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Computers and Internet in Bioinformatics

Computers and Internet in Bioinformatics. Dr Tan Tin Wee Director Bioinformatics Centre. Internet and Bioinformatics. Computing Technology in Biology - biocomputing

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Computers and Internet in Bioinformatics

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  1. Computers and Internet in Bioinformatics Dr Tan Tin Wee Director Bioinformatics Centre

  2. Internet and Bioinformatics • Computing Technology in Biology - biocomputing • Molecular biology was one of first to use latest Internet technologies such as mailing list, newsgroups, WAIS, Gopher and World Wide Web • Internet Boom occurred at the same time as Genome Project data explosion • Close synergies between the two

  3. Scope of Introductory Bioinformatics • Database Searching • Sequence Alignment • Gene finding • Functional Genomics • Protein Classification • Phylogenetic inference ComputingTechnology Internet

  4. What is a Computer? User Interface E.g.Microsoft OfficePowerpoint, Eudora, Excel Software Applications Operating System Win95, Win98, Unix, VMS Printer Speaker Scanner DiskDrive Hardware Peripherals CPU, Memory, Harddisk, I/O interface

  5. What is a Computer Program • Set of instructions which tells the computer • Machine language eg. 010011010010 • Assembly Language eg. MOV AX,2 command for programming chips eg Intel SPARCs, Digital Alpha chip, Z80, Motorola 6008 • Higher level Programming languageInterpreted - BASIC, PERLByteCode - JavaCompilable - C, C++, COBOL, PASCAL etc

  6. Programming Language • 1GL - Machine • 2GL - Assembly • 3GL - Structured Programming - Fortran, Pascal, C, C++ (Object Oriented), PERL, BASIC, etc • 4GL - Functional Programming - LISP, Standard ML, Prolog

  7. Program Development Environment • Visual Basic (BASIC) • Visual C (C programming) • Visual J++ (Java) • Delphi (Pascal) • Assists software developer to develop programs faster.

  8. Example • Microsoft Word • Developers use a variety of environments writing software for Windows operating system • Compile the code • End result is an executable .exe which when you double-click, powers up the application • Application allows you to compose document and save into harddisk or floppy

  9. What is the Internet? • A world wide collection of networks of computers • A network of computer networks • A network based on the TCP/IP protocol

  10. Standalone Computer PC Printer A typical setup at home Speakers

  11. LAN A Small Local Area Network of two computers and one printer in your office

  12. InterDepartmental Network

  13. Campus Wide Network

  14. Campus Network Wide Area Network National Network InterCountry Network Global Network The INTERNET

  15. How do you connect to Internet? ISP IAP The INTERNET Internet Service Provider Internet Access Provider ILC International Leased Circuit Local Phone Company Telephone Line Modem

  16. Office connection to Internet? ISP IAP The INTERNET Internet Service Provider Internet Access Provider ILC International Leased Circuit Local Phone Company Leased Telephone Line Office Local Area Network Router

  17. What can you do with Internet? • INTERNET APPLICATIONS • Electronic Mail (Email) • Internet Talk/Chat (IRC) • File Transfer (FTP) • Remote Login (Telnet) • Internet News (Usenet) • Info retrieval (Gopher, World Wide Web) • Virtual Reality (VRML) • AudioVideo Conferencing (CU-SeeMe, Mbone) • Internet Phone

  18. Client Application Server software Client and Server Front end Application Connected by Network Communicating by a Protocol CPU/Harddisk RemoteBackEnd Same Machine Separate Machines

  19. Networks and Protocols • Many networks - BITNET, SNA (for IBM) and most famous and de facto global information infrastructure - INTERNET • Many different protocols - most famous is TCP/IP - a set of protocols for transferring information packets through a network • Transmission Control Protocol/Internet Protocol

  20. Technical Notes • IP number 137.132.9.61 • Userid tinwee • Domain Name biomed.nus.sg • Email address tinwee@biomed.nus.sg • URL http://biomed.nus.sg:80/welcome.html

  21. Internet Access in Singapore For Dialup, you will need: • An Internet account • PC / Macintosh based computer • Modem • Phone line • Communications Software For NUS, you will need: • Network card • configure built-in software

  22. Internet Access in Singapore Internet Providers • Pacific Internet • Cyberway • Singnet • Internet resellers • Through Singapore ONE • NUS, NTU and other educational institutions

  23. Power of the Internet and Emergence of WWW • Hypertext • Ted Nelson’s Project Xanadu (1969) • CDROMs and Hypermedia • Distributed Hypertext • Distributed Hypermedia • Mosaic, Netscape, Internet Explorer

  24. What is Hypertext? • Non-Linear Text • Links embedded in the text • Jumps to other locations in the document/db Fence ...... ...... ...... ...... the quick brown fox jumps over the fence

  25. Hypermedia & CDROMs • Ted Nelson’s visionary ideas in 1969 • Project Xanadu • Combine Text with Graphics, Pictures, Audio, Video, Movie clips etc • CDROMs

  26. Distributed Hypertext the quick brown fox leaps over the fence again.

  27. Distributed Hypertext World Wide Web of Information Servers the quick brown fox leaps over the fence again. Client Netscape Web Browser application

  28. Distributed Hypertext/Hypermedia Tim Berners-Lee CERN, Geneva 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

  29. Mosaic, Netscape, Internet Explorer WWW Browsers

  30. Web and Documents Apache Web server Directory of Files etc etc Netscape Web browser Form Filling Front end

  31. Web and Databases Apache Web server Common Gateway Interface CGI interface Netscape Web browser Form Filling Front end Database Search Engine • Flat Files • Relational Dbs • Object Oriented Dbs

  32. Biological Databases • DNA sequence databases • Protein sequence databases • Gene Map databases • Motifs databases • Bibliographic databases • Biochemical databases • Enzyme databases etc etc

  33. BioInformaticsStart-Ups in USA - market hype Pharma’sRush ??? EBI ICGEBnet NCBI EMBnet/EMBL Advanced networking Biocomputing Internet boom Genetic Revolution 1970s 1980s 1990s 2000s NABBINet Australian Institutes APBioNet IMCB India DDBJ ANGIS BIC GenomeNet PekingU BC/HKBIC

  34. Parallel Development APEC Survey APAN- APBioNet NUS bionetwork BIC ASTNET EMBnet- APBioNet APBioNet Bioinformatics Infrastructure Development 94 95 96 97 98 99 00 01 Synergy Push-Pull Network Infrastructure Development 94 95 96 97 98 99 00 01 APAN- APBioNet APNG AI3 APAN SINGAREN TRANSPAC

  35. Life Scientists • Communication with each other through email, mailing lists, newsgroups and video conferencing • Information when and where needed • Rapid dissemination of information for global collaborations • Access to software applications freely • Access to computational resources freely

  36. Conclusion • Computer and Internet Technologies has tremendous applications in the Life Sciences • Tremendous impact on the growth and evolution of Bioinformatics

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