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BMS2062
Introduction to
Bioinformatics
Use of information technology and
telecommunications in bioinformatics
Topic 1: Practical uses of Internet services
Ros Gibson
IT Staff
• Lecturer:
Ros Gibson
[email protected]
• Demonstrators :
IT - Silvia and Natalia
Biomed
http://www.sims.monash.edu.au/subjects/bms2062/
Slides prepared by Kathy Lynch (SIMS, Monash University) with modifications by Ros Gibson.
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IT module assessment
• Numerous small practical tasks
• Multiple Choice questions in exam
• Web page and PowerPoint Presentation
layouts and interface (not content)
Attendance:
• the roll will be marked each practical class
Slides prepared by Kathy Lynch (SIMS, Monash University) with modifications by Ros Gibson.
•Kathy Lynch, SIMS. Monash University
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Module outline
Lectures:
• Practical uses of internet services (22/7)
• Internet, web and multimedia (28/7)
• Digitised images and image compression (29/7)
Practical:
• Practical use of internet services (Week 2)
• Web pages – design and use (Week 3)
• Using PowerPoint (Week 4)
Questions?
OK, let’s start…………..
Slides prepared by Kathy Lynch (SIMS, Monash University) with modifications by Ros Gibson.
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Practical uses of Internet services
Biologists are one of the largest research
communities using the Internet. The
internet provides
• a simple means to distribute data
• allows easy access to data sources and
analysis services.
Overview
• Communication and information
• The Internet as a communication means
• Protocols, Internet and Web services
Slides prepared by Kathy Lynch (SIMS, Monash University) with modifications by Ros Gibson.
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Communication
and information
Communication is
• “The imparting or interchange of thoughts,
opinions or information by speech, writing, or
signs”
• “The science or process of conveying information
especially by electronic or mechanical means”
(www.macquariedictionary .com.au)
• Purposes business / social interaction / infotainment /
education / research / personal fulfillment
• Immediacy
• Distance
• Power / impact / effectiveness
Slides prepared by Kathy Lynch (SIMS, Monash University) with modifications by Ros Gibson.
•Kathy Lynch, SIMS. Monash University
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Communication
Representation
• Physical objects / actuality
• Written /spoken words
• Sound - music, sound effects
• Pictures - diagrams, photographs, charts,
maps, animated pictures, moving pictures
Transmission
• Direct: Face-to-face contact (speech/non verbal), telephone
• Indirect: Radio, Printed word/pictures newspapers/books/magazines/etc, film/TV
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Slides prepared by Kathy Lynch (SIMS, Monash University) with modifications by Ros Gibson.
Issues
• What method of representation is the
most accurate and appropriate for the
intended information?
• What method of transmission is the
most effective and efficient?
• How suitable are the different
representation and transmission methods
to the needs and capabilities of the
sender and receiver - in particular in
bioinformatics ?
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Slides prepared by Kathy Lynch (SIMS, Monash University) with modifications by Ros Gibson.
Same information - different
representations
During the LAG PHASE, the
bacteria in the original
inoculum adapt to their new
environment (e.g. synthesise
enzymes required for
growth). The number of cells
does not increase during this
time . During the
EXPONENTIAL or
LOGARITHMIC PHASE of
growth, the number of
bacteria doubles at regular
intervals. During the
STATIONARY PHASE, the
bacteria have exhausted one
or more critical requirements
for growth. Growth slows as
wastes accumulate and/or
nutrients are depleted.
Growth curve of E.coli in batch culture
Time (h):
Viable cells/ml:
1.0
3.2x10 1
2.0
2.58x10 2
3.0
2.11x10 3
4.0
2.04x10 4
5.0
1.90x10 5
6.0
1.71x10 6
7.0
1.42x10 7
8.0
8.70x10 7
9.0
1.04x10 9
10.0
9.68x10 8
11.0
1.03x10 9
12.0
4.45x10 8
Slides prepared by Kathy Lynch (SIMS, Monash University) with modifications by Ros Gibson.
•Kathy Lynch, SIMS. Monash University
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Communication
and the Internet
• The Internet is a relatively new form of
communication
• It is perceived as a means of
communicating
• Standards and expectations are still being
developed
But what is the Internet?
Slides prepared by Kathy Lynch (SIMS, Monash University) with modifications by Ros Gibson.
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What is the Internet?
Standard definition:
• The interconnection of networked computers.
• A computer network is a group of two or more
computers that are connected together and are
able to share resources (hardware/software/data)
• The Internet is the world’s largest computer
network, connecting thousands of networks and
millions of computers all over the world enabling
a global sharing of information.
Slides prepared by Kathy Lynch (SIMS, Monash University) with modifications by Ros Gibson.
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A little Internet history
• 1969 - ARPANet installed (4 nodes)
• 1972 - introduction of email, telnet and
TCP/IP, (32 servers)
• 1973 - first international connections
• 1980 - hypertext concept developed by
Tim Berners-Lee (CERN)
• 1989 - 100,000 users
• 1990 - Hypertext program commercialised
• 2002 - 605.60 million users
References:
www.nua.ie/surveys/how_many_online/
www.webopedia.com/quick_ref/timeline.asp
Slides prepared by Kathy Lynch (SIMS, Monash University) with modifications by Ros Gibson.
•Kathy Lynch, SIMS. Monash University
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Some Internet basics
• Computers on the Internet use a number of
protocols or rules to send and received
‘packets’ of data.
• TCP/IP – Transmission Control Protocol /
Internet Protocol, is the main suite of protocols
used on the Internet. It allows for the connection
(and understanding) between two hosts to
exchange data
• An internet address or IP address is a unique
address of a computer linked to the Internet. IP
address are technically a series of numbers, eg
130.194.11.125
Slides prepared by Kathy Lynch (SIMS, Monash University) with modifications by Ros Gibson.
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The Web is NOT the Internet
The INTERNET
•Text based
The WEB
•Graphical
•Multimedia capabilities
http://www. webopedia.com/DidYouKnow/Internet/2002/Web_vs_Internet.asp
Slides prepared by Kathy Lynch (SIMS, Monash University) with modifications by Ros Gibson.
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What is the Web?
• “A system of Internet servers that support specially
formatted documents.”
(www.webopedia.com/TERM/W/World_Wide_Web.html)
• The documents are formatted using the basic language of
the Web; HTML / hypertext markup language. (XML is the
new language of the Web)
• Allows for the transfer of information (documents) with
consistent and quality appearance regardless of the
operating system e.g. Windows, Mac, Unix.
• Documents use links or hyperlinks to other content.
• Web documents may contain graphics, sounds, text and
video (GUI).
• The Web is uncontrolled but there are standards, eg W3
consortium.
Slides prepared by Kathy Lynch (SIMS, Monash University) with modifications by Ros Gibson.
•Kathy Lynch, SIMS. Monash University
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Some Web basics
• A URL is the Universal (or uniform) Resource
Locator for a file on the Web. It usually contains
the domain name of the organisation, the type of
organisation and country
www.sims.monash.edu.au
.edu, .gov, .com, .org, .net, .mil
.au, .at, .uk, .fr, .jp, .de.
• Email addresses are based on domain names, eg
[email protected]
• Prefixing the URL is the type of protocol used for
transmission; http, ftp
http://www.monash.edu.au
• Home page has filename of index.html
(index.htm , or default.html / .htm )
Slides prepared by Kathy Lynch (SIMS, Monash University) with modifications by Ros Gibson.
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How it all works
• Client computer (nodes)
• Servers (hosts)
• Protocols - rules and regulations for
transmitting the data – which then allows
for a number of different services
Slides prepared by Kathy Lynch (SIMS, Monash University) with modifications by Ros Gibson.
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Internet and Web services
•
•
•
•
•
•
•
•
ftp and archie
telnet
http
Email (SMTP)
Web searching
audio – video – text conferencing
discussion lists (threaded and listservs)
rich media; video, audio, virtual reality,
3D modeling/simulations
Slides prepared by Kathy Lynch (SIMS, Monash University) with modifications by Ros Gibson.
•Kathy Lynch, SIMS. Monash University
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Service: ftp
[1]
file transfer protocol (an Internet service)
• Transfers any sort of file between local
and a remote computer. A file can
contain just about anything – text,
image, video, sound, source code …
• Often uses anonymous ftp
(prac activity)
Slides prepared by Kathy Lynch (SIMS, Monash University) with modifications by Ros Gibson.
Service: ftp
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[2]
Need to know:
• the domain name or IP address of the
computer, and the pathname of where
the files are located.
• ASCII (text, source code) or binary
(executable, application files,
compressed files) file type. (Common
type is Binary)
• the file type compatibility (operating
system, application)
Slides prepared by Kathy Lynch (SIMS, Monash University) with modifications by Ros Gibson.
Service: ftp
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[3]
using WS_FTP LE ftp.monash.edu.au/pub/
Slides prepared by Kathy Lynch (SIMS, Monash University) with modifications by Ros Gibson.
•Kathy Lynch, SIMS. Monash University
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Service: ftp
[4]
using a Web browser
ftp://ftp.monash.edu.au/pub/
Slides prepared by Kathy Lynch (SIMS, Monash University) with modifications by Ros Gibson.
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Service: archie
• Project of the McGill University School of
Computer Science.
• A tool that allows you to perform keyword
searches on a database for files available on the
Internet through anonymous ftp.
• Most archie servers are now accessed using a
web browser
• Some search engines provide facilities for finding
ftp files
e.g. www.alltheweb.com
Slides prepared by Kathy Lynch (SIMS, Monash University) with modifications by Ros Gibson.
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Service: telnet
• A terminal emulation program – connects
the users computer to a server on the
network
• Enter commands on the users computer
connected using telnet and it works as if
you were at the server’s console
Slides prepared by Kathy Lynch (SIMS, Monash University) with modifications by Ros Gibson.
•Kathy Lynch, SIMS. Monash University
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Service: http
Hyper text transfer protocol (a Web service)
Web browsers
• Two common examples include Internet Explorer
and Netscape Communicator
• Contact and retrieve content from a server
• Display the content
• View, compose and manage email, address book,
diary information, and html documents
• Navigate through content
• https – now available which has additional
security
(Developing web content is covered in IT Module - lecture 2)
Slides prepared by Kathy Lynch (SIMS, Monash University) with modifications by Ros Gibson.
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Service: email
Electronic mail (an Internet service)
• Messages sent from the client to the server and
from one server to another using SMTP protocol
(Simple Mail Transfer Protocol)
• Messages are then retrieved by an email client
on the users computer (e.g. Outlook Express or
Netscape Messenger) using either POP (Post
Office Protocol) or IMAP (Internet Message
Access Protocol).
• Text interface has been superceded by a Web
interface
Slides prepared by Kathy Lynch (SIMS, Monash University) with modifications by Ros Gibson.
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Service: others
• Synchronous audio – video – text
conferencing (chat)
• Instant messaging (internet relay chat)
• Discussion lists (threaded and listservs /
usernet)
• Rich media uses: video, audio, virtual
reality, 3D modeling/simulations
Slides prepared by Kathy Lynch (SIMS, Monash University) with modifications by Ros Gibson.
•Kathy Lynch, SIMS. Monash University
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Rich media
• VRML (Virtual Reality Modeling Language)
http://www.nyu.edu/pages/ mathmol/library/dna/dna.wrl
(Requires Cosmo World View Player)
• Web microscope
http://micro.magnet.fsu.edu/optics/ intelplay/ liveview/index.ht
ml
• General advertising
http://www.macromedia.com/resources/ richmedia/examples/
Slides prepared by Kathy Lynch (SIMS, Monash University) with modifications by Ros Gibson.
Web searching
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[1]
Search Engines
• Web-crawlers / spiders: Automatically browse
web pages for data. This data is then used as
a listing from which a user searches
• Human indexes: Web site administrators (or
similar) submit a short description about the
site/page. This data is then used as a listing
from which a user searches
• Hybrid Search Engines: Search engines today
commonly use a combination of web-crawlers
and human indexes
Slides prepared by Kathy Lynch (SIMS, Monash University) with modifications by Ros Gibson.
Web searching
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[2]
Ranking:
• One of the the main rules in a ranking
algorithm involves the location and frequency
of keywords on a web page.
Popularity:
• Relates to the number of other sites that link
to the site
The tools:
• Databases
• Indexes (title, major heading, body text, ‘deep crawl’)
• Metadata (keywords, author, description)
Slides prepared by Kathy Lynch (SIMS, Monash University) with modifications by Ros Gibson.
•Kathy Lynch, SIMS. Monash University
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Web searching
[2]
Using the data:
• Hyperlinks
• Saving to local computer
• Inserting into own work (files, links)
Points to Consider
•
•
•
•
Plagiarism
Copyright
Validity
Citation Manager
Slides prepared by Kathy Lynch (SIMS, Monash University) with modifications by Ros Gibson.
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The last 60 minutes…..
• What was it about – you tell me
• What didn’t you understand?
Slides prepared by Kathy Lynch (SIMS, Monash University) with modifications by Ros Gibson.
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What’s next
• Week 2 Monday lecture:
The Internet and multimedia
• Week 2 Tuesday lecture:
Digital images and image compression
• Week 2 practical:
Internet services
• Bring a floppy disk
• Read through prac exercises before class
Slides prepared by Kathy Lynch (SIMS, Monash University) with modifications by Ros Gibson.
•Kathy Lynch, SIMS. Monash University
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Resources
Cosmo World View Player (12 MB)
www.cai.com/cosmo/
Slides prepared by Kathy Lynch (SIMS, Monash University) with modifications by Ros Gibson.
•Kathy Lynch, SIMS. Monash University
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