Selasa, 18 November 2014

HISTORY OF INTERNET

The history of the Internet begins with the development of electronic computers in the 1950s. Initial concepts of packet networking originated in several computer science laboratories in the United States, Great Britain, and France. The US Department of Defense awarded contracts as early as the 1960s for packet network systems, including the development of the ARPANET (which would become the first network to use the Internet Protocol.) The first message was sent over the ARPANET from computer science Professor Leonard Kleinrock's laboratory at University of California, Los Angeles (UCLA) to the second network node at Stanford Research Institute (SRI)

Moreover, internet is a global system of interconnected computer networks that use the standard Internet protocol suite (TCP/IP) to link several billion devices worldwide. It is an international network of networks that consists of millions of private, public, academic, business, and government packet switched networks, linked by a broad array of electronic, wireless, and optical networking technologies. The Internet carries an extensive range of information resources and services, such as the inter-linked hypertext documents and applications of the World Wide Web (WWW), the infrastructure to support email, and peer-to-peer networks for file sharing and telephony.

 



 

Internet Timeline

1969

ARPA (Advanced Research Projects Agency) goes online in December, connecting four major U.S. universities. Designed for research, education, and government organizations, it provides a communications network linking the country in the event that a military attack destroys conventional communications systems.
1972
Electronic mail is introduced by Ray Tomlinson, a Cambridge, Mass., computer scientist. He uses the @ to distinguish between the sender's name and network name in the email address.
1973
Transmission Control Protocol/Internet Protocol (TCP/IP) is designed and in 1983 it becomes the standard for communicating between computers over the Internet. One of these protocols, FTP (File Transfer Protocol), allows users to log onto a remote computer, list the files on that computer, and download files from that computer.
1976
Presidential candidate Jimmy Carter and running mate Walter Mondale use email to plan campaign events.
Queen Elizabeth sends her first email. She's the first state leader to do so.
1982
The word “Internet” is used for the first time.
1984
Domain Name System (DNS) is established, with network addresses identified by extensions such as .com, .org, and .edu.
Writer William Gibson coins the term “cyberspace.”
1985
Quantum Computer Services, which later changes its name to America Online, debuts. It offers email, electronic bulletin boards, news, and other information.
1988
A virus called the Internet Worm temporarily shuts down about 10% of the world's Internet servers.
1989
The World (world.std.com) debuts as the first provider of dial-up Internet access for consumers.
Tim Berners-Lee of CERN (European Laboratory for Particle Physics) develops a new technique for distributing information on the Internet. He calls it the World Wide Web. The Web is based on hypertext, which permits the user to connect from one document to another at different sites on the Internet via hyperlinks (specially programmed words, phrases, buttons, or graphics). Unlike other Internet protocols, such as FTP and email, the Web is accessible through a graphical user interface.
1990
The first effort to index the Internet is created by Peter Deutsch at McGill University in Montreal, who devises Archie, an archive of FTP sites.
1991
Gopher, which provides point-and-click navigation, is created at the University of Minnesota and named after the school mascot. Gopher becomes the most popular interface for several years.
Another indexing system, WAIS (Wide Area Information Server), is developed by Brewster Kahle of Thinking Machines Corp.
1993
Mosaic is developed by Marc Andreeson at the National Center for Supercomputing Applications (NCSA). It becomes the dominant navigating system for the World Wide Web, which at this time accounts for merely 1% of all Internet traffic.
1994
The White House launches its website, www.whitehouse.gov.
Initial commerce sites are established and mass marketing campaigns are launched via email, introducing the term “spamming” to the Internet vocabulary.
Marc Andreessen and Jim Clark start Netscape Communications. They introduce the Navigator browser.
1995
CompuServe, America Online, and Prodigy start providing dial-up Internet access.
Sun Microsystems releases the Internet programming language called Java.
1996
Approximately 45 million people are using the Internet, with roughly 30 million of those in North America (United States and Canada), 9 million in Europe, and 6 million in Asia/Pacific (Australia, Japan, etc.). 43.2 million (44%) U.S. households own a personal computer, and 14 million of them are online.
1997
On July 8, 1997, Internet traffic records are broken as the NASA website broadcasts images taken by Pathfinder on Mars. The broadcast generates 46 million hits in one day.
The term “weblog” is coined. It’s later shortened to “blog.”
1998
Google opens its first office, in California.
1999
College student Shawn Fanning invents Napster, a computer application that allows users to swap music over the Internet.
The number of Internet users worldwide reaches 150 million by the beginning of 1999. More than 50% are from the United States. 
“E-commerce” becomes the new buzzword as Internet shopping rapidly spreads.

MySpace.com is launched.
2000
To the chagrin of the Internet population, deviant computer programmers begin designing and circulating viruses with greater frequency. “Love Bug” and “Stages” are two examples of self-replicating viruses that send themselves to people listed in a computer user's email address book. The heavy volume of email messages being sent and received forces many infected companies to temporarily shut down their clogged networks.
The Internet bubble bursts, as the fountain of investment capital dries up and the Nasdaq stock index plunges, causing the initial public offering (IPO) window to slam shut and many dotcoms to close their doors.America Online buys Time Warner for $16 billion. It’s the biggest merger of all time.

2001
Napster is dealt a potentially fatal blow when the 9th U.S. Circuit Court of Appeals in San Francisco rules that the company is violating copyright laws and orders it to stop distributing copyrighted music. The file-swapping company says it is developing a subscription-based service. 
About 9.8 billion electronic messages are sent daily.

Wikipedia is created.
2002
As of January, 58.5% of the U.S. population (164.14 million people) uses the Internet. Worldwide there are 544.2 million users.The death knell tolls for Napster after a bankruptcy judge ruled in September that German media giant Bertelsmann cannot buy the assets of troubled Napster Inc. The ruling prompts Konrad Hilbers, Napster CEO, to resign and lay off his staff.
2003
It's estimated that Internet users illegally download about 2.6 billion music files each month.
Spam, unsolicited email, becomes a server-clogging menace. It accounts for about half of all emails. In December, President Bush signs the Controlling the Assault of Non-Solicited Pornography and Marketing Act of 2003 (CAN-SPAM Act), which is intended to help individuals and businesses control the amount of unsolicited email they receive.Apple Computer introduces Apple iTunes Music Store, which allows people to download songs for 99 cents each.Spam, unsolicited email, becomes a server-clogging menace. It accounts for about half of all emails.Apple Computer introduces Apple iTunes Music Store, which allows people to download songs for 99 cents each.

2004
Internet Worm, called MyDoom or Novarg, spreads through Internet servers. About 1 in 12 email messages are infected.Online spending reaches a record high—$117 billion in 2004, a 26% increase over 2003.
2005
YouTube.com is launched.
2006
There are more than 92 million websites online.
2007
Legal online music downloads triple to 6.7 million downloads per week.
Colorado Rockies' computer system crashes when it receives 8.5 million hits within the first 90 minutes of World Series ticket sales.The online game, World of Warcraft, hits a milestone when it surpasses 9 million subscribers worldwide in July.
2008
In a move to challenge Google's dominance of search and advertising on the Internet, software giant Microsoft offers to buy Yahoo for $44.6 billion.In a San Fransisco federal district court, Judge Jeffrey S. White orders the disabling of Wikileaks.org, a Web site that discloses confidential information. The case was brought by Julius Baer Bank and Trust, located in the Cayman Islands, after a disgruntled ex-employee allegedly provided Wikileaks with stolen documents that implicate the bank in asset hiding, money laundering, and tax evasion. Many web communities, who see the ruling as unconstitutional, publicized alternate addresses for the site and distributed bank documents through their own networks. In response, Judge White issues another order to stop the distribution of bank documents.Microsoft is fined $1.3 billion by the European Commission for further abusing its dominant market position, and failing to comply to their 2004 judgment, which ordered Microsoft to give competitors information necessary to operate with Windows. Since 2004, Microsoft has been fined a total of $2.5 billion by the Commission for not adhering to their ruling.
URL
 
URL is an acronym that stands for Uniform Resource Locator and is a reference (an address) to a resource on the Internet. URL strings consist of three parts (substrings):
1. network protocol
2. host name or address
3. file or resource location
4.These substrings are separated by special characters as follows: protocol :// host / location
URL Protocol
The 'protocol' substring defines a network protocol to be used to access a resource. These strings are short names followed by the three characters '://' (a simple naming convention to denote a protocol definition). Typical URL protocols include http://, ftp://, and mailto://.
URL Host
The 'host' substring identifies a computer or other network device. Hosts come from standard Internet databases such as DNS and can be names or IP addresses. For example, compnetworking.about.com is the host for this Web page.
URL Location
The 'location' substring contains a path to one specific network resource on the host. Resources are normally located in a host directory or folder. For example, /od/internetaccessbestuses/bldef-url.htm is the location of this Web page including two subdirectories and the file name.

The Domain Name System

The DNS translates Internet domain and host names to IP addresses. DNS automatically converts the names we type in our Web browser address bar to the IP addresses of Web servers hosting those sites.
 DNS implements a distributed database to store this name and address information for all public hosts on the Internet. DNS assumes IP addresses do not change (are statically assigned rather than dynamically assigned).
 The DNS database resides on a hierarchy of special database servers. When clients like Web browsers issue requests involving Internet host names, a piece of software called the DNS resolver (usually built into the network operating system) first contacts a DNS server to determine the server's IP address. If the DNS server does not contain the needed mapping, it will in turn forward the request to a different DNS server at the next higher level in the hierarchy. After potentially several forwarding and delegation messages are sent within the DNS hierarchy, the IP address for the given host eventually arrives at the resolver, that in turn completes the request over Internet Protocol.


Examples of top level domains:

Generic top level domains:
  • .com
  •  .biz
  •  .info
  • .edu
  •  .mil
  •  .net, etc.

Country codes (2 character codes):

  •  .jp,
  •  .sw, 
  • .us,
  •  etc.
Most common webpage that people browse using internet
  • Google
  • Wikipedia
  • Facebook
  • Twitter
More info about history of internet: INTERNET

Rabu, 12 November 2014

XML

Asalamualaikum everyone! Today we would like to share what we had learn on computer in science class just now. A new topic and interesting which is XML. XML stand for Extensible Markup Language and was design to describe data. XML also a software-hardware independent tools for carrying information.

Three types of XML
  1. XML document
  2. XML tree
  3. XML table

XML document

Example of information or data stored as xml called xml documents:

<note>
<to>Flor</to>
<from>Janea</from>
<heading>PS</heading>
<body>I've seen suspicious movement from Black Brigade Group</body>

XML is usually used in many aspect of web development and simplify data storage and sharing

XML tree
XML documents have a hierarchical structure and can conceptually be interpreted as a tree structure called an XML tree. Xml documents must contain a root elements ( one that is the parent of all other elements). All elementss in an XML document can contain sub elements, text and attributes.



Rules for Naming Elements

  • Names can contain letters, numbers, and other characters
  • Names cannot start with a number 
  • Names cannot start with the letters like letters xml, XML or etc.

COMPARISON BETWEEN HTML AND XML

HTML XML
COMPARISON
  • Markup languange for displaying web pages in a web browser. Designed to display data with focus on how the data look
  • Displaying information
  • Designed to display data, with focus on how data looks
  • Markup language defines a set of rules for encoding documents that can be read by noth humans and machines. Designed with focus on storing and transporting data
  • Carrying information
  • Designed to transport and store data with focus on what data is
LEARN MORE ABOUT XML THROUGH THIS VIDEO: XML

Selasa, 04 November 2014

PROTEIN DATA BANK

Protein Data Bank is a repository for 3-D biological macro-molecular structure. it is an important source for research in the academic, pharmaceutical and biotechnology.

PDB data
  • Information required includes
  1. Coordinates of all the atoms
  2. Chemical description of the various molecules in the crystal
  3. Experimental information about the structure
  4. Structural description of the biological molecule
Result of Protein images



SOFTWARE TOOLS
- To minimize the amount of manual labor
- Help scientist deposit their results quicker
- Help validate results

Commonly used software
  1. pdb_extract
  2. ADIT (Autodep Input Tool)
  3. PDB Validation Suite


Example of Table for Data Query

Search Fields Example
PDB ID 4HHB, 2MHR
Deposition/Release Date September 1 1996
Contains Chain Type Protein: Ignore, Enzyme: Yes, DNA
Citation Author S.S. Taylor
MORE INFORMATION ABOUT PROTEIN DATA BANK: PDB

SMILES 


Today's lecture is about SMILES AND PDB. The Simplified Molecular Input Line Entry Specification or SMILES is a specification for unambiguously describing the structure of chemical molecules using short ASCII strings.  

SMILES
  • Simplified Molecular Input Line Entry Specification
  • Widely used and computationally efficient
  • Uses atomic symbols and a set of intuitive rules
  • Uses hydrogen-suppressed molecular graphs (HSMG)
Types of smiles
  1. Canonical SMILES refers to the version of the SMILES specification that includes rules for ensuring that every distinct chemical molecules has a single unique SMILES reprisentation
  2. Isomeric SMILES refers to the version of SMILES specification that includes extensions to support the specification of isotopes, chiralty and configuration about double bond.
RESULTS OF SMILES



  • TABLE FOR SMILES BOND
Chemical molecules Molecular formula
Ethene C=C
Chloroethene CIC=C
1,1-Dichloroethene CIC(CI)=C
Cis-1,2-Dichloroethene CIC=CCI
Trichloroethene CIC(CI)=CCI
TUTORIAL ON HOW TO USE SMILES: SMILES