Information technology deals with the use of electronic computers and computer software to process data and information. It has many applications including e-commerce, healthcare, weather forecasting, computational biology, and environmental management. The internet is a worldwide network that connects billions of computers and allows for sharing of resources and information across large distances. It has transformed how people communicate and access information.

1. A. COMPUTER APPLICATION

2. 1).
Computer in Science with special
reference to Biology, the scope and
prospects.

3. OVERVIEW OF INFORMATION
TECHNOLOGY
• The term "information technology" or "infotech" evolved in the
1970s
• computer and communication technologies are combined.
• Information technology is a general term that describes any
technology which helps to produce, manipulate, store, cummunicate,
and disseminate information.
• According to Information Technology Association of America (ITAA),
Information technology (IT) is "the study, design, development,
implementation , support or management computer-based
information systems, particularly software application and computer
hardware."
• IT deals with the use of electronic computers and computer software
to convert, store, protect, process, transmit and securely retrieve
information.
• In the broadest sense, information technology refers to both the
hardware and software that are used to store, retrieve, and
manipulate information.

4. Scope and applications of Information
Technology
• Computers serve as a powerful information-processing tool. Some of them are:
1. Railways, Air and sea networks
• Are connected with the help of IT.
• The information is very vital for running all these smoothly.
• Even if we do not have information for one minute it may result into a big disaster.
2. E-commerce
• Is one of the largest applications of computers in keeping and managing business
and financial records.
• It helps in transaction of any amount of money from one part of the world to
another.
• We can purchase anything online with the help of debit and credit cards
• Most of the large companies keep the employment records of all their workers in
large databases that are managed by computer programs.
• The other applications are billing to customers tracking payments received and
payments to be made and tracking supplies needed and items produced, stored,
shipped, and sold, etc.

5. 3. Forensics IT (FIT)
• Offers computer and network forensic services in civil and criminal matters.
• FIT provides complete, non-invasive computer investigation, analysis, recovery,
evidence handling and search techniques on computer or network storage
media.
• There are many reasons to employ the techniques of computer forensics:
1) In legal cases, computer forensic techniques are frequently used to analyze
computer systems belonging to defendants (in criminal cases) or litigants (in
civil cases).
2) To recover data in the event of a hardware or software failure.
3) To analyze a computer system after a break-in, for example, to determine how
the attacker gained access and what the attacker did.
4) To gather evidence against an employee that an organization wishes to
terminate.
5) To gain information about how computer systems work for the purpose of
debugging, performance optimization, or reverse-engineering.

6. 4. Agroinformatics
• Offers the solutions to solve the major problems of human world in 21st century
like food problem and preservation of environment and natural resources.
IT in Agriculture include:
• Management of Database in Agriculture Application of the Internet Technology in
Agriculture
• Electronic Commerce in Agriculture
• Education and Training in Agroinformatics
• Rural Communication and Agroinformatics
• Internet Technology in Regional Agriculture
• Agroinformatics in Agricultural Extension Services.
• Precision Agriculture and Information Technology
• Geographic Information System and Global Positioning System.
• Remote Sensing and Image Processing Artificial Intelligence and Expert System
• Modelling Agricultural Systems
• PC Application Software for Agriculture.
5. E-retailing/internet retailing
• combines new technology with store and direct mail model.
• The most common sites in this area are amazon.com, and rediffshopping.com.

7. 6. Computational biology/Bioinformatics:
• It is the application of computer science and allied aspects to
solve the problems of biologists about the mysteries of life.
• It mainly deals with the data emerging form cell, like DNA,
RNA and Protein sequencing.
• Biologists who specialised in the use of computational tools
and systems to answer the problems of biology are
bioinformaticians.
• Computer scientists, mathematicians, statisticians and
engineers who specialize in developing theories and
algorithms and techniques for such tools and systems are
computational biologists.
• Genomics, Proteomics, Computer aided drug design, Bio
Databases and Data Mining, Molecular phylogenetics,
Microarray Informatics and Systems biology are the branches
of Bioinformatics.

8. 7. Computers in Medicine
• Is the most promising result of IT. In the medical field
scanning of body and body organ, drug discovery, drug
design etc. are the important aspects of IT.
• Computer aided drug design has cut the cost and time of
drug discovery with great effect.
• It is possible to select candidate drug molecule from huge
available databases and check whether it can bind to the
active site of the troublesome molecule using the docking
softwares like Gold, ArgusLab, Hex, and Autodock .
• A small number of molecules from a few dozens thus
predicted computationally only have to be passed for
clinical tests and trials.

9. 8. Weather forecasting
• Is to predict the state of the atmosphere for a future time and
a given location.
• The National Centre Medium Weather Forecasting (NCMRWF)
is a premier institution of India to render Agro Advisory
Services (AAS) to farmers, providing a medium weather
forecast.
• A major part of modern weather forecasting is used to give
the severe weather alerts and advisories for air traffic,
military, utility companies like gas and electricity.
9. Healthcare
• Applications of IT fall into three main categories:
1) administrative and financial systems that facilitate billing,
accounting, and other administrative tasks.
2) clinical systems that facilitate or provide input into the care
process and
3) infrastructure that supports both the administrative and
clinical applications.

10. Technologies used in healthcare information technology are:
1) Electronic health record (EHR): an electronic file cabinet for patient data from
various sources.
2) Computerized provider order entry (CPOE): It is a medication ordering and
fulfilment system such as lab orders, radiology studies, procedures,
discharges,transfers, and referrals.
3) Clinical decision support system (CDSS): provides physicians and nurses with
real-time diagnostic and treatment recommendations.
4) Picture archiving and communication system (PACS): captures and integrates
diagnostic and radiological images from various devices (e.g., X-ray, MRI,
computed tomography scan), stores them, and disseminates them to a medical
record, a clinical data repository, or other points of care.
5) Radio frequency identification (RFID): tracks patients throughout the hospital,
and links lab and medication tracking through a wireless communication system
6) Automated dispensing machines (ADMs): This technology distributes medication
doses
7) Electronic materials management (EMM): track and manage inventory of
medical supplies, pharmaceuticals, and other materials.
8) Interoperability: This concept refers to electronic communication among
organizations so that the data in one IT system can be incorporated into another

11. 10. Business Process outsourcing (BPO)
• for product and business related customer provides superior customer service and
reduces cost of operation.
11. IT in Environment management:
• Global nature of environment concern makes it necessary for all to be familiar
with world geography and culture.
• Information technology (IT) makes this an easy task through worldwide
network.
• There are many government and private network to manage and provide
information about biodiversity in each and every country.
• Some important environmental networks are:
1. The Canadian Environmental Network (CEN)
• Is an organization forEnvironmental non-Governmental Organizations (ENGOs)
located across Canada.
• This non-profit organization is mainly funded by Environment Canada and helps
to facilitate networking and communication between environment
organizations, and coordinate ENGO participation in consultations with
government.
• The CEN also works to educate the public on major issues and policy-making in
regards to the environment. http://www.cen-rce.org

12. 2. World Conservation Monitoring Center (WCMC)
• Is collaboration between UK based charity, WCMC 2000 and the United Nations
Environment Programme.
• The functions of WCMC are Monitoring compliance with international agreements
in the field of biodiversity conservation of nature and natural resources;
• Promoting the formation and implementation by appropriate bodies of policies
concerning the conservation of nature and natural resources,
• compiling data on matters of relevance to the conservation of nature and natural
resources,
• promoting establishment of national and regional conservation data centers,
particularly in developing countries,
• with a view to increasing access to reliable information for enlightened
management in the field of the conservation of nature and natural resources:
• Storing, processing, analyzing and interpreting such data with a view to increasing
the fund of knowledge and
• understanding relating to the conservation of nature and natural resources and
• Monitoring developments in and
• identifying areas of particular concern in the field of the conservation of nature and
natural resources.
• http://www.wcmc.org.uk

13. 3. The National Biodiversity Data Centre
• Is the national centre dedicated to the collation, management, analysis and
dissemination of data and information on Ireland's biological diversity.
• It serves as a hub for the exchange of data between governmental
organizations, Non-governmental organizations, research institutions and
volunteer recorders.
• http://www.biodiversityireland.iel
4. The National Biological Information Infrastructure (NBII)
• Is a broad,collaborative program to provide increased access to data and
information on the nation's biological resources.
• The NB II links diverse, high-quality biological databases, information products,
and analytical tools maintained by NB II partners and other contributors in
government agencies, academic institutions, non-government organizations,
and private industry.
• NBII examines the priority biological resources challenges specific to various
regions of the United States, and places special emphasis on providing content
relevant to those challenges.
• http://www.nbii.gov/portal/server.pt/community/nbii_home/236

14. 5. Environmental Information System (ENVIS):
• The ENVIS centers work for generating a network of database
in area like pollution control, clean technologies, remote
sensing, coastal ecology, biodiversity, Western Ghats and
Eastern Ghats, environmental management, media related to
environment, renewable energy desertification, mangroves,
wildlife, Himalayan ecology, mining etc.
Further remote sensing satellite provide useful services through
IT in soil resource management, crop health monitoring,
production, forecasting, monitoring in seasonal agricultural
process, watershed management, forest cover etc. Thus IT
helps in extraction of environmental information for
awareness education, and conservative action at individual
level.

15. 2). Information Super Highway
( INTERNET )
Information Net Works :
• INTERNET
• WORLD WIDE WEB
• WEB BROWSERS
• HTTP
• HTML
• URLs
• Biological Networks

16. INTERNET

17. WHAT IS THE INTERNET ?
• The Internet or “Net” (network of networks) is the
largest computer network in the world that connects
billions of computer users.
• The word internet comes from combination between
“interconnection” and “Network”.
• Network is a collection of computers and devices
connected via communication channels and
transmission media allow to share resources
(hardware, software, data, information).
• Generally nobody own internet.
• The vast collection of computer networks which form
and act as a single huge networks for transport of data
and messages across distances which can be anywhere
from the same office to anywhere in the world

18. • The internet is made up of millions of computers linked
together around the world in such a way that information can
be sent from any computer to any other 24 hours a day.
• It is also known as “loose connection of related networks”
• These computers can be in homes, schools, universities,
government departments, or businesses small and large. They
can be any type of computer and be single personal
computers or workstations on a school or a company
network.
• The internet is often described as 'a network of networks'
because all the smaller networks of organizations are linked
together into the one giant network called the internet.
• All computers are pretty much equal once connected to the
internet, the only difference will be the speed of the
connection which is dependent on your Internet Service
Provider and your own modem.

19. • The Internet can be seen as having two major
components: network protocols and hardware.
• The protocols, such as the TCP/IP suite, present sets of rules
that devices must follow in order to complete tasks.
• Without this common collection of rules, machines would not
be able to communicate.
• The protocols are also responsible for translating the
alphabetic text of a message into electronic signals that can
be transmitted over the Internet, and then back again into
legible, alphabetic text.
• The process of transferring information from once device to
another relies on packet switching. Each computer connected
to the Internet is assigned a unique IP address that allows the
device to be recognized.
• When one device attempts to send a message to another
device, the data is sent over the Internet in the form of
manageable packets.

20. • Each packet is assigned a port number that will connect it to
its endpoint.
• A packet that has both a unique IP address and port number
can be translated from alphabetic text into electronic signals
by travelling through the layers of the OSI model from the
top application layer to the bottom physical layer.
• The message will then be sent over the Internet where it is
received by the Internet service provider's (ISP) router. The
router will examine the destination address assigned to each
packet and determine where to send it.
• Eventually, the packet reaches the client and travels in reverse
from the bottom physical layer of the OSI model to the top
application layer.
• During this process, the routing data -- the port number and
IP address -- is stripped from the packet, thus allowing the
data to be translated back into alphabetic text and
completing the transmission process.

21. • Hardware, the second major component of the
Internet, includes everything from the computer
or smartphone that is used to access the Internet to the
cables that carry information from one device to
another.
• Additional types of hardware include satellites, radios,
cell phone towers, routers and servers.
• These various types of hardware are the connections
within the network.
• Devices such as computers, smart phones
and laptops are end points, or clients, while the
machines that store the information are the servers.
• The transmission lines that exchange the data can
either be wireless signals from satellites or 4G and cell
phone towers, or physical lines, such as cables and fiber
optics.

22. HISTORY
• ARPA – Advanced Research Project Agency.
• 1969 January 2 – started an experimental Computer Network.
• Concept – No Server, but equal importance/participation to every
computer in the Network.
• Even if, one or two node destroyed that will not affect the Network.
• In 1982 the word internet started.
• 1986: First “freenet” created in Case Western Reserve University
• 1991: US government allowed business agencies to connect to
internet.
• Now all peoples can connect to internet and improve their life and
work quality.
• The internet support various aspects in our life.
• Father of Internet- Vinton CerfVinton Cerf
• Co-designer of the TCP/IP networking protocol.

23. Father of Internet Vint Cerf
Born June 23, 1943 New Haven, Connecticut
Citizenship American
Fields Computer science
Institutions IBM, UCLA, Stanford University, DARPA, MCI, CNRI, Google
Known for TCP/IP Internet Society
Notable awards Presidential Medal of Freedom Turing Award

24. Uses of the Internet
• In general, the Internet can be used to communicate across
large or small distances, share information from any place in
the world and access information or answers to almost any
question in moments.
• Some specific examples of how the Internet is used include:
• E-mail and other forms of communication, such Internet
Relay Chat (IRC), Internet telephony, instant messaging, video
conferencing and social media;
• education and self-improvement through access to online
degree programs, courses and workshops and
• searching for jobs -- both the employer and applicant use the
Internet to post open positions, apply for jobs and recruit
individuals found on social networking sites like LinkedIn.

25. • Other examples include:
• Online discussion groups and forums
• Online dating
• Online gaming
• Research
• Reading electronic newspapers and magazines
• Online shopping

26. Frequent Uses of Internet
• World wide web E mail
• FTP Web chat
• News group Usenet
• Telnet Bulletin boards
• Fax (facsimile) Telephony
• Collaborative multimedia computing Net show
• Virtual corporation Telecommunicating
• Commercial videoconferencing Telephone
conferencing
• Other forms of conferencing Net meeting

27. Internet Basics
• IP Number : An unambiguous way to specify a single
computer
• IP address is made up of four numbers.
• Example : IP address for the main server at NCBI
(National Center for Biotech. Information) at NIH is
130.14.25.1
• Left to right 130.14 = NIH .25 = Library of Medicine & .1
= The machine itself
• FQDN (Fully Qualified Domain Name) :
ncbi.nlm.nih.gov
Computer.domain
• In 1981 – 213 hosts In 2001- 60 Mn Live hosts
• Doubling time for the no. of hosts is 18 months

28. Top Level Domain Names
• .com Commercial site
• .edu Educational site
• .gov Government site
• .mil Military site
• .net Gateway or network host
• .org Private (usually nonprofit) organizations
Domain names used outside US…
• .ca Canadian site
• .ac.uk Academic site in UK
• .ac.in Academic site in India
• .co.in Commercial site in India

29. GENERIC TOP LEVEL DOMAINS
PROPOSED BY IAHC :
(International Ad Hoc Committee)
• .firm Firms or businesses
• .shop Businesses offering goods to purchase
(stores)
• .web Entities emphasizing activities relating to
the World Wide Web
• .arts Cultural and entertainment organizations
• .rec Recreational organizations
• .info Information sources
• .nom Personal names (e.g., yourlastname.nom)

30. Connecting to the internet
What You Will Need…….
• A STANDARD COMPUTER - this can be a Personal
Computer (PC) .The computer itself doesn't have to
be a high powered machine to access most things
on the internet but to properly experience some of
the newer multimedia dealing with sounds, digital
movies and interactive software however, you may
require one of the more powerful machines
available.

32. • A MODEM - which takes the digital information
from your computer, converts it to an analog
signal so that it can travel over the telephone
lines to another modem at the other end which
then coverts it back into digital information for
the receiving computer. Modems can be either
internal (inside your computer) or external
(linked by a cable). Modems are rated by the
speed that they are able to send and receive
information.

34. • A TELEPHONE LINE - a separate telephone line
is preferable as you are unable to make voice
telephone calls when you are connected and
people will receive a busy signal if they are
trying to call you - unless you have call waiting
where you will then lose your internet
connection and your telephone will ring for you
to pick up. This can be pretty annoying if you
are in the middle of downloading a 10MB file.

36. • AN INTERNET ACCESS ACCOUNT - which you can obtain
through an Internet Service Provider. The Internet Service
Provider that you choose will provide you with disks or paper
instructions on how to set up your internet connection. With
this type of set up you pay for the time that you use the
internet. Either a fixed amount for a fixed amount of time or
on a per usage basis.
• Once you are connected to the internet you will need a few
extra things such as Web Browser software and Email
Software which you can download or purchase from a
software supplier.
• In order to explore the web you will need a special piece of
software known as a web browser. The two most commonly
used web browsers are Netscape Navigator and Internet
Explorer. They both operate in a similar manner using menus
and buttons to help you navigate around the web.

38. Internet Service Providers (ISPs)
• Small ISPs hook into regional ISP, which themselves
link into major backbones.
• In order to get online, we need to contract with ISP
to deliver an internet connection through our
modem.
ISPs in India :
• Videshsancharnigamlimited (VSNL)
• MTNL
• Satyamonline
• Icenet etc.

39. • Internet connection type
• Dial Up : Oldest and most widely used type
• ISDN (Integrated Service Digital Network) :Much
faster. Voice, data, pictures, videos etc can be
transmitted quickly.
• Leased line : 9.6 Kbps – 155 Mbps
• Internet over cable
• DSL ( Digital Subscriber Line )

40. Security and the Internet
• Large amounts of information, both public and private, is
collected across the Internet, opening users up to the risk
of data breaches and other security threats.
• Hackers and crackers can break into networks and systems
and steal information such as login information or bank and
credit card account records. Some steps that can be taken to
protect online privacy include:
• Installing antivirus and antimalware
• Creating difficult, varied passwords that are impossible to
guess.
• Using a virtual private network (VPN) or, at least, a private
browsing mode, such as Google Chrome's Incognito window.
• Only using HTTPS
• Making all social media accounts private.
• Deactivating autofill.
• Turning off the device's GPS.

41. • Updating cookies so an alert is sent anytime a cookie is
installed.
• Logging out of accounts instead of just closing the tab or
window.
• Using caution with spam emails and never opening or
downloading content from unknown sources.
• Using caution when accessing public Wi-Fi or hotspots.
• Additionally, there is an element of the Internet called
the dark web. The dark web is hidden and inaccessible
through standard browsers.
• Instead, it uses the Tor and I2P browsers which allow users to
remain entirely anonymous.
• While this anonymity can be a great way to protect an online
user's security and free speech or for the government to keep
classified data hidden, the dark web also creates an
environment that facilitates cybercrime, the transfer of illegal
goods and terrorism.

42. Benefits of the Internet
• Access to endless information, knowledge and education.
• An increased ability to communicate, connect and share.
• The ability to work from home, collaborate and access a global
workforce.
• The chance to sell and make money as a business or individual.
• Access to an unlimited supply of entertainment sources, such as
movies, music, videos and games.
• The ability to amplify the impact of a message, allowing charities
and other organizations to reach a wider audience and increase
the total amount of donations.
• Access to the internet of things (IoT), which allows home
appliances and devices to connect and be controlled from a
computer or smartphone.
• The ability to save data and easily share files with cloud storage.
• The ability to monitor and control personal accounts instantly,
such as bank accounts or credit card bills

43. WWW
WORLD WIDE WEB

44. • Limitations of FTP : one can only see the names of the
directory/files.
• The contents within the files can not be viewed.
• For that, downloading is necessary.
• Development of DDDS (distributed document delivery
systems )
• WWW is the most evolved DDDS.
• Research at CERN (european nuclear research council) in 1989
led the development of www.
• It began in the late 1980's when physicist Dr. Berners-Lee
wrote a small computer program for his own personal use.
• This program allowed pages, within his computer, to be linked
together using keywords.
• It soon became possible to link documents in different
computers, as long as they were connected to the Internet.

45. • The document formatting language used to link documents is
called HTML (Hypertext Markup Language.)
• The Web remained primarily text based until 1992.
• Two events occurred that year that forever changed the way
the Web looked.
• Marc Andreesen developed a new computer program called
the NCSA Mosaic and gave it away! The NCSA Mosaic was the
first Web browser.
• The browser made it easier to access the different Web sites
that had started to appear.
• Soon Web sites contained more than just text, they also had
sound and video files.
• The development of the WWW has been the catalyst for the
popularity of the internet and is also the easiest part of the
internet to use.
• We now have Internet Chat, Discussion Groups, Internet
Phone capabilities, Video conferencing, News Groups,
Interactive Multimedia, Games and so much more.

47. CONCEPT OF WWW
URL
• Uniform resource locator
• The last part of the puzzle required to allow the web to work is a
URL.
• This is the address which indicates where any given document lives
on the web
HTML
• Hypertext markup language
• A standardized system for tagging text files to achieve font, color,
graphic & hyperlink effects on WWW pages.
HTTP
• Hypertext Transfer Protocol
• This protocol requests the 'HTML' document from the server and
serves it to the browser.

48. HYPERLINK:-
• A hyperlink is a word, phrase, or image that you can click on to
jump to a new document or a new section within the current
document.
• Hyperlinks are found in nearly all Web pages, allowing users to
click their way from page to page. Text hyperlinks are often blue
and underlined
HYPERTEXT:-
• Hypertext is text that links to other information. By clicking on a
link in a hypertext document, a user can quickly jump to different
content.
• Hypertext is usually associated with Web pages. Today nearly
every web page includes links to other pages and both text and
images can be used as links to more content
WEB PAGE:-
• A web page or webpage is a resource of information that is
suitable for the world wide web and can be accessed through a
web browser.
• This information is usually in HTML or XHTML format and may
provide navigation to other web pages via hypertext links.

49. World Wide Web Components
Structural Components :
• Clients/Browsers – to dominant implementations.
• Servers – Run on sophisticated hardware.
• Caches – Many interesting implementations.
• Internet – The global infrastructure which facilitates
data transfer.
Semantic Components :
• Hyper Text Transfer Protocol (HTTP)
• Hyper Text Markup Language (HTML)
• Extensible Markup Language (XML)
• Uniform Resource Identifiers (URIs)

50. The Fundamental Concept of
World Wide Web
The Hypertext Concept :
• Hypertext is text which contains links to other
texts. The term was first coined by Ted Nelson
around 1965 .
The Hypermedia Concept :
• Hypermedia is term used for Hypertext which
is not constrained to be text; it can include
video and sound.

51. Web Browser :
• A web browser is a software program that allows a user
to access, and display web pages. Browsers are used
primarily for displaying and accessing websites on the
internet, as well as other content created using
languages such as Hypertext Markup Language (HTML)
and Extensible Markup Language (XML).
Web Server :
• This program that waits patiently for the browser to
request a Web Page. The servers looks for the
requested information, retrieves it and send it to the
browser or sends an error message if the file is not
found.
Uniform Resource Locator (URL) :
• These are the web addresses. The resource locator is an
addressing system.

52. WEBSITES
• A website is a collection of web pages, images,
videos or other digital assets that is hosted on
one or more web servers, usually accessible via
the internet.
• All publicly accessible web sites are seen
collectively as constituting the world wide web.

53. A) Classification according to STYLE:
Static Website
• A Static Website is one that has web pages stored on the server in
the same form as the user will view them.
• It is primarily coded in HTML and it simply presents pre-defined
information to the user
Dynamic Website
• A Dynamic Website is one that does not have web pages stored on
the server in the same form as the user will view them.
• Instead, the web page content changes automatically
B) Classification according to FUNCTION:
1) Personal website: These are World Wide Web pages created by an
individual to contain content of a personal nature rather than on
behalf of a company, organization or institution.
2) Commercial Websites: A website that generates revenue or cash
flow of any type that isn’t under a non profit organizations filed
with that state.

54. 3) Government Website: These are websites created
by government to cope up with the need of new
generation and make things easily available and
convenient for them as well as the users
4) Not-Profit Organization Websites : These are the
websites which are used by not for profit
organization to promote there cause of work and
spread there work of kindness all over the world to
help more people and also to get more
investments.

55. C) Classification according to Content:

57. Navigation on the WORLD WIDE WEB
• Does not require advanced knowledge of the location of
information.
• Hyperlinks : Clickable items.
• Web Page : Each document displayed on the www is called
web page
• Web Site : Collection of all the related web pages.
• Web Surfing : Navigation through hyperlinks
• Browsers : Programs to view web pages
• URL : Uniform Resource Locator : “ protocol : //
computer.domain ”
• HTTP : Hypertext transfer protocol
• Portal : Web page that can be customized to the needs of user
as he can jump to other sources of news or entertainment.

58. Finding Information on www
• Old fashioned way : Using the list of references or
by following hyperlinks.
• Continuously clicking may be highly ineffective
when desired information is very specific.
• Concept of “virtual library”
1) www virtual library at Harvard
www.mcb.harvard.edu/BioLinks.html
2) EBI bio catalog, at European Bioinformatics Inst.
www.ebi.ac.uk/biocat/biocat.html
3) NAR database collection www.nar.oupjournals.org

59. ADVANTAGES
• Mainly free information.
• Low cost of initial connection.
• Rapid interactive communication.
• Facilitates the exchange of huge volumes of data.
• Has become the global media.
DISADVANTAGES
• Danger of overload & excess information.
• Difficult to filter & prioritize information.
• No guarantee of finding what one is looking for.
• No regulation.
• No quality control over available data.

60. Search Engine
• “A specialized program that performs full text or keyword
searches on databases that catalog web content.”
• Result : in hyperlinked format.
• Web crawling : to capture all the text of every web page.
• Another technique : to capture only title of each web page.
• Therefore different search engines can produce different
results.
• AltaVista : www.altavista.com
• Excite : www.excite.com
• Google : www.google.com
• HotBot : www.hotbot.lycos.com
• Infoseek : www.infoseek.go.com
• Lycos : www.lycos.com
• Northern Light : www.northernlight.com

62. Meta Search Engines
1. They take user’s query and poll anywhere from 5-10 of the
traditional search engines.
2. Collect the results.
3. Filter out duplicates.
4. Return a single list to user.
• “A meta search engine is also known as all in one search engine.
• It performs a search by calling on more than one other search
engine to do the actual work. The results are collected, duplicate
retrievals are eliminated and the results are ranked according to
how well they match your query. You will be then presented a list
of URLs.
• Popular meta search engines:
• Metasearch : www.metasearch.com
• Metacrawler : www.metacrawler.com
• Metafind : www.metafind.com
• savvy search : guaraldi.ca.colostate.edu:2000

63. Internet V/s intranet
• Web : communication between people at distance.
• Same principle can be used to connect people in
the same organization.
• Easy communication. Easy access to information.
• Concept of “paperless industry.”
• Confidential communication between physically
distant people.
• Intranets are protected : other people who don’t
belong to organization can not access the internal
web pages.
• Additional protections using passwords are also
applied.

64. Difference between the World Wide
Web and the Internet
• The key difference between the Internet and the World Wide Web (WWW or the
Web) is that the Internet is a global connection of networks while the Web is a
collection of information that can be accessed using the Internet.
• In other words, the Internet is the infrastructure and the Web is a service on top.
• The Web is the most widely used part of the Internet. Its outstanding feature
is hypertext, a method of instant cross-referencing.
• In most Web sites, certain words or phrases appear in text of a different color than
the rest; often this text is also underlined.
• When a user selects one of these words or phrases, they will be transferred to the
related site or page.
• Buttons, images, or portions of images are also used as hyperlinks.
• The Web provides access to billions of pages of information.
• Web browsing is done through a Web browser, the most popular of which
are Google Chrome, Firefox and Internet Explorer.
• The appearance of a particular Web site may vary slightly depending on the
browser used.
• Later or more updated versions of a particular browser are able to render more
complex features, such as animation, virtual reality, sound and music files.

65. WEB BROWSERS

66. INTRODUCTION
• A Web browser acts as an interface between the
user and Web server
• Software application that resides on a computer
and is used to locate and display Web pages.
• Web user access information from web servers,
through a client program called browser.
• A web browser is a software application for
retrieving, presenting, and traversing information
resources on the World Wide Web

67. FEATURES
• All major web browsers allow the user to open
multiple information resources at the same time,
either in different browser windows or in different
tabs of the same window
• A refresh and stop buttons for refreshing and
stopping the loading of current documents
• Home button that gets you to your home page
• Major browsers also include pop-up blockers to
prevent unwanted windows from "popping up"
without the users consent.

68. COMPONENTS OF WEB BROWSER
1. User Interface
• This includes the address bar, back/forward
button , bookmarking menu etc
2. Rendering Engine
• Rendering, that is display of the requested
contents on the browser screen.
• By default the rendering engine can display
HTML and XML documents and images

69. HISTROY
• The history of the Web browser dates back in to the late
1980s, when a variety of technologies laid the
foundation for the first Web browser, World Wide Web,
by Tim Berners-Lee in 1991.
• Microsoft responded with its browser Internet Explorer
in 1995 initiating the industries first browser war
• Opera first appeared in 1996; although it have only 2%
browser usage share as of April 2010, it has a
substantial share of the fast-growing mobile phone
Web browser market, being preinstalled on over 40
million phones.
• In 1998, Netscape launched Mozilla

70. TYPES OF WEB BROWSER
 Internet Explorer
 Google Chrome
 Tor Browser
 AOL Explorer
 Uc Browser
 Elinks for Mac
 Arlington Kiosk
 Konqueror
 Dillo
 Links
 Epiphany
 Lynx
 Flock
 Maxthon
 Galeon
 Mosaic
 iCab
 Mozilla
 K-Meleon
 Mozilla Firefox
 KioWare
 Netscape
 SeaMonkey
 OmniWeb
 Safari
 Opera
 Microsoft Edge
 Amaya

71. 1.Internet Explorer

72. Internet Explorer
• Internet Explorer (IE) is a product from software giant
Microsoft.
• This is the most commonly used browser in the
universe.
• This was introduced in 1995 along with Windows 95
launch and it has passed Netscape popularity in 1998.
• Currently internet explorer is discontinued by
microsoft.
• Internet Explorer was one of the most widely used web
browsers, attaining a peak of about 95% usage share
during 2002 and 2003.
• Now it holds less than 16% share in worldwide desktop
browser usage.

73. Features:-
● 33 language support.
● Intelligent search suggestion.
● Better find on page.
● Increased performance.
● Smart address bar.
● Reader mode for viewing and uncluttered of
web page.
● History view and private browsing.

74. 2.MIcrosoft Edge

75. MIcrosoft Edge
• Microsoft Edge is a web browser developed by
Microsoft and included in the company's
Windows 10 operating systems, replacing
Internet Explorer as the default web browser
on all device.
• Edge is the default browser on windows 10
with internet explorer on the side.

76. Features of Microsoft edge
● Integration of Cortana.
● Doodle directly on webpage and save to one
note.
● Reading view.
● Integrated Share Panel to share contents on a
web page.
● Weather and important news feed on startup
page.
● Latest version also has Extension support.

77. 3.Netscape Navigator

78. Netscape Navigator
• Netscape Navigator is a discontinued proprietary
web browser, Netscape announced in its first press
release (13 October 1994) that it would make
Navigator available without charge to all non-
commercial users.
• It was the flagship product of the Netscape
Communications Corp and was the dominant web
browser in terms of usage share in the 1990s, but
by 2002 its usage had almost disappeared due to
the increased usage of Microsoft's Internet Explorer.

79. Features of Netscape Navigator
● Ability to use two render engines i.e. Trident or
Gecko.
● Improved Tabbed Browsing.
● Support for live contents like RSS feed.
● Includes Widgets to improve browsing experience
like local weather info, stocks, movie times and
reviews, etc.
● And also features, such as ID Theft Protection and
Spyware Protection have been integrated.

80. 4.Mozilla Firefox

81. Mozilla Firefox
• Firefox is a new browser derived from Mozilla. It
was released in 2004 and has grown to be the
second most popular browser on the Internet.
• It is free and open source.Firefox is available for
Windows, macOS and Linux operating systems, with
its Firefox for Android available for Android.
• Firefox was released in November 2004, and was
highly successful with 60 million downloads within
nine months

82. Features of Mozilla firefox
● 75 language support.
● Powered by gecko engine.
● Private browsing and tabbed browsing.
● Security & high performance.
● Super speed and faster page loading.
● Themes and extension support.
● Inbuilt download manager

83. 5.Google Chrome

84. Google Chrome
• Google Chrome is a freeware web browser developed
by Google and its beta version was first released on
September 2, 2008 for Microsoft Windows.
• As of September 2016, StatCounter estimates that
Google Chrome has a 60% worldwide usage share of
web browsers as a desktop browser.
• Chrome features a minimalistic user interface, with
its user-interface principles later being implemented
into other browsers.
• Chrome also has a reputation for strong browser
performance.

85. Features of Chrome
● 50 language support.
● Theme support.
● New tabs and incognito mode.
● Simple and minimal interface design.
● Fast ,secure.
● Fast startup and page loading.

86. 6.Safari

87. Safari
• Safari is a web browser developed by Apple Inc.
and included in Mac OS X. It was first released as a
public beta in January 2003.
• A mobile version has been included in iOS devices
since the introduction of the iPhone in 2007.
• It is the default browser on Apple devices.
• A Windows version which is now discontinued,was
available from 2007 to 2012.
• Safari has very good support for latest
technologies like XHTML, CSS2 etc.
• It is written in C++.

88. Features of Safari
● Reader mode removes ads and formatting on web page.
● Smarter Address bar .
● Improved support for HTML5.
● Full screen video, closed caption, geolocation.
● Faster Nitro JavaScript Engine.
● Extension Support for customizing browsing experience.
● Private Browsing.
● Text Search & Spell Checking.
● Tabbed Browsing and Pop-up ads Blocking.
● Improved Web Inspector.
● Improved Graphics Hardware acceleration on Windows.

89. 7.Opera Browser

90. Opera
• Opera is smaller and faster than most other
browsers, yet it is full- featured.
• Fast, user-friendly, with keyboard interface, multiple
windows, zoom functions, and more.
• Java and non Java-enabled versions available. Ideal
for newcomers to the Internet, school children,
handicap and as a front-end for CD- Rom and kiosks.
• Opera Mini is a web browser designed primarily for
mobile phones, smartphones and personal digital
assistants.
• It was light weight and most Mobile phones came
preloaded with opera mini.
• It used Java ME platform. Right now opera holds 4.2
% desktop usage share.

91. Features of Opera
● Built-in Tabbed browsing.
● Bookmark bar and Download manager.
● Turbo Mode Compresses webpages upto 80%
before sending to user.
● Faster page loading.
● Incognito mode and Improved Privacy and
security.
● First browser to support Cascading Style Sheets
(CSS).

92. 8.UC Browser

93. UC Browser
• UC Browser is a mobile browser developed by
Chinese mobile Internet company UCWeb and is
owned by AliBaba of China.
• Originally launched in April 2004 for java platform
only Now is available for Android, ios and also
windows.
• It uses cloud acceleration and data compression
technology. This browser is used by more than
400 million users.

94. Features of UC Browser
● Data compression reduces data consumption while
users are browsing.
● supports simultaneous downloads and includes a
download manager. It supports pause-and-resume
downloads.
● It has HTML5 web app and cloud syncing features.
● The cloud system used by the browser distributes
data from the closest servers. As a result, the
loading process is quicker and smoother.
● A "View it later" mode caches web pages with their
videos, images and text for offline viewing.

95. 9.Tor Browser

96. Tor Browser
• Tor works on the concept of Onion routing. Onion routing
resemble to onion in structure.
• In onion routing the layers are nested one over the other
similar to the layers of onion.
• This nested layer is responsible for encrypting data several
times and sends it through virtual circuits.
• On the client side each layer decrypt the data before passing
it to the next level.
• The last layer decrypts the innermost layer of encrypted data
before passing the original data to the destination.
• In this process of decryption all the layers function so
intelligently that there is no need to reveal IP and
Geographical location of User thus limiting any chance of
anybody watching your internet connection or the sites you
are visiting.

97. Features of Tor Browser
● Cross Platform Availability.
● Complex Data encryption before it it sent over Internet.
● It is a combination of Firefox Browser + Tor Project.
● Provides anonymity to servers and websites.
● Makes it possible to visit locked websites.
● Performs task without revealing IP of Source.
● Portable – Run browser directly from the USB Device.
No need to install it.
● Tor is capable of handling thousands of relay and
millions of users.

98. 10.Maxthon Browser

99. Maxthon Browser
• Maxthon is a freeware web browser for
Windows, OS X and Linux, developed by Chinese
company Maxthon Ltd based in Beijing.
• It is also available on Windows Phone 8, iOS and
Android.Maxthon supports both the Trident and
the WebKit rendering engines.
• Maxthon won CNET WebWare 100 Awards in
2008 and 2009,and was #97 in PCWorld's list of
the 100 Best Products of 2011.

100. Features of Maxthon Browser
● Split screen option: divides open tabs into left and right of
screen.
● Saves open tabs in case of program shutdown or system crash.
● Support for custom skins.
● Customizable tabs and user interface.
● Programmable mouse gestures.
● Partial Gecko engine support with the use of a third-party
program.
● Simple collector – a small notepad-like utility, used to collect
text from web pages.
● Supports many Internet Explorer plugins as well as plugins of
its own.
● Cloud sync of data like passwords,history,bookmarks across
devices.

101. HTTP

102. What is HTTP?
• HTTP (Hypertext Transfer Protocol) is the set of
rules for transferring files (text, graphic images,
sound, video, and other multimedia files) on the
World Wide Web.
• Communication between client computers and web
servers is done by sending HTTP Requests and
receiving HTTP Response.
• HTTP is an application layer protocol
• Connectionless protocol
• Stateless

103. TERMINOLOGY
• IP Address: An Internet Protocol address (IP address) is a
numerical label assigned to each device (e.g., computer,
printer) participating in a computer network that uses the
Internet Protocol for communication.
• TCP :Transmission Control Protocol (TCP) is one of the two
original core protocols of the Internet Protocol Suite (IP), and
is so common that the entire suite is often called TCP/IP. TCP
provides reliable, ordered, error-checked delivery of a stream
of octets between programs running on computers connected
to an intranet or the public Internet.
• Port Number : A port number is a 16 bit number which when
associated with IP address , completes the destination
address for a communications session.
• Socket : A socket is nothing but a combination of IP address
and port number. It is simply an end while communication.

104. HTTP Connections :
Non Persistant HTTP
• At most one object send over a TCP
connections
Persistant HTTP
• Multiple objects can be send over single TCP
connections between client and server

105. HTTP session consist of three phases:
• The client establishes a TCP connection
• The client sends its request and then waits for
the answer
• The server processes the request and sends
back its answer, containing a status code and
the appropriate data.
• The connection is closed.

106. METHODS
1.HTTP SUPPORTS SEVERAL DIFFERENT
REQUEST COMMANDS, CALLED HTTP
METHODS. EVERY HTTP REQUEST MESSAGE
HAS A METHOD.
2.THE METHOD TELLS THE SERVER WHAT
ACTION TO PERFORM.

107. HTTP Methods
 GET method means retrieve whatever information. Is
identified by the Request-URI
 POST - used to send data to the server for updates.
 PUT - method requests that the enclosed entity be stored
under the supplied Request-URI.
 DELETE - requests that the origin server delete the
resource identified by the Request-URI.
 HEAD - identical to GET except that the server MUST NOT
return a message-body in the response.
 TRACE - Allows the client to see what is being received at
the other end of the request chain and use that data for
testing
 OPTION – used to determine servers capabilities

108. HTTP REQUEST MESSAGE
• The first line of an HTTP request message is called the request
line; the subsequent lines are called the header lines.
• The request line has three fields: the method field, the URL
field, and the HTTP version field.
• The method field can take on several different values,
including GET, POST, HEAD, PUT, and DELETE etc.
• The great majority of HTTP request messages use the GET
method.
• The GET method is used when the browser requests an
object, with the requested object identified in the URL field.
HTTP RESPONSE MESSAGES
• It has three sections: an initial status line, header lines, and
then the entity body.
• The entity body contains the requested object itself.
• The status line has three fields: the protocol version field, a
status code, and a corresponding status message.

109. HTTP Request / Response Communication
between clients and servers is done by
requests and responses:
1. A client ( a browser) sends an HTTP request to
the web
2. An web server receives the request
3. The server runs an application to process the
request
4. The server returns an HTTP response (output)
to the browser
5. The client (the browser) receives the response

110. The HTTP Request Circle A typical
HTTP request/ response circle:
• The browser requests an HTML page.
• The server returns an HTML file.
• The browser requests a style sheet.
• The server returns a CSS file.
• The browser requests an JPG image. The
server returns a JPG file.

111. The message format consists of the
following 3 items:
1) Start-line
2) Header Fields
3) Message Body

112. HTTPS
• The Secure Sockets Layer (SSL) was designed to
encrypt any TCP/IP based network traffic and
provide the following capabilities
• Prevents eavesdropping
• Prevents tampering or replaying of messages
• Uses certificates to authenticate servers and
optionally clients
• The HTTPS protocol is the same text based
protocol as HTTP but is run over an encrypted SSL
session.

114. HTML Hyper Text Markup Language
What is HTML?
• HTML is the standard markup language for creating
Web pages.
• HTML stands for Hyper Text Markup Language
• HTML describes the structure of Web pages using
markup
• HTML elements are the building blocks of HTML pages
• HTML elements are represented by tags
• HTML tags label pieces of content such as "heading",
"paragraph", "table", and so on
• Browsers do not display the HTML tags, but use them
to render the content of the page

115. History
In 1980, physicist Tim Berners-Lee, a contractor at
CERN, proposed and prototyped ENQUIRE, a system for
CERN researchers to use and share documents.
In 1989, Berners-Lee wrote a memo proposing an
Internet- based hypertext system.
Berners-Lee specified HTML and wrote the browser and
server software in late 1990.
That year, Berners-Lee and CERN data systems engineer
Robert Cailliau collaborated on a joint request for
funding, but the project was not formally adopted by
CERN.
In his personal notes from 1990 he listed "some of the
many areas in which hypertext is used" and put an
encyclopedia first.

116. HTML Versions
Version Year
HTML 1991
HTML 2.0 1995
HTML 3.2 1997
HTML 4.01 1999
XHTML 2000
HTML5 2014

117. STRUCTURE

118. The <!DOCTYPE> Declaration
•The <!DOCTYPE> declaration represents the
document type, and helps browsers to display
web pages correctly.
•It must only appear once, at the top of the
page (before any HTML tags).
•The <!DOCTYPE> declaration is not case
sensitive.

119. Tags or Elements

120. Attributes
• Attributes provide additional information about
the contents of an element. They appear on the
opening tag of the element and are made up of
two parts: a name and a value, separated by an
equals sign.

121. HTML Editors
• Write HTML Using Notepad or TextEdit
• Web pages can be created and modified by using professional
HTML editors.
• However, for learning HTML we recommend a simple text editor
like Notepad (PC) or TextEdit (Mac).
• We believe using a simple text editor is a good way to learn HTML.
Save the HTML Page
• Save the file on your computer. Select File > Save as in the Notepad
menu.
• Name the file "index.htm" and set the encoding to UTF-8 (which is
the preferred encoding for HTML files).
View the HTML Page in Your Browser
• Open the saved HTML file in your favorite browser (double click on
the file, or right-click - and choose "Open with").
• The result will look much like this:

122. Comments
• Comment tags are used to insert comments in the
HTML source code.
• Notice that there is an exclamation point (!) in the
opening tag, but not in the closing tag.
• Comments are not displayed by the browser, but they
can help document your HTML source code. <!-- Write
your comments here -->
Links
• HTML links are hyperlinks.
• You can click on a link and jump to another document.
• When you move the mouse over a link, the mouse
arrow will turn into a little hand. Note: A link does not
have to be text. It can be an image or any other HTML
element.

123. Images
• In HTML, images are defined with the <img> tag.
• The <img> tag is empty, it contains attributes only, and
does not have a closing tag. <img src="url“ >
Tables
• An HTML table is defined with the <table> tag.
• Each table row is defined with the <tr> tag. A table
header is defined with the <th> tag. By default, table
headings are bold and centered. A table data/cell is
defined with the <td> tag.
<table>
<tr>
<td>Something…</td>
</tr>
</table>

124. Lists
•Ordered lists
•Unordered lists
Blocks
• The <div> Element
• The <div> element is often used as a container for other HTML elements.
• The <div> element has no required attributes, but both style and class are
common.
• When used together with CSS, the <div> element can be used to style blocks
of content
Forms
• • The <form> Element
• • The HTML <form> element defines a form that is used to collect user
input:
<form>
.
form elements
.
</form>

125. The Action Attribute
•The action attribute defines the action to be
performed when the form is submitted.
• Normally, the form data is sent to a web page on the
server when the user clicks on the submit button.
• In the example above, the form data is sent to a
page on the server called "action_page.php". This
page contains a server-side script that handles the
form data: <form action="action_page.php">
• If the action attribute is omitted, the action is set to
the current page.

126. Audio
Audio on the Web
• Before HTML5, audio files could only be played in a browser
with a plug-in (like flash).
• The HTML5 <audio> element specifies a standard way to
embed audio in a web page.
HTML Audio - How It Works
• The controls attribute adds audio controls, like play, pause,
and volume.
• The <source> element allows you to specify alternative audio
files which the browser may choose from. The browser will
use the first recognized format.
• The text between the <audio> and </audio> tags will only be
displayed in browsers that do not support the <audio>
element.

127. Video
Playing Videos in HTML:
• Before HTML5, a video could only be played in a browser with a
plug-in (like flash).
• The HTML5 <video> element specifies a standard way to embed a
video in a web page.
How it Works:
• The controls attribute adds video controls, like play, pause, and
volume.
• It is a good idea to always include width and height attributes. If
height and width are not set, the page might flicker while the
video loads.
• The <source> element allows you to specify alternative video files
which the browser may choose from. The browser will use the first
recognized format.
• The text between the <video> and </video> tags will only be
displayed in browsers that do not support the <video> element.

128. URL(Universal Resource Locator)

129. • URL(Universal Resource Locator) is a string of
charactersthat sets the location to a resource on
a network.
• This tutorial focus will be breaking down the
parts of a url tohelp better understand the
composition of the string.
• Each part being discussed will be highlighted in a
light blue like the example below.

130. Protocol
• Protocol can be described as the type of connection.
• Thenormal protocol is http but other protocols
include https, ftp,and ssh.
• Protocols have default ports that they communicate
over.
• Http: Port 80
• Https : 221
• FTP: Port 20 Protocol

131. Subdomain
• The subdomain is the first part of the
hostname, which can be found between ‘//’
and the first ‘.’ . The subdomain www is the
default subdomain used but can be change
tost ring of alpha numeric characters, such as
our example below.

132. Domain Name
• The domain name is the parts of the domain
after the subdomain and before the port or
path. It will include the top-level domain or
second level domain.

133. Top Level Domain
• The top level domain(TLD) is the country code
for thedomain. In the example below the TLD
is the uk. In otherinstances it is com, net, org,
biz and even edu.

134. Second Level Domain and Country
Code SLD.
• The second level domain(SLD) is the part of the url before
the top level domain. In our example, it is prodigy view. The
country code second level domain (ccSLD) is the part of the
url directly before the top level domain and after the SLD.
1. Second Level Domain
2. Country Code Second Level Domain

135. Port
• The normal port that a web server runs on is port
80, but your web server can be configured to run on
any port such as 9000.
• Remember that if you change the port, make sure
another program is also not using that port.

136. Path
• The path refers to a file or location on the web
server. Many of today’s web server paths are
actually dynamic urls that are used to generate
code depending on the path. The beginning of
the path starts with a ‘/’.

137. Parameters
• Urls have parameters that are generally
designated after the ? symbol and separated
with an & symbol. Normally parameters are
parsed by a scripting language such as php.

138. Search Engine Friendly Parameters
• A lot of servers today perform a cool trick where they take
in parameters, and rewrite them as paths. This makes both
search engine friendly and user friendly urls.
Example
www.example.com/index.php?action=view&video=5
Becomes
www.example.com/view/5

139. Fragment/Anchors
• The last part of the url is what can either be
known as fragment or anchor.
• The variable is define after a the ‘#’symbol.
Fragments normally act as a location to go to
on a page.

140. Biological Networks

141. Basic Components
• Nodes
o DNA/RNA/Protein/Metabolite/Ontology
• Edges
• Directed
o Dis)nc)on between source and target
-‐ Ac)va)on (direct/indirect)
-‐ Repression (direct/indirect)
• Undirected
o No dis)nc)on between source and target
-‐ Co-‐expression (indirect)
-‐ Binding (direct)
-‐ Similarity/strength

142. Basic Features
• Degree
• Number of connec)ons that a node has
• Distance
• Number of connec)ons between two
nodes, in a shortest path
• Path
• A sequence of connec)ons
• Is there a path (reachability)
• Mean Shortest Path distance (closeness)
• In how many shortest paths (betweenness)

143. • Size of a network (Number of nodes)
• Density of a network (Propor)on of the connec)ons)
• Mo)fs/Cliques/Clusters/Sub-‐networks
Loops Chains Parallels
Multi-input Single input

144. Types of Biological Networks
• DNA-‐Protein
• Transcrip)onal regulatory networks
• Methyla)on networks
• RNA-‐RNA
• miRNA regulatory networks
• RNA-‐Protein
• Splicing regulatory networks
• Protein-‐Protein
• Co-‐expression networks
• Co-‐localization networks
• Co-‐evolution networks
• Structure networks
• Pathway networks
• Protease regulatory networks
• Signal transduction networks
• Gene Ontology networks

145. Why Build/Analyze Biological Networks ?
Single gene List of genes
o Regulators/Co-‐regulators
o Upstream/Downstream elements in the network
o Global connec)vity/interconnec)vity
o Func)onal features
o Differen)ally expressed subnetworks
o One gene – one disease : bunch of genes –
pathways
o Nextgen sequencing data
o Meta-‐analysis

146. How to Build Biological Networks
• Search/Retrieve from knowledge bases
• Predict from genome sequences
• Predict from “omics” data
• Predict from literature
• Integrate and analyze
• Meta-‐networks from genome scale data analysis

147. 3.
Online publications with
special reference to biology

148. • Electronic journals
• E books
• Downloading and uploading
• Open archive initiative
• Biomedcentral
• Pubmedcentral
• Freedom of scientific information access
• E- access
• Free software movement
• Free software foundation
• GNU/ Linux
• Online archive
• Databases
• Public Library of Science

150. • Electronic journals, also known as ejournals, e-journals,
and electronic serials, are scholarly journals or
intellectual magazines that can be accessed via electronic
transmission.
• Some journals are 'born digital' in that they are solely published on
the web and in a digital format, but most electronic journals
originated as print journals, which subsequently evolved to have
an electronic version, while still maintaining a print component.
• As academic research habits have changed in line with the growth
of the internet, the e-journal has come to dominate the journals
world.
• An e-journal closely resembles a print journal in structure: there is
a table of contents which lists the articles, and many electronic
journals still use a volume/issue model, although some titles now
publish on a continuous basis.
• Online journal articles are a specialized form of electronic
document: they have the purpose of providing material for
academic research and study, and they are formatted
approximately like journal articles in traditional printed journals.

151. • Often a journal article will be available for download in two
formats - as a PDF and in HTML format, although other electronic
file types are often supported for supplementary material.
• Articles are indexed in bibliographic databases, as well as by
search engines.
• E-journals allow new types on content to be included in journals,
for example video material, or the data sets on which research has
been based.
• With the growth and development of the internet, there has been
a growth in the number of new journals, especially in those that
exist as digital publications only.
• A subset of these journals exist as Open Access titles, meaning
that they are free to access for all, and have Creative
Commons licences which permit the reproduction of content in
different ways.
• High quality open access journals are listed in Directory of Open
Access Journals.
• Most however continue to exist as subscription journals, for which
libraries, organisations and individuals purchase access.

152. • It consists of Full-text and Bibliographic Databases.
• Full- text databases contain the whole content of an article
such as citation information, text, illustrations, diagrams and
tables.
• Bibliographic databases only contain citation information of an
article, such as author’s name, journal title, publication date
and page numbers.
• An e-database is an organized collection of information. It
supports flexible and in-depth searching of different fields, e.g.
journal title, article title, author, abstract, year, etc.
• We can only search for journal title in the Library Catalogues,
but not the title or author of individual articles.
• Therefore, e-database is extremely useful to find out the articles
on particular topics, e.g. Peer assessment in classroom.
• A particular journal articles can retrieve from e-database, which
could not find the same information via the Library Catalogue.

153. • Libraries have been exploring easily to cope up with the problems of ever
increasing prices of the journals, space requirements and decreasing level of usage
as the journals get older.
• Nevertheless, libraries are required to maintain back the issues of the journals,
usually in bound form.
• Electronic Journal helps the librarians in addressing these problems to a great
extent without significantly affecting the service levels.
• Electronic journals can be accessed via inter-net from any web enabled PC.
• Depending on the type of subscription, one or more users can access the service
simultaneously, either directly from an independent web enabled PC or in a local
area network through a proxy server (IP addresses based access).
• Electronic journals also offer benefit of full text searching and downloading of
articles.
• Many publishers of electronic journals offer their journals through consortia of
libraries at much lower rates.
• INDEST and INFLIBNET are two such consortia operating in India.
• Access to articles in electronic journals can also be made through aggregator
services which offer searchable databases of contents of e-journals from several
publishers, and links to journal site for full text.
• Emerald, OCLC and J-Gate are some of the example of e-journal aggregator
services.
• The main disadvantage of electronic journal is that libraries cannot physically
posses the journals.

154. Categories of E-Journals:
• Based on the level of content e-journal can be classified as:
a. Scholarly or research e-journal.
b. Popular or general public e-journal.
c. Industry or Trade e-journals.
• Based on availability and pricing e-journals may be categorized as
followings:
• Free online e-journal: The journals, which are totally free in online.
Such as Fulltext Database/ service.
• Free along with print subscription e-journal: The journals, which
online access are free and also provide print subscription. i.e.
Cambridge University Press, John Hopkins University Press, Oxford
University press.
• Priced e-journal: The journals, which are online and priced marginally
less than the printed version. i.e. Blackwell, Blackwell Navigator etc.

155. Advantages of E-Journals:
• E-journals are becoming increasingly in demand both as a means
of rapid desktop access to current research materials and as a way
to view past volumes. E-journals offer a range of potential
advantages to libraries and end-users:
• Allows remote access.
• Can be used simultaneously by more than one user.
• Provides timely access and at the rate of 24 X 7 X 365 formula.
• Supports different searching capabilities.
• Accommodates unique features (e.g. Links to related items,
reference linking)
• Saves physical storage space.
• Supports multimedia information.
• As a result of the above advantages, libraries today buy licenses
for an ever-increasing number of Electronic Journals from a range
of different publishers and providers, and use a diverse set of
technologies for information delivery

156. Examples for e-journals
• The website e.journals.org, provides the links to
world electronic journals.
• Examples for some of the e-journals in botany are:
• http://www.sciencedirect.com/science/journal/
• http:// www.springerlink.com/link
• http://www.springerlink.com/link
• http:// www.genetics.org/

158. Introduction
• Electronic book (E-Book) a term coined by
VanDam of Brown University during the
1960s, is is nothing but a book in electronic
form.
• But, e-book differs from a book in print as it
requires some kind of electronic device to
read.
• One can download thousand of free e-books
from the Internet.

159. Definition
• The term “e-book” stands for “Electronic Book”.It is
exactly the same as a regular book; however e-
books can be read on your PC and are usually
delivered via email.
• An electronic book or e-book, is the presentation of
electronic files in digital displays.
• The World Wide Web contains a huge quantity and
variety of electronic text forms.
• Increasingly, though an e-book is becoming are
precisely defined in terms of text that can be read
via the use of e-book software and hardware.

160. History
• The electronic book (e-book) was born in 1971, with the first
steps of Project Gutenberg, a digital library for books from
public domain.
• It is nearly 40 years old already.
• From 1994 onwards, the internet quickly spread worldwide.
• It created its own space as a new medium, to get information,
access documents, broaden our knowledge and communicate
across borders and languages.
• Book sellers began selling book online within and outside
their home country, offering experts on their websites.
• Though e-books are now becoming very popular in
developing countries, the development of e-books began in
the 1960s.
• According to what is techtarget.com, an e-book is an
electronic version of a traditional print book that can be read
by using a personal computer or by using an e-book reader.

161. Features
• Mobility
• Accessed Indefinitely
• Ability and storage
• Language accessibility
• Type Faces
• Sound E-book
• Cost
• Distribution
• Environmental concern

162. Advantages
• For readers, e-books have those benefits.
• They‟re cheaper.
• They‟re quick to download.
• They take very little computer space to store.
• They‟re easy to navigate when looking for particular
information.
• They can be printed if necessary.
• If one likes the e-book, can buy the moac expensive
printed version.
• They‟re cheaper to publish.
• The royalties are higher.
• Sales and marketing are Internet based, which is
always cheaper.

163. • They‟re easier to distribute.
• International distribution is much easier and more
accessible than for printed books.
• One can test the market before investing in an
expensive print run.
• 24 Hours, 7 Weeks and 365 Days access ensures
enhanced availability.
• Multimedia resources provided such as picture, video,
audio.
• Availability via Intranet.
• Saving shelf space in the libraries.
• Keyword searching provided.
• E-book cannot be damaged, lost or stolen.
• Multiple accesses can be provided.

164. Disadvantages
• Cost of hardware or e-book readers is high.
• Problems with printing a downloading.
• People may dislike reading text on computers.
• Lack of awareness of software/hardware.
• E-books might be hacked, copied or distributed
without the author’s or publisher’s permission.
• A major worry of reading form an e-book reader
could hurt the eyes.

165. Types
• There are four types of E-books.
• Downloadable e-books - Contents are available on the internet for
downloading to the user’s PC; No special reading device is required.
• Dedicated e-book readers - Contents are downloaded to a dedicated
hardware device with a high quality screen and special capabilities for
book reading.
• Print-on-demand books - Contents are stored in a system connected to
a high speed; high quality printer and bound copies are produced on
demand.
• Web- accessible e-book - Published on the providers web site and may
be accessed for a free or purchase the books to receive in definite
access.
• According to Crawford there are also number of types of e-books.
• Proprietary e-book devices.
• Open e-books.
• Free books or public domain e-books.
• Instabooks.

166. Examples
1. Oxford Advanced Learner’s Dictionary or Encyclopedia
• by A.S. Hornby.
• (http://www.mobipocket.com)
• This is easier to use and includes links within entries to
help the user more to the right place quickly.
2. Darkstar :
• The Java Game Server by Brendan Burns.
• (http://oreilly.com)
• This is among the innumerable gaming e-books
available in the virtual library of downloadable delights.

167. Best Sites free e-books to download
• Free E-books.net (www.free-ebooks.net)
• Get Free EBooks (www.getfreebooks.com)
• Free Tech Books (www.freetechbooks.com)
• Online Free E books.net
(www.onlinefreeebooks.net)
• Snip files (www.snipfiles.com)
• E Books Directory (www.e-booksdirectory.com)

168. E-book Reader
• E-book reader, also called an e-book device or e-reader.
• An e-book reader is a portable electronic device that is
designed primarily for the purpose of reading digital
books and periodicals.
• E-book readers are similar in form to a tablet computer.
• A tablet computer typically has a faster screen capable
of higher refresh rates which makes them more
suitable for interaction.
• The main advantages of e-book readers are better
readability of their screens especially in bright sunlight
and longer battery life.

169. E-book Reader Examples
Company Model
Amazon Kindle, Kindle 2, Kindle 3, etc.
Apple Ipad
Barnes & Noble Nook
Samsung Papyrus
Sony Pocket Reader Edition PRS - 300
Kobo Inc. Kobo
Pocket Book Pocket Book Pro 602

170. Amazon’s Kindle
• The Kindle, a portable e-book reader Amazon’s Kindle developed
by Amazon and launched in 2007.
• Created by the net’s bookseller, Amazon.com
• Thin, Lightweight, Electronic reading device
• Download your favorite book, newspaper, or magazine
• Kindle screen simulates paper
• read in bright sunlight with no glare
• costs much less to download than buy to the book
Sony Reader
• first to market in 2005 with its e-Sony Reader book reader.
• Sony sells e-books for the Reader from the Sony e-Book Library
store in the US, UK, Japan, Germany, Austria, Canada and it will be
coming to France.
• There have been ten models to date.
• Hold effortlessly in one hand Browse and download a huge range
of eBooks via Wi-Fi

171. Conclusion
• E- Book is a new concept here which is already
popular in the West.
• The present situation is growing and our future of e
books is bright.
• The cost of readers will also come down.
• E books never go out of stock and its supply chain is
very efficient.

172. Downloading and uploading

173. What Does It Mean to Upload
Something?

174. • In the context of the web, upload = send. You can think of it
like loading the data "upward" to the cloud/internet.
• When you upload something to a website, another user's
computer, a network location, etc., you're sending data from
your device to the other device.
• Files can be uploaded to a server, such as a website, or
directly to another device, like when using a P2P transfer
utility.
• For example, if you upload an image to Facebook, you're
sending the picture from your device to
the Facebook website.
• The file started with you and ended up somewhere else, so
it's considered an upload.
• This is true for any transfer like this, no matter the file type.
• You can upload documents to your teacher via email, upload
a video to YouTube, upload music to your online music
collection, etc.

175. What Does It Mean to Download
Something?

176. • In opposition to upload, download = save. You're taking
data from elsewhere and putting it onto your device,
essentially bringing it "down" from the internet.
• Downloading something from the web means that
you're transferring data from the other location to your
own device, whether it be your phone,
computer, tablet, smartwatch, etc.
• All sorts of information can be downloaded from the
web: books, movies, software, etc.
• For example, you can download movies to your
phone to watch while you're on the go, which means
that the actual data that makes up the movie is
transferred from the site you got it from and saved to
your phone, making it locally available.

177. Upload vs. Download: How They Relate
• Considering that an upload is sending data, and a download is saving data, you
might have caught on already that this goes on all the time when you use the web.
• Open your web browser and go to Google.com, and you immediately requested the
site (uploading tiny bits of data in the process) and got the Google search engine in
return (it downloaded the correct web page to your browser).
• Here's another example: when you browse YouTube for music videos, each search
term you enter is sending tiny bits of data to the site to request the video you're
looking for.
• Each of those requests you send are uploads since they started on your device and
ended up on YouTube's end.
• When the results are understood by YouTube and sent back to you as web pages,
those pages are being downloaded to your device for you to see.
• For a more concrete example, think about an email.
• You're uploading the pictures to an email server when you send someone photos
over an email.
• If you save photo attachments from someone who sent you an email, you're
downloading them to your device.
• Another way to see it: you upload the images so that the recipient can view them,
and when they save them, they're downloading them.

178. It's Important to Know the Difference
• Uploads and downloads happen all the time in the background.
You don't usually need to understand when something is
uploading or downloading or what they really refer to, but
knowing how they differ is important in some situations.
• For example, if a website tells you to upload your resume using
their online form, but you don't know if that means to save
something to your computer or send them a file, it can get
confusing and delay the overall process you're trying hard to finish.
• Or, maybe you're buying a home internet plan and you see one
advertised as offering 50 Mbps download speeds and another
with 20 Mbps upload speeds.
• Most people don't need a fast upload speed unless they're often
sending large amounts of data over the internet.
• However, not knowing the difference between upload and
download might leave you paying for way more than you need, or
paying a smaller amount for speeds too slow for what you need.

179. It's Important to Know the Difference
• Uploads and downloads happen all the time in the background.
• You don't usually need to understand when something is
uploading or downloading or what they really refer to, but
knowing how they differ is important in some situations.
• For example, if a website tells you to upload your resume using
their online form, but you don't know if that means to save
something to your computer or send them a file, it can get
confusing and delay the overall process you're trying hard to finish.
• Or, maybe you're buying a home internet plan and you see one
advertised as offering 50 Mbps download speeds and another with
20 Mbps upload speeds.
• Most people don't need a fast upload speed unless they're often
sending large amounts of data over the internet.
• However, not knowing the difference between upload and
download might leave you paying for way more than you need, or
paying a smaller amount for speeds too slow for what you need.

180. What About Streaming?

181. • Since the speed at which you can download things from the
internet is determined by what you're paying your ISP for, some
people opt to stream data versus download it.
• They're similar, but not technically the same, and there are
benefits of both.
• For example, there are movie streaming sites that let you watch
movies online instead of download them, and web apps that can
be used in a browser instead of saved to your device.
• Downloading is useful if you want the entire file for offline use, like
if you plan to watch movies, edit documents, view photos, listen to
music, etc., without an internet connection.
• The entire file is saved on your device since you downloaded it,
but to use it, you have to wait for the whole download to finish.
• Streaming, on the other hand, is useful if you want to use the file
before it's finished downloading.
• You can stream Netflix shows on your tablet, for example, without
needing to download the whole episode first.
• However, the file isn't usable offline because after the stream
completes, it's completely deleted from your device (unless you
specifically choose to download the episode).

182. Other Facts About Uploading and
Downloading
• The terms download and upload are usually reserved
for transfers that take place between a local device and
something else on the internet.
• For example, you won't say that you've "uploaded data
to your flash drive" when copying a file to it from your
computer.
• There are network protocols that support data uploads
and downloads.
• One is FTP, which utilizes FTP servers and FTP clients to
send and receive data between devices.
• Another is HTTP, which is the protocol used when you
upload/download data through your web browser.

183. Open Archives Initiative (OAI)
www.openarchives.org

184. • The Open Archives Initiative (OAI) is an organization to
develop and apply technical interoperability standards for
archives to share catalog information (metadata).
• It attempts to build a "low-
barrier interoperability framework" for archives (institutional
repositories) containing digital content (digital libraries).
• It allows people (service providers) to harvest metadata (from
data providers).
• This metadata is used to provide "value-added services",
often by combining different data sets.
• OAI has been involved in developing a technological
framework and interoperability standards for enhancing
access to eprint archives, which
make scholarly communications like academic
journals available, associated with the open
access publishing movement.
• The relevant technology and standards are applicable beyond
scholarly publishing.

185. • The OAI technical infrastructure, specified in the Protocol for
Metadata Harvesting (OAI-PMH) version 2.0, defines a
mechanism for data providers to expose their metadata.
• This protocol mandates that individual archives map their
metadata to the Dublin Core, a common metadata set for this
purpose.
• OAI standards allow a common way to provide content, and
part of those standards is that the content has metadata that
describes the items in Dublin Core format.
• Object Reuse and Exchange (OAI-ORE) defines standards for
the description and exchange of aggregations of web
resources.
• Funding for the initiative comes from the
• Andrew W. Mellon Foundation,
• Coalition for NetworkedInformation (CNI),
• Digital Library Federation (DLF),
• National Science Foundation (NSF),
• Alfred P. Sloan Foundation, and other organizations.

186. Purpose of Open Archives Initiative
• “develops and promotes interoperability standards
that aim to facilitate the efficient dissemination of
content”
• “has its roots in the open access and institutional
repository movements”
• “Archive” defined broadly: “as a repository for
stored information”

187. History of the Open Archives Initiative
• Originally defined a “metadata harvesting
protocol” – OAI-PMH
• Grew out of efforts to share e-prints
Original work supported by:
• Digital Library Federation (DLF)
• Coalition for Networked Information (CNI)
• National Science Foundation (NSF)

188. OAI-PMH
Protocol history
Version 1.0 released January 2001
Version 1.1 released July 2001
 Version 2.0 released June 2002
• No further major revisions planned
• Protocol for harvesting metadata, not content
• No inherent assumption that the metadata
describes digital content

189. How OAI-PMH works

190. Data providers
• Set up a server that responds to harvesting requests
• Required to expose metadata in simple Dublin Core
(DC) format
• Can supplement DC with metadata in any other format
expressible with an XML schema (e.g., CDWA Lite)
Service providers
• Harvest and store metadata
• Generally provide search/browse access to this
metadata
• Can be general or domain-specific
• Can choose to collect metadata in formats other than
DC
• Can provide value-added services
• Sometimes re-expose metadata to other aggregations

193. OAI Object Re-Use and Exchange
• Develop, identify, and profile extensible standards and
protocols to allow repositories, agents, and services to
interoperate in the context of use and reuse of compound
digital objects beyond the boundaries of the holding
repositories.
• Aim for more effective and consistent ways:
o to facilitate discovery of these objects,
o to reference (link to) these objects (and parts thereof),
o to obtain a variety of disseminations of these objects,
o to aggregate and disaggregate these objects,
o Enable processing by automated agents

196. BIOMED CENTRAL
• Biomed central is united kingdom based, for profit
scientific publisher specialising in open access
journal publication.
• Biomed central and its sister companies chemistry
central and physmath central publish over 200
scientific journals.
• Most biomed central describes itself as the first
and largest open access science publisher.
• Its is owned by Springer science + Business Media.

197. BioMed Central – who are we?
BioMed Central is the open access publisher
committed to the free widespread dissemination
of research, publishing peer-reviewed research
across all areas of biology and medicine, with
immediate, barrier-free open access for all
BioMed Central’s business models to maintain our
open access policy: – Open access journals with
article-processing charges and Membership –
Subscription-based content to value-added
secondary resources
e.g. Critical Care, Biology Image Library –
Institutional repository service - Open Repository

198. About BioMed Central
• Launched in 1999
• Publishes 200 journals; 74 tracked by ISI; 43 with impact factors
• Has approximately 300 member institutions in over 30 countries
• We encourage institutions to create central funds to cover open access
costs and become advocates open access
• Biomed central was founded in 2000 as part of the current science group
• The first director of the company was Jan Vetterop.
• In 2002, the company’s business model evolved to include article process
charges.
• In October 2008, it was announced that Biomed central had been acquired
by spring science + Business media, the second largest STM publisher.
• In 2007 Yale University libraries stopped subsiding page charges for affiliates
of Yale whose using Biomed central as the publisher of their works.
• In November 2008 Biomed central became an official supporting
organization of Healthcare Information.

199. JOURNAL
• Biomed central owns and produces in house five journals :
i. Genome biologus
ii. Genome medicine
iii. Arthritis Research and Therapy
iv. Breast cancer Research
v. Critical care
• It also produces the BMC journal series of 65 journals
covering the fields of biology and medicine.
• Chemistry central journal and Physmath series of journals are
also produces by the company.
• Most of the other journals published by Biomed central are
owned and produced independently by societies and
academic editorial boards, with Biomed central providing the
hosting publishing platform and marketing.

200. BIOMED CENTRAL JOURNALS ARE
ARCHEIVED IN SEVERAL WAYS :
• On the company’s own servers on Pubmed central’s
serves, through CD- ROM collections developed by
national libraries through the archive etc.,
• Since the material is available without registration
or subscription search engines such as Google also
index much of the research material.

201. AIM AND SCOPE
• Unreported or unusual side effects or adverse interaction
involving medications.
• Unexpected or unusual presentations of a disease
• New associations or variations on disease process
• Presentations, diagnoses and management of new and
emerging diseases.
• an unexpected association between diseases or symptoms.
• An unexpected event in the course of observing or treating a
patients.
• Findings that shed new light on the possible pathogenesis of a
disease or an adverse effect.
• Authors should indicate in the abstract and cover letter how
the case report adds to the medical literature.
• Submissions that do not indicate this information be returned
to authors prior to peer review.

202. OPEN ACCESS
• Open access publishing allows free distribution and access to
published articles
• The author retains copyright of their work a creative
commons attribution licence.
• So, all articles are made freely available to the widest
audience possible.
• Biology, medicine, health are the areas include in biomed
central.
TIME FOR CHANGING
• Fifteen years ago, the business model for scientific publishers
was to charge users to view the articles they published.
• This subscription based model for scientific publishers was to
charge users to view the articles they published.
• Biomed central open access publishing model changed all
that.

203. BIOMED CENTRAL THE FIRST OPEN
ACCESS PUBLISHERS
• Part of current science group
• Published first article in mid-2000
• Strict policy of immediate open access to all
research article.
THE BENEFITS :
• All articles are free to read,
• copy,
• distribute and use(with attribution).

204. Open access is an important step towards
open science
 Enhances scholarly communication
 Research has more impact
 Increases Authors profile
 Readers get better access to funded research
 Improves visibility of an institutions research
 No subscription barriers
Open access publishing
 Publisher makes full text version of article immediately
freely available online.
Self archiving: Author posts “author-copy” on open
access websites or any other open access repository
Achieving Open Access

205. Open Access Mandates
Funding Agency Mandates
• http://www.biomedcentral.com/info/about/apcfaq#grants
• – NIH
• – Wellcome Trust UK and British Councils
• – Howard Hughes Medical Institutes
• – National Science Foundation, Canada
Institutional Mandates
• – University of California, Berkeley
• – Harvard University
Mandates
• The US National Science Foundation (NSF)
• The US National Research Council
• Canadian Cancer Research Institutes
• Norwegian Research Council open access mandate
• German government to re-evaluate the open access proposal rejected in 2006.
• Australia's draft research assessment system requires research to be deposited in
institutional repositories
• The Wellcome Trust is auditing the level of compliance with its open access mandate and
plans to contact non-complying grantees individually.
• UK Research Councils

207. PubMed Central
• PubMed Central (PMC) is a free digital repository that archives open
access full-text scholarly articles that have been published
in biomedical and life sciences journals.
• As one of the major research databases developed by the National Center
for Biotechnology Information (NCBI), PubMed Central is more than a
document repository.
• Submissions to PMC are indexed and formatted for
enhanced metadata, medical ontology, and unique identifiers which enrich
the XML structured data for each article
• Content within PMC can be linked to other NCBI databases and accessed
via Entrez search and retrieval systems, further enhancing the public's
ability to discover, read and build upon its biomedical knowledge
• PubMed Central is distinct from PubMed
• PubMed Central is a free digital archive of full articles, accessible to anyone
from anywhere via a web browser (with varying provisions for reuse).
• Conversely, although PubMed is a searchable database of biomedical
itations and abstracts, the full-text article resides elsewhere (in print or
online, free or behind a subscriber paywall).

208. HISTORY
• Launched in February 2000, the repository has grown rapidly as the NIH
Public Access Policy is designed to make all research funded by the National
Institutes of Health (NIH) freely accessible to anyone, and, in addition, many
publishers are working cooperatively with the NIH to provide free access to
their works.
• In late 2007, the Consolidated Appropriations Act of 2008 (H.R. 2764) was
signed into law and included a provision requiring the NIH to modify its
policies and require inclusion into PubMed Central complete electronic
copies of their peer-reviewed research and findings from NIH-funded
research.
• These articles are required to be included within 12 months of publication.
• This is the first time the US government has required an agency to
provide open access to research and is an evolution from the 2005 policy, in
which the NIH asked researchers to voluntarily add their research to
PubMed Central.
• A UK version of the PubMed Central system, UK PubMed Central (UKPMC),
has been developed by the Wellcome Trust and the British Library as part of
a nine-strong group of UK research funders.
• This system went live in January 2007.

209. • On 1 November 2012, it became Europe PubMed Central.
• The Canadian member of the PubMed Central International
network, PubMed Central Canada, was launched in October 2009.
• The National Library of Medicine "NLM Journal Publishing Tag Set"
journal article markup language is freely available.
• The Association of Learned and Professional Society
Publishers comments that "it is likely to become the standard for
preparing scholarly content for both books and journals".
• A related DTD is available for books.
• The Library of Congress and the British Library have announced
support for the NLM DTD.
• It has also been popular with journal service providers.
• With the release of public access plans for many agencies beyond
NIH, PMC is in the process of becoming the repository for a wider
variety of articles.
• This includes NASA content, with the interface branded as
"PubSpace"

211. How they works ?
• Articles are sent to PubMed Central by publishers in XML or SGML, using a
variety of article DTDs.
• Older and larger publishers may have their own established in-house DTDs,
but many publishers use the NLM Journal Publishing DTD (see above).
• Received articles are converted via XSLT to the very similar NLM Archiving
and Interchange DTD.
• This process may reveal errors that are reported back to the publisher for
correction.
• Graphics are also converted to standard formats and sizes. The original and
converted forms are archived.
• The converted form is moved into a relational database, along with
associated files for graphics, multimedia, or other associated data.
• Many publishers also provide PDF of their articles, and these are made
available without change.
• Bibliographic citations are parsed and automatically linked to the relevant
abstracts in PubMed, articles in PubMed Central, and resources on
publishers' Web sites.
• PubMed links also lead to PubMed Central.

212. • Unresolvable references, such as to journals or particular articles
not yet available at
• one of these sources, are tracked in the database and
automatically come "live" when the resources become available.
• An in-house indexing system provides search capability, and is
aware of biological and medical terminology, such as generic vs.
proprietary drug names, and alternate names for organisms,
diseases and anatomical parts.
• When a user accesses a journal issue, a table of contents is
automatically generated by retrieving all articles, letters, editorials,
etc. for that issue.
• When an actual item such as an article is reached, PubMed Central
converts the NLM markup to HTML for delivery, and provides links
to related data objects.
• This is feasible because the variety of incoming data has first been
converted to standard DTDs and graphic formats.
• In a separate submission stream, NIH-funded authors may deposit
articles into PubMed Central using the NIH Manuscript Submission
(NIHMS). Articles thus submitted typically go through XML markup
in order to be converted to NLM DTD.

213. PMCID
• The PMCID (PubMed Central identifier), also
known as the PMC reference number, is
a bibliographic identifier for the PubMed Central
database, much like the PMID is the bibliographic
identifier for the PubMed database. The two
identifiers are distinct however.
• It consists of "PMC" followed by a string of seven
numbers. The format is :
• PMCID: PMC1852221
• Authors applying for NIH awards must include the
PMCID in their application.

214. Example of a PMC journals
Example of a PMC journal in which at least one author manuscript was
published:
• JrId: 38224
• JournalTitle: Advanced powder technology : the international journal of the Society
of Powder Technology, Japan
• MedAbbr: Adv Powder Technol
• ISSN (Print): 0921-8831
• ISSN (Online): 1568-5527
• IsoAbbr: Adv Powder Technol
• NlmId: 101535104
Example of a PMC journal that is not a MEDLINE title, as of Jan. 2016:
• JrId: 36751J
• ournalTitle: Allergy, asthma, and clinical immunology : official journal of the
Canadian Society of Allergy and Clinical Immunology
• MedAbbr: Allergy Asthma Clin Immunol
• ISSN (Print): 1710-1484
• ISSN (Online): 1710-1492
• IsoAbbr: Allergy Asthma Clin Immuno
• lNlmId: 101244313

215. The freedom of scientific information
access

216. Open Access to Scientific Information
• Scientific information is both a researcher’s greatest output and
technological innovation’s most important resource.
• UNESCO promotes and supports OA—the online availability of scholarly
information to everyone, free of most licensing and copyright barriers—for
the benefit of global knowledge flow, innovation and socio-economic
development.
• At least 10 out of the 17 Sustainable Development Goals (SDGs) comprising
the 2030 Agenda for Sustainable Development require constant scientific
input.
• Given that these goals must be achieved globally, there is an absolute need
to remove restrictions in order to disseminate research outputs to intended
stakeholders.
• UNESCO thus believes that OA has a fundamental role to support
the SDGs and is committed to making OA one of the central supporting
agendas to achieve the SDGs.
• UNESCO’s OA initiatives are built around the SDGs to recognize the need
for ensuring that scientific research addresses the needs of society and
responds to current and future sustainability challenges.

217. UNESCO promotes Open Access (OA)
• Open Access logo, originally designed by Public Library of Science
• UNESCO promotes Open Access (OA), with particular emphasis on scientific
information (journal articles, conference papers and datasets of various
kinds) emanating from publicly funded research.
• Working with partners, UNESCO works to improve awareness about the
benefits of OA among policy makers, researchers and knowledge managers.
• Through its global network of Field Offices, Institutes and Centers, UNESCO
facilitates the development and adoption of OA-enabling policies.
• In addition, UNESCO engages in global OA debates and cooperates with
local, regional and global initiatives in support of OA.
• UNESCO’s OA programme pays particular attention to African and other
developing countries where, notwithstanding important gains in ICT
availability, OA prevalence, both in terms of output and usage, remains low.
• Open Access benefits researchers, innovators, teachers, students, media
professionals and the general public.
• It promotes global knowledge flow for the benefit of scientific discovery,
innovation and socio-economic development.

218. Open Access logo, originally designed
by Public Library of Science

219. The Global Open Access Portal (GOAP)
• The Global Open Access Portal (GOAP) funded by the
Governments of Colombia, Denmark, Norway, and the United
States Department of State, presents a current snapshot of the
status of Open Access (OA) to scientific information in 158
countries worldwide.
• For countries that have been more successful in implementing
Open Access, the portal highlights critical success factors and
aspects of the enabling environment.
• For countries and regions that are still in the early stages of Open
Access development, the portal identifies key players, potential
barriers and opportunities.
• The Global Open Access Portal is designed to provide necessary
information for policy-makers to:
• Learn about the global Open Access environment;
• View their country’s status; and
• Understand where and why Open Access has been most
successful.

221. E-Access
• An E-Access Service is an OVC-based service with at
least one UNI OVC End Point and one ENNI End
Point.
• Currently only point-to-point E-Access Services are
defined - namely Access EPL, Access EVPL, and
Access E-Line - which contain exactly one UNI and
exactly one ENNI.
• Examples:
• Access EPL Service
• Access EVPL Service

222. Access EPL Service
• A Service Provider can use the Access EPL service from
an Access Provider to deliver the port-based Ethernet
services: Ethernet Private Line (EPL) and Ethernet
Private LAN (EP-LAN). The following diagram shows two
Access EPL services being used to facilitate a multi-CEN
EP-LAN service.

223. Access EVPL Service
• A Service Provider can use the Access EVPL service from an
Access Provider to deliver the C-VLAN-mapped Ethernet services:
Ethernet Virtual Private Line (EVPL) and Ethernet Virtual Private
LAN (EVP-LAN). The following diagram shows two multi-CEN EVPL
services built from one Access-EPL and two Access-EVPL services.

224. Free software movement

225. Free software movement
• The free software movement is a social
movement with the goal of obtaining and
guaranteeing certain freedoms for software users,
namely the freedom to run the software, to study
and change the software, and to redistribute copies
with or without changes.
• Although drawing on traditions and philosophies
among members of the 1970s hacker culture and
academia, Richard Stallman formally founded the
movement in 1983 by launching the GNU Project.
• Stallman later established the Free Software
Foundation in 1985 to support the movement.

226. Richard Stallman

227. • Richard Matthew Stallman (/ˈstɔːlmən/; born March 16,
1953), often known by his initials, rms, and occasionally
upper-case RMS, is an American free software
movement activist and programmer.
• He campaigns for software to be distributed in a manner such
that its users receive the freedoms to use, study, distribute,
and modify that software.
• Software that ensures these freedoms is termed free
software.
• Stallman launched the GNU Project, founded the Free
Software Foundation, developed the GNU Compiler
Collection and GNU Emacs, and wrote the GNU General
Public License.
• Stallman launched the GNU Project in September 1983 to
create a Unix-like computer operating system composed
entirely of free software.
• With this, he also launched the free software movement.

228. • He has been the GNU project's lead architect and
organizer, and developed a number of pieces of widely
used GNU software including, among others, the GNU
Compiler Collection, GNU Debugger, and GNU Emacs
text editor.
• In October 1985 he founded the Free Software
Foundation (FSF).
• In September 2019, he resigned as president of the FSF
and left his "visiting scientist" role at MIT.
• Stallman remains head of the GNU Project.
• Stallman pioneered the concept of copyleft, which uses
the principles of copyright law to preserve the right to
use, modify, and distribute free software, and is the
main author of free software licenses which describe
those terms, most notably the GNU General Public
License (GPL), the most widely used free software
license.

229. Purpose of FSM
• The philosophy of the movement is that the use of computers
should not lead to people being prevented from cooperating
with each other.
• In practice, this means rejecting "proprietary software",
which imposes such restrictions, and promoting free
software, with the ultimate goal of liberating everyone in
cyberspace – that is, every computer user.
• Stallman notes that this action will promote rather than
hinder the progression of technology, since "it means that
much wasteful duplication of system programming effort will
be avoided.
• This effort can go instead into advancing the state of the art".
• Members of the free software movement believe that all
users of software should have the freedoms listed in The Free
Software Definition.

230. • Many of them hold that it is immoral to prohibit or prevent people
from exercising these freedoms and that these freedoms are
required to create a decent society where software users can help
each other, and to have control over their computers.
• Some free software users and programmers do not believe
that proprietary software is strictly immoral, citing an increased
profitability in the business models available for proprietary
software or technical features and convenience as their reasons.
• The Free Software Foundation also believes all software
needs free documentation, in particular because conscientious
programmers should be able to update manuals to reflect
modification that they made to the software, but deems the
freedom to modify less important for other types of written works.
• Within the free software movement, the FLOSS
Manuals foundation specializes on the goal of providing such
documentation.
• Members of the free software movement advocate that works
which serve a practical purpose should also be free.

231. ACTIONS
• Writing and spreading free software
• The core work of the free software movement focused on software
development.
• The free software movement also rejects proprietary software, refusing to
install software that does not give them the freedoms of free software.
• According to Stallman, "The only thing in the software field that is worse
than an unauthorised copy of a proprietary program, is an authorised copy
of the proprietary program because this does the same harm to its whole
community of users, and in addition, usually the developer, the perpetrator
of this evil, profits from it."
• Building awareness
• Some supporters of the free software movement take up public speaking,
or host a stall at software-related conferences to raise awareness of
software freedom.
• This is seen as important since people who receive free software, but who
are not aware that it is free software, will later accept a non-free
replacement or will add software that is not free software.

232. Free Software Foundation

233. • The Free Software Foundation (FSF) is a non-profit
organization founded by Richard Stallman on 4 October 1985
to support the free software movement, which promotes the
universal freedom to study, distribute, create, and
modify computer software,with the organization's preference
for software being distributed under copyleft ("share alike")
terms,such as with its own GNU General Public License.
• The FSF was incorporated in Boston, Massachusetts, US,
where it is also based.
• From its founding until the mid-1990s, FSF's funds were
mostly used to employ software developers to write free
software for the GNU Project.
• Since the mid-1990s, the FSF's employees and volunteers
have mostly worked on legal and structural issues for the free
software movement and the free software community.
• Consistent with its goals, the FSF aims to use only free
software on its own computers.

234. History
• The Free Software Foundation was founded in 1985 as a non-
profit corporation supporting free software development.
• It continued existing GNU projects such as the sale of manuals
and tapes, and employed developers of the free software
system.
• Since then, it has continued these activities, as well as
advocating for the free software movement.
• The FSF is also the steward of several free software licenses,
meaning it publishes them and has the ability to make
revisions as needed.
• The FSF holds the copyrights on many pieces of
the GNU system, such as GNU Compiler Collection.
• As holder of these copyrights, it has the authority to enforce
the copyleft requirements of the GNU General Public
License (GPL) when copyright infringement occurs on that
software.

235. Current and ongoing activities
• The GNU Project
• GNU licenses
• GNU Press
• The Free Software Directory
• Maintaining the Free Software Definition
• Project hosting
• h-node ("Hardware-Node“ )
• Advocacy
• Annual awards
• LibrePlanet

236. Endorsements
Operating systems
• The FSF maintains a list of approved Linux operating systems that
maintain free software by default:
• Dragora GNU/Linux-Libre
• dyne:bolic
• gNewSense
• GNU Guix system
• Hyperbola GNU/Linux-libre
• Parabola GNU/Linux-libre
• PureOS
• Trisquel
• Ututo
• LibreCMC
• ProteanOS
The project also maintains a list of operating systems that are not versions of
the GNU system:
• Replicant

237. • Discontinued operating systems
• The following are previously endorsed operating
systems that are no longer actively maintained:
• BLAG Linux and GNU
• Musix GNU+Linux
• Hardware endorsements (RYF)
• The FSF maintains a "Respects Your Freedom"
(RYF) hardware certification program. To be
granted certification, a product must use 100%
Free Software, allow user installation of modified
software, be free of backdoors and conform with
several other requirements.

238. Board
• The FSF's board of governors includes amongst themselves
professors at leading universities, senior engineers, and
founders.
• A few high-profile activists, and software businessmen are
admitted as well.
• Currently on the board there is one high-profile activist,
and one world-class, software-campaign strategist .
• There was once a majorly contributing programmer (Mono
and Gnome) and businessman who lost favor badly.
• Founders are also major software developers of the free
software in the GNU Project.
• John Sullivan is the current FSF executive director.
• Previous members that occupied the position were Peter T.
Brown (2005–2010) and Bradley M. Kuhn (2001–2005).