN) ,000 users Hypertext program commercialised million users References:

5 Some Internet basics Computers on the Internet use a number of protocols or rules to send and received packets of data. TCP/IP Transmission Control Protocol / Internet Protocol, is the main suite of protocols used on the Internet. It allows for the connection (and understanding) between two hosts to exchange data An internet address or IP address is a unique address of a computer linked to the Internet. IP address are technically a series of numbers, eg The Web is NOT the Internet The INTERNET Text based The WEB Graphical Multimedia capabilities 14 What is the Web? A system of Internet servers that support specially formatted documents. ( The documents are formatted using the basic language of the Web; HTML / hypertext markup language. (XML is the new language of the Web) Allows for the transfer of information (documents) with consistent and quality appearance regardless of the operating system e.g. Windows, Mac, Unix. Documents use links or hyperlinks to other content. Web documents may contain graphics, sounds, text and video (GUI). The Web is uncontrolled but there are standards, eg W3 consortium. 15

6 Some Web basics A URL is the Universal (or uniform) Resource Locator for a file on the Web. It usually contains the domain name of the organisation, the type of organisation and country addresses are based on domain names, eg gibson@acslink.aone.net.au Prefixing the URL is the type of protocol used for transmission; http, ftp Home page has filename of index.html (index.htm, or default.html /.htm ) 16 How it all works Client computer (nodes) Servers (hosts) Protocols - rules and regulations for transmitting the data which then allows for a number of different services 17 Internet and Web services ftp and archie telnet http (SMTP) Web searching audio video text conferencing discussion lists (threaded and listservs) rich media; video, audio, virtual reality, 3D modeling/simulations 18

7 Service: ftp [1] file transfer protocol (an Internet service) Transfers any sort of file between local and a remote computer. A file can contain just about anything text, image, video, sound, source code Often uses anonymous ftp (prac activity) 19 Service: ftp [2] Need to know: the domain name or IP address of the computer, and the pathname of where the files are located. ASCII (text, source code) or binary (executable, application files, compressed files) file type. (Common type is Binary) the file type compatibility (operating system, application) 20 Service: ftp [3] using WS_FTP LE ftp.monash.edu.au/pub/ 21

8 Service: ftp [4] using a Web browser ftp://ftp.monash.edu.au/pub/ 22 Service: archie Project of the McGill University School of Computer Science. A tool that allows you to perform keyword searches on a database for files available on the Internet through anonymous ftp. Most archie servers are now accessed using a web browser Some search engines provide facilities for finding ftp files e.g Service: telnet A terminal emulation program connects the users computer to a server on the network Enter commands on the users computer connected using telnet and it works as if you were at the server s console 24

9 Service: http Hyper text transfer protocol (a Web service) Web browsers Two common examples include Internet Explorer and Netscape Communicator Contact and retrieve content from a server Display the content View, compose and manage , address book, diary information, and html documents Navigate through content https now available which has additional security (Developing web content is covered in IT Module - lecture 2) 25 Service: Electronic mail (an Internet service) Messages sent from the client to the server and from one server to another using SMTP protocol (Simple Mail Transfer Protocol) Messages are then retrieved by an client on the users computer (e.g. Outlook Express or Netscape Messenger) using either POP (Post Office Protocol) or IMAP (Internet Message Access Protocol). Text interface has been superceded by a Web interface 26 Service: others Synchronous audio video text conferencing (chat) Instant messaging (internet relay chat) Discussion lists (threaded and listservs / usernet) Rich media uses: video, audio, virtual reality, 3D modeling/simulations 27

10 Rich media VRML (Virtual Reality Modeling Language) (Requires Cosmo World View Player) Web microscope ml General advertising 28 Web searching [1] Search Engines Web-crawlers / spiders: Automatically browse web pages for data. This data is then used as a listing from which a user searches Human indexes: Web site administrators (or similar) submit a short description about the site/page. This data is then used as a listing from which a user searches Hybrid Search Engines: Search engines today commonly use a combination of web-crawlers and human indexes 29 Web searching [2] Ranking: One of the the main rules in a ranking algorithm involves the location and frequency of keywords on a web page. Popularity: Relates to the number of other sites that link to the site The tools: Databases Indexes (title, major heading, body text, deep crawl ) Metadata (keywords, author, description) 30

11 Web searching [2] Using the data: Hyperlinks Saving to local computer Inserting into own work (files, links) Points to Consider Plagiarism Copyright Validity Citation Manager 31 The last 60 minutes.. What was it about you tell me What didn t you understand? 32 What s next Week 2 Monday lecture: The Internet and multimedia Week 2 Tuesday lecture: Digital images and image compression Week 2 practical: Internet services Bring a floppy disk Read through prac exercises before class 33

12 Resources Cosmo World View Player (12 MB) 34