Wednesday 26 December 2012

What is XML???

Assalamu'alaikum...



How are you today? Hope all of you have a nice day!!




Today, we want to introduce about XML. Do you know what is XML? Actually, XML is stand for Extensible Markup Language. It was designed to describe data and focus what data is

It is different with HTML that was designed to display data, with focus on how the data looks.



XML Simplifies Data Sharing



In the real world, computer systems and databases contain data in incompatible formats. XML data is stored in plain text format. This provides a software- and hardware-independent way of storing data.

 This makes it much easier to create data that can be shared by different applications.


XML Does Not DO Anything



Maybe it is a little hard to understand, but XML does not DO anything. XML was created to structure, store, and transport information.




The following example is a note to Ali, from Ahmad, stored as XML:

_____________________________________
<note>
<to>Ali</to>
<from>Ahmad</from>
<heading>Reminder</heading>
<body>Don't forget me this weekend!</body>
</note>
_____________________________________

The note above is quite self descriptive. It has sender and receiver information, it also has a heading and a message body. But still, this XML document does not DO anything. 

It is just information wrapped in tags. Someone must write a piece of software to send, receive or display it.


With XML You Invent Your Own Tags



The tags in the example above (like <to> and <from>) are not defined in any XML standard. These tags are "invented" by the author of the XML document. That is because the XML language has no predefined tags.




The tags used in HTML are predefined. HTML documents can only use tags defined in the HTML standard (like <p>, <h1>, etc.).




XML allows the author to define his/her own tags and his/her own document structure.



There is an example of XML document (in form of tree structure):
_________________________________________________________
<bookstore>
  <book category="COOKING">
    <title lang="en">Everyday Italian</title>
    <author>Giada De Laurentiis</author>
    <year>2005</year>
    <price>30.00</price>
  </book>
  <book category="CHILDREN">
    <title lang="en">Harry Potter</title>
    <author>J K. Rowling</author>
    <year>2005</year>
    <price>29.99</price>
  </book>
  <book category="WEB">
    <title lang="en">Learning XML</title>
    <author>Erik T. Ray</author>
    <year>2003</year>
    <price>39.95</price>
  </book>
</bookstore>
________________________________________________________



Entity References



Some characters have a special meaning in XML.




If you place a character like "<" inside an XML element, it will generate an error because the parser interprets it as the start of a new element.




This will generate an XML error:




<message>if salary < 1000 then</message>


To avoid this error, replace the "<" character with an entity reference:



<message>if salary &lt; 1000 then</message>




There are 5 predefined entity references in XML:

< < less than
>
>
greater than
&
&
ampersand
'
apostrophe
"
quotation mark


XML is Not a Replacement for HTML



XML is a complement to HTML.




It is important to understand that XML is not a replacement for HTML. In most web applications, XML is used to transport data, while HTML is used to format and display the data.




My best description of XML is this:




XML is a software- and hardware-independent tool for carrying information.





XML is Everywhere




XML is now as important for the Web as HTML was to the foundation of the Web.




XML is the most common tool for data transmissions between all sorts of applications.



XML is Used to Create New Internet Languages



A lot of new Internet languages are created with XML.




Here are some examples:

  • XHTML 
  • WSDL for describing available web services
  • WAP and WML as markup languages for handheld devices
  • RSS languages for news feeds
  • RDF and OWL for describing resources and ontology
  • SMIL for describing multimedia for the web 


#  Do you want to have a TUTORIAL for XML???  Try it here.

Friday 14 December 2012

HYPERTEXT MARKUP LANGUAGE (HTML)

Bismillahirrahmanirrahim..

To begin with,
Let us watch this video that describe about the basic of HTML...


So do you get the idea of what HTML really is???
That was just part of the video. You can continue to watch it here.


HyperText Markup Language (HTML) is the main markup language for displaying web pages and other information that can be displayed in a web browser.


HTML is written in the form of HTML element consisting of tags enclosed in angle brackets (like <html>), within the web page content. HTML tags most commonly come in pairs like <h1> and </h1>, although some tags, known as empty elements, are unpaired, for example <img>

The first tag in a pair is the start tag, the second tag is the end tag (they are also called opening tags and closing tags). In between these tags web designers can add text, tags, comments and other types of text-based content.


The purpose of a web browser is to read HTML documents and compose them into visible or audible web pages. The browser does not display the HTML tags, but uses the tags to interpret the content of the page.



HTML elements form the building blocks of all websites. HTML allows images and objects to be embedded and can be used to create interactive forms. 

It provides a means to create structured documents by denoting structural semantics for text such as headings, paragraphs, lists, links, quotes and other items.

 It can embed scripts in languages such as JavaScript which affect the behavior of HTML webpages.

Markup


HTML markup consists of several key components, including elements (and their attributes), character-based data types, character references and entity references. Another important component is the document type declaration, which triggers standards mode rendering.

Example




(The text between <html> and </html> describes the web page, and the text between <body> and </body> is the visible page content. The markup text '<title>Hello HTML</title>' defines the browser page title.)

Elements




HTML documents are composed entirely of HTML elements that, in their most general form have three components: a pair of tags, a "start tag" and "end tag"; some attributes within the start tag; and finally, any textual and graphical content between the start and end tags, perhaps including other nested elements.



 The HTML element is everything between and including the start and end tags. Each tag is enclosed in angle brackets.



The general form of an HTML element is therefore: <tag attribute1="value1" attribute2="value2">content</tag>. Some HTML elements are defined as empty elements and take the form <tag attribute1="value1" attribute2="value2" >.



 Empty elements may enclose no content. The name of an HTML element is the name used in the tags. 



Note that the end tag's name is preceded by a slash character, "/", and that in empty elements the end tag is neither required nor allowed. If attributes are not mentioned, default values are used in each case.

For addition, there are some types of special character and its HTML code:


Desired Character     HTML required
<  &lt;
> &gt;
 &  &amp;
  &quot;
  non breaking space &nbsp;

There are much more knowledge about HTML that cannot be explained here...

For more info..visit here


PROTEIN DATA BANK(PDB)

Assalamu'alaikum ....

For this post, we will share a brief information about ..

"PROTEIN DATA BANK"

Do you know what is PDB?...


It is actually a repository for 3-D  biological macromolecular structure
It includes proteins,nucleic acids and viruses. PDB is obtained by X-Ray crystallography (80%) or NMR spectroscopy (16%) and all data are available to the public.This structure is actually submitted by biologists and biochemists from around the world.


PDB was founded in 1971 by Brookhaven National Laboratory, New York. The first set of data were entered on punched cards. Then with magnetic tapes.After that it is  transferred to the Research Collaboratory for Structural Bioinformatics (RCSB) in 1998.Currently it holds 29,000 released structures.

PDB an important resource for research in the academic, pharmaceutical, and biotechnology sectors

Example:
  • Will this molecule turns into a cancer cell?
  • Can this combination of molecules cure common cold?
  • How does radiation affect the RNA and DNA?

Protein Images






Structure of Squash Trypsin Inhibitor:





Structure of the Alpha Amylase





Structure of Phospholipase





Structure of clpp:





PDB data format

PDB data format is used to contain the coordinates and related information . In the late 1990’s macromolecular Crystallographic Information file (mmCIF) evolved. It conforms to well-documented standards and facilitates automated data management

Software Tools

There are various software tools can minimize the amount of manual labor
It helps scientists deposit their results quicker and also help validate their results


Commonly used software:
Data Query

Search Fields Example
PDB ID
4HHB,2MHR
Contains Chain Type
Protein: IGNORE,Enzyme:YES
Citation Author
Stuart Taylor
Compound Information
Myoglobin
Number of chains
1-5
Structure Content
Present of Alpha

PDB Beta

Includes three tiers architecture: relational database, presentation 
tier and an object-relational J2EE middle tier. It also a
dded XML as a file format



Uses freely distributed Java components:
  • Lucene – Text indexing system
  • JfreeChart – Charts generation
  • Hibernate – Object/relational persistence
  • Jboss – J2EE application server

Data Integration


Users are interested in enzymes, diseases and others beside macro molecular structure.


External data are included in PDB Beta

  • Gene Ontology – Vocabularies of all known gene and protein
  • Enzyme Commission – Repository of Enzymes
  • KEGG Pathways – Molecule interaction networks




  • Data are collected and integrated weekly.


    > Visit Protien Data Bank Website: RCHB Protein Data Bank