Computers and Internet in Bioinformatics
Dr Tan Tin Wee
Director
Bioinformatics Centre
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
Scope of Introductory Bioinformatics
• Database Searching
• Sequence Alignment
• Gene finding
• Functional Genomics
• Protein Classification
• Phylogenetic inference
ComputingTechnology
Internet
What is a Computer?
Hardware Peripherals
PrinterSpeakerScannerDiskDrive
Operating System
Software Applications
User Interface
CPU, Memory, Harddisk, I/O interface
Win95, Win98, Unix, VMS
E.g.Microsoft OfficePowerpoint, Eudora, Excel
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
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
Program Development Environment
• Visual Basic (BASIC)
• Visual C (C programming)
• Visual J++ (Java)
• Delphi (Pascal)
• Assists software developer to develop programs faster.
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
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
Standalone Computer
A typical setup at homeSpeakers
PC Printer
LAN
A Small Local Area Networkof two computersand one printerin your office
InterDepartmental Network
Campus Wide Network
Campus Network
Wide Area Network
National Network
InterCountry Network
Global Network
The INTERNET
How do you connect to Internet?
The INTERNET
Modem
TelephoneLine
Local Phone Company
ISP IAP
ILCInternationalLeasedCircuit
Internet Service Provider
Internet Access Provider
Office connection to Internet?
The INTERNET
Router
Leased TelephoneLine
Local Phone Company
ISP IAP
ILCInternationalLeasedCircuit
Internet Service Provider
Internet Access Provider
Office Local Area Network
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
Client and Server
Application
CPU/Harddisk
Same Machine
Client Application
Server software
Front end
RemoteBackEnd
Separate Machines
Connected by NetworkCommunicating by a Protocol
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
Technical Notes
• IP number 137.132.9.61
• Userid tinwee
• Domain Name biomed.nus.sg
• Email address [email protected]
• URL http://biomed.nus.sg:80/welcome.html
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
Internet Access in Singapore
Internet Providers• Pacific Internet• Cyberway• Singnet • Internet resellers• Through Singapore ONE• NUS, NTU and other educational institutions
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
What is Hypertext?• Non-Linear Text
• Links embedded in the text
• Jumps to other locations in the document/db
the quick brown foxjumps overthe fence
Fence........................
Hypermedia & CDROMs
• Ted Nelson’s visionary ideas in 1969
• Project Xanadu
• Combine Text with Graphics, Pictures, Audio, Video, Movie clips etc
• CDROMs
Distributed Hypertext
the quickbrown foxleapsover the fence again.
Distributed Hypertext
the quickbrown foxleapsover the fence again.
Client Netscape Web Browser application
World Wide Web of Information Servers
Distributed Hypertext/Hypermedia
Uniform Resource Locator:http://www.sg/welcome.htmlhttp://www.whitehouse.gov/welcome.auhttp://biomed.nus.sg/logo.gif
Document File Name
+
Internet Address
Tim Berners-LeeCERN,Geneva
Mosaic, Netscape, Internet Explorer WWW Browsers
Web and Documents
Netscape Web browser FormFilling Front end
Apache Web server
Directory of Filesetc etc
Web and Databases
Netscape Web browser FormFilling Front end
Apache Web server
Database Search Engine
Common Gateway InterfaceCGI interface
•Flat Files•Relational Dbs•Object Oriented Dbs
Biological Databases
• DNA sequence databases
• Protein sequence databases
• Gene Map databases
• Motifs databases
• Bibliographic databases
• Biochemical databases
• Enzyme databases etc etc
1970s 1980s 1990s 2000s
Biocomputing
BioInformaticsStart-Ups in
USA - market hype
NCBI
EBI
EMBnet/EMBL
ICGEBnet
???Pharma’s
Rush
Internet boom
GeneticRevolution
IMCB
AustralianInstitutes
DDBJ ANGIS
APBioNet
BIC
NABBINet
GenomeNet PekingU BC/HKBIC
Advancednetworking
India
Parallel Development
94 95 96 97 98 99 00 01
94 95 96 97 98 99 00 01NetworkInfrastructureDevelopment
BioinformaticsInfrastructureDevelopment
Synergy
APNG AI3 APAN SINGAREN TRANSPACAPAN-
APBioNet
NUS bionetworkAPECSurveyBIC
APBioNet
Push-Pull
APAN-APBioNet
EMBnet-APBioNet
ASTNET
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
Conclusion
• Computer and Internet Technologies has tremendous applications in the Life Sciences
• Tremendous impact on the growth and evolution of Bioinformatics