Computers and Internet in Bioinformatics

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

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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.

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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

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Standalone Computer
PC
Printer
A typical setup at home
Speakers
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LAN
A Small Local Area Network of two computers and
one printer in your office
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InterDepartmental Network
13
Campus Wide Network
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Campus Network Wide Area
Network National
Network
InterCountry Network
Global
Network
The INTERNET
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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
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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

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

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Technical Notes

• IP number 137.132.9.61
• Userid tinwee
• Domain Name biomed.nus.sg
• Email address tinwee_at_biomed.nus.sg
• URL http//biomed.nus.sg80/welcome.html

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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

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Internet Access in Singapore

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

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Power of the Internet and Emergence of WWW

• Hypertext
• Ted Nelsons Project Xanadu (1969)
• CDROMs and Hypermedia
• Distributed Hypertext
• Distributed Hypermedia
• Mosaic, Netscape, Internet Explorer

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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
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Hypermedia CDROMs

• Ted Nelsons visionary ideas in 1969
• Project Xanadu
• Combine Text with Graphics, Pictures, Audio,
  Video, Movie clips etc
• CDROMs

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

• Document File Name
• Internet Address

Tim Berners-Lee CERN, Geneva
Uniform Resource Locator http//www.sg/welcome.ht
ml http//www.whitehouse.gov/welcome.au http//bio
med.nus.sg/logo.gif
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Mosaic, Netscape, Internet Explorer WWW Browsers
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Web and Documents
Apache Web server
Directory of Files etc etc
Netscape Web browser Form Filling Front end
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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

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Biological Databases

• DNA sequence databases
• Protein sequence databases
• Gene Map databases
• Motifs databases
• Bibliographic databases
• Biochemical databases
• Enzyme databases etc etc

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BioInformaticsStart-Ups in USA - market hype
PharmasRush
???
EBI
ICGEBnet
NCBI
EMBnet/EMBL
Advanced networking
Biocomputing
Internet boom
Genetic Revolution
1970s
1980s
1990s
2000s
NABBINet
Australian Institutes
APBioNet
IMCB
DDBJ
ANGIS
BIC
GenomeNet
PekingU BC/HKBIC
India
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Parallel Development
APEC Survey
APAN- APBioNet
NUS bionetwork
BIC
EMBnet- APBioNet
ASTNET
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
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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