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
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
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
ISP IAP
ILC
International
Leased
Circuit
Internet Service
Provider
Internet Access
Provider
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. 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
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
30. Web and Documents
Netscape Web browser Form
Filling Front end
Apache Web server
Directory of Files
etc 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
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
