Transcript internet - Bioinformatics Modules for Life Sciences Teaching, NUS

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
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Database Searching
Sequence Alignment
Gene finding
Functional Genomics
Protein Classification
Phylogenetic inference
Computing
Technology
Internet
What is a Computer?
User Interface
E.g.Microsoft Office
Software Applications Powerpoint, Eudora, Excel
Operating System
Win95, Win98,
Unix, VMS
Hardware
CPU, Memory,
Harddisk, I/O interface
Printer
Speaker
Peripherals
Scanner
DiskDrive
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
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
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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
PC
Standalone Computer
Printer
A typical setup at home
Speakers
LAN
A Small Local Area Network
of two computers
and one printer
in 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?
ISP
Internet Service
Provider
IAP
The INTERNET
Internet Access
Provider
ILC
International
Leased
Circuit
Local Phone Company
Telephone
Line
Modem
Office connection to Internet?
ISP
Internet Service
Provider
IAP
The INTERNET
Internet Access
Provider
ILC
International
Leased
Circuit
Local Phone Company
Leased Telephone
Line
Office Local Area Network
Router
What can you do with Internet?
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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
Front end
Application
Client Application
Connected by Network
Communicating by a Protocol
CPU/Harddisk
Server software
Same Machine
Separate Machines
Remote
BackEnd
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
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IP number
Userid
Domain Name
Email address
137.132.9.61
tinwee
biomed.nus.sg
[email protected]
• URL http://biomed.nus.sg:80/welcome.html
Internet Access in Singapore
For Dialup, you will need:
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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
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Pacific Internet
Cyberway
Singnet
Internet resellers
Through Singapore ONE
NUS, NTU and other educational institutions
Power of the Internet and
Emergence of WWW
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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 fox
jumps over
the fence
Fence
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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 quick
brown fox
leaps
over the
fence again.
Distributed Hypertext
World Wide Web of Information Servers
the quick
brown fox
leaps
over the
fence again.
Client Netscape Web Browser application
Distributed
Hypertext/Hypermedia
Document File Name
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Internet Address
Tim Berners-Lee
CERN,
Geneva
Uniform Resource Locator:
http://www.sg/welcome.html
http://www.whitehouse.gov/welcome.au
http://biomed.nus.sg/logo.gif
Mosaic, Netscape, Internet
Explorer WWW Browsers
Web and Documents
Apache Web server
Netscape Web browser Form
Filling Front end
Directory of Files
etc etc
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
Biological Databases
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DNA sequence databases
Protein sequence databases
Gene Map databases
Motifs databases
Bibliographic databases
Biochemical databases
Enzyme databases etc etc
EBI
BioInformatics
Start-Ups in
USA market hype
Pharma’s
Rush
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ICGEBnet
NCBI
EMBnet/EMBL
Advanced
networking
Biocomputing
Internet boom
Genetic
1970s
1980sRevolution
1990s
2000s
NABBINet
Australian
Institutes
IMCB
APBioNet
India
DDBJ
ANGIS
BIC
GenomeNet
PekingU BC/HKBIC
Parallel Development
NUS bionetwork BIC ASTNET
Bioinformatics
Infrastructure
Development
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APEC
Survey
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Synergy
Network
Infrastructure
Development
APNG
AI3
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APANAPBioNet APBioNet
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Push-Pull
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APAN SINGAREN
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APANAPBioNet
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TRANSPAC
EMBnetAPBioNet
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