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 Computing Technology Internet

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. 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 language Interpreted - BASIC, PERL ByteCode - Java Compilable - 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 A typical setup at home Speakers PC Printer

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? The INTERNET Modem Telephone Line Local Phone Company ISPIAP ILC International Leased Circuit Internet Service Provider Internet Access Provider

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

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

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

28. Distributed Hypertext/Hypermedia Uniform Resource Locator: http://www.sg/welcome.html http://www.whitehouse.gov/welcome.au http://biomed.nus.sg/logo.gif Document File Name + Internet Address Tim Berners-Lee CERN, Geneva

29. Mosaic, Netscape, Internet Explorer WWW Browsers

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

31. Web and Databases Netscape Web browser Form Filling Front end Apache Web server Database Search Engine Common Gateway Interface CGI interface 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. 1970s1980s1990s2000s 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. Parallel Development 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. 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