internet.ppt

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internet.ppt

  1. 1. Computers and Internet in Bioinformatics Dr Tan Tin Wee Director Bioinformatics Centre
  2. 2. Internet and Bioinformatics <ul><li>Computing Technology in Biology - biocomputing </li></ul><ul><li>Molecular biology was one of first to use latest Internet technologies such as mailing list, newsgroups, WAIS, Gopher and World Wide Web </li></ul><ul><li>Internet Boom occurred at the same time as Genome Project data explosion </li></ul><ul><li>Close synergies between the two </li></ul>
  3. 3. Scope of Introductory Bioinformatics <ul><li>Database Searching </li></ul><ul><li>Sequence Alignment </li></ul><ul><li>Gene finding </li></ul><ul><li>Functional Genomics </li></ul><ul><li>Protein Classification </li></ul><ul><li>Phylogenetic inference </li></ul>Computing Technology Internet
  4. 4. What is a Computer? Hardware Peripherals Printer Speaker Scanner DiskDrive Operating System Software Applications User Interface CPU, Memory, Harddisk, I/O interface Win95, Win98, Unix, VMS E.g.Microsoft Office Powerpoint, Eudora, Excel
  5. 5. What is a Computer Program <ul><li>Set of instructions which tells the computer </li></ul><ul><li>Machine language eg. 010011010010 </li></ul><ul><li>Assembly Language eg. MOV AX,2 command for programming chips eg Intel SPARCs, Digital Alpha chip, Z80, Motorola 6008 </li></ul><ul><li>Higher level Programming language Interpreted - BASIC, PERL ByteCode - Java Compilable - C, C++, COBOL, PASCAL etc </li></ul>
  6. 6. Programming Language <ul><li>1GL - Machine </li></ul><ul><li>2GL - Assembly </li></ul><ul><li>3GL - Structured Programming - Fortran, Pascal, C, C++ (Object Oriented), PERL, BASIC, etc </li></ul><ul><li>4GL - Functional Programming - LISP, Standard ML, Prolog </li></ul>
  7. 7. Program Development Environment <ul><li>Visual Basic (BASIC) </li></ul><ul><li>Visual C (C programming) </li></ul><ul><li>Visual J++ (Java) </li></ul><ul><li>Delphi (Pascal) </li></ul><ul><li>Assists software developer to develop programs faster. </li></ul>
  8. 8. Example <ul><li>Microsoft Word </li></ul><ul><li>Developers use a variety of environments writing software for Windows operating system </li></ul><ul><li>Compile the code </li></ul><ul><li>End result is an executable .exe which when you double-click, powers up the application </li></ul><ul><li>Application allows you to compose document and save into harddisk or floppy </li></ul>
  9. 9. What is the Internet? <ul><li>A world wide collection of networks of computers </li></ul><ul><li>A network of computer networks </li></ul><ul><li>A network based on the TCP/IP protocol </li></ul>
  10. 10. Standalone Computer A typical setup at home Speakers PC Printer
  11. 11. LAN A Small Local Area Network of two computers and one printer in your office
  12. 12. InterDepartmental Network
  13. 13. Campus Wide Network
  14. 14. Campus Network Wide Area Network National Network InterCountry Network Global Network The INTERNET
  15. 15. How do you connect to Internet? The INTERNET Modem Telephone Line Local Phone Company ISP IAP ILC International Leased Circuit Internet Service Provider Internet Access Provider
  16. 16. Office connection to Internet? The INTERNET Router Leased Telephone Line Local Phone Company ISP IAP ILC International Leased Circuit Internet Service Provider Internet Access Provider Office Local Area Network
  17. 17. What can you do with Internet? <ul><li>INTERNET APPLICATIONS </li></ul><ul><li>Electronic Mail ( Email ) </li></ul><ul><li>Internet Talk/Chat (IRC) </li></ul><ul><li>File Transfer ( FTP ) </li></ul><ul><li>Remote Login ( Telnet ) </li></ul><ul><li>Internet News ( Usenet ) </li></ul><ul><li>Info retrieval ( Gopher, World Wide Web ) </li></ul><ul><li>Virtual Reality ( VRML ) </li></ul><ul><li>AudioVideo Conferencing ( CU-SeeMe, Mbone ) </li></ul><ul><li>Internet Phone </li></ul>
  18. 18. Client and Server Application CPU/Harddisk Same Machine Front end Remote BackEnd Separate Machines Connected by Network Communicating by a Protocol Client Application Server software
  19. 19. Networks and Protocols <ul><li>Many networks - BITNET, SNA (for IBM) and most famous and de facto global information infrastructure - INTERNET </li></ul><ul><li>Many different protocols - most famous is TCP/IP - a set of protocols for transferring information packets through a network </li></ul><ul><li>Transmission Control Protocol/Internet Protocol </li></ul>
  20. 20. Technical Notes <ul><li>IP number 137.132.9.61 </li></ul><ul><li>Userid tinwee </li></ul><ul><li>Domain Name biomed.nus.sg </li></ul><ul><li>Email address [email_address] </li></ul><ul><li>URL http://biomed.nus.sg:80/welcome.html </li></ul>
  21. 21. Internet Access in Singapore <ul><li>For Dialup, you will need: </li></ul><ul><li>An Internet account </li></ul><ul><li>PC / Macintosh based computer </li></ul><ul><li>Modem </li></ul><ul><li>Phone line </li></ul><ul><li>Communications Software </li></ul><ul><li>For NUS, you will need: </li></ul><ul><li>Network card </li></ul><ul><li>configure built-in software </li></ul>
  22. 22. Internet Access in Singapore <ul><li>Internet Providers </li></ul><ul><li>Pacific Internet </li></ul><ul><li>Cyberway </li></ul><ul><li>Singnet </li></ul><ul><li>Internet resellers </li></ul><ul><li>Through Singapore ONE </li></ul><ul><li>NUS, NTU and other educational institutions </li></ul>
  23. 23. Power of the Internet and Emergence of WWW <ul><li>Hypertext </li></ul><ul><li>Ted Nelson’s Project Xanadu (1969) </li></ul><ul><li>CDROMs and Hypermedia </li></ul><ul><li>Distributed Hypertext </li></ul><ul><li>Distributed Hypermedia </li></ul><ul><li>Mosaic, Netscape, Internet Explorer </li></ul>
  24. 24. What is Hypertext? <ul><li>Non-Linear Text </li></ul><ul><li>Links embedded in the text </li></ul><ul><li>Jumps to other locations in the document/db </li></ul>the quick brown fox jumps over the fence Fence ...... ...... ...... ......
  25. 25. Hypermedia & CDROMs <ul><li>Ted Nelson’s visionary ideas in 1969 </li></ul><ul><li>Project Xanadu </li></ul><ul><li>Combine Text with Graphics, Pictures, Audio, Video, Movie clips etc </li></ul><ul><li>CDROMs </li></ul>
  26. 26. Distributed Hypertext the quick brown fox leaps over the fence again.
  27. 27. Distributed Hypertext the quick brown fox leaps over the fence again. Client Netscape Web Browser application World Wide Web of Information Servers
  28. 28. Distributed Hypertext/Hypermedia Document File Name + Internet Address Uniform Resource Locator: http:// www.sg / welcome.html http:// www.whitehouse.gov / welcome.au http:// biomed.nus.sg / logo.gif Tim Berners-Lee CERN, Geneva
  29. 29. Mosaic, Netscape, Internet Explorer WWW Browsers
  30. 30. Web and Documents Netscape Web browser Form Filling Front end Apache Web server Directory of Files etc etc
  31. 31. Web and Databases Netscape Web browser Form Filling Front end Apache Web server Database Search Engine Common Gateway Interface CGI interface <ul><li>Flat Files </li></ul><ul><li>Relational Dbs </li></ul><ul><li>Object Oriented Dbs </li></ul>
  32. 32. Biological Databases <ul><li>DNA sequence databases </li></ul><ul><li>Protein sequence databases </li></ul><ul><li>Gene Map databases </li></ul><ul><li>Motifs databases </li></ul><ul><li>Bibliographic databases </li></ul><ul><li>Biochemical databases </li></ul><ul><li>Enzyme databases etc etc </li></ul>
  33. 33. 1970s 1980s 1990s 2000s Biocomputing BioInformatics Start-Ups in USA - market hype NCBI EBI EMBnet/EMBL ICGEBnet ??? Pharma’s Rush Internet boom Genetic Revolution IMCB Australian Institutes DDBJ ANGIS APBioNet BIC NABBINet GenomeNet PekingU BC/HKBIC Advanced networking India
  34. 34. Parallel Development 94 95 96 97 98 99 00 01 94 95 96 97 98 99 00 01 Network Infrastructure Development Bioinformatics Infrastructure Development Synergy APNG AI3 APAN SINGAREN TRANSPAC APAN- APBioNet NUS bionetwork APEC Survey BIC APBioNet Push-Pull APAN- APBioNet EMBnet- APBioNet ASTNET
  35. 35. Life Scientists <ul><li>Communication with each other through email, mailing lists, newsgroups and video conferencing </li></ul><ul><li>Information when and where needed </li></ul><ul><li>Rapid dissemination of information for global collaborations </li></ul><ul><li>Access to software applications freely </li></ul><ul><li>Access to computational resources freely </li></ul>
  36. 36. Conclusion <ul><li>Computer and Internet Technologies has tremendous applications in the Life Sciences </li></ul><ul><li>Tremendous impact on the growth and evolution of Bioinformatics </li></ul>

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