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 tinwee@biomed.nus.sg

• 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