CTS Pro: December 2012

Thursday, 27 December 2012

H T M L

H T M L

The World Wide Web

It is the set of computers on the internet that support http.

HTTP
HTTP is the initials for the hypertext transfer protocol. It is the language used by a www client to request documents from a www server.

HTML

HTML is the initials for HyperText MarkUp Language. It is the main markup language for displaying web pages and other information that can be displayed in a web browser.

Creating and Publishing a web page

Steps for creating and publishing a web page:

1. Firstly, create an HTML document.

2. Secondly, place the document in world accessible directory.

3. Then, access the web page through:

http://hostname/~username/filename

4. Lastly, validate the document

-check the syntax a formal HTML validator

An example of a simple HTML document:


<!DOCTYPE html>

<html>

  <head>

    <title>Hello HTML</title>

  </head>

  <body>

    <p>Hello World!</p>

  </body>

</html>

Preformatted Paragraphs

• The PRE Element

– <PRE>….</PRE>

• Attributes: WIDTH

– Expected width in characters. Not widely supported.

• Problem: Special Characters

<PRE>

if (a<b>{

doThis();

} else {

doThat();
}

Desired Character HTML Required

<
<

> >

&
&

" "

Non-breaking Space
&nbsp

We can try the HTML at HTML Tutorial.

Is a markup language much like HTML and was designed to describe data and focus what data is. In XML tags are not predefined. It uses a DTD or an XML schema to describe the data and both is designed to self-descriptive.

The Difference between XML and HTML :

XML is not a replacement for HTML.
XML and HTML were designed with different goals:
– XML was designed to transport and store data, with focus on what data is
– HTML was designed to display data, with focus on how data looks
HTML is about displaying information, while XML is about carrying information.

DIFFERENCES	HTML	XML
CLOSING TAG	<p>This is a paragraph <p>This is another paragraph	<p>This is a paragraph</p> <p>This is another paragraph </p>
NESTING	<b><i>*This text is bold and italic*</b></i>	<b><i>*This text is bold and italic*</i></b>

XML Does not DO Anything

1. XML was created to structure, store, and transport information

2. The following example is a note to Tove from Jani, stored as XML:

<note>
<to>Tove</to>
<from>Jani</from>
<heading>Reminder</heading>
<body>Don't forget me this weekend!</body>
</note>

X M L

XML Documents Form a Tree Structure

l . XML documents must contain a root element

2. This element is "the parent" of all other elements

3. The elements in an XML document form a document tree

4. The tree starts at the root and branches to the lowest level of the tree

5. All elements can have sub elements (child elements):

6. The terms parent, child, and sibling are used to describe the relationships between elements

7. Parent elements have children

8. Children on the same level are called siblings (brothers or sisters)

9. All elements can have text content and attributes (just like in HTML)

The image above represents one book in the XML below:

<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>

XML Tutorial

Sunday, 16 December 2012

Protein Data Bank

Assalamualaikum,
today we learn about Protein Data Bank (PDB) using RasWin software. It's quite complicated, but interesting. We can observe the structure of protein in 3D with different kind of display such as wireframe, backbone, ball&stick and etc. We can also customize the colour according to temperature, structure, shapely and etc.

Image of PDB

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.

Image of PDB

The Protein Data Bank (PDB) is a repository for the 3-D structural data of large biological molecules, such as protein and nucleic acids.The data, typically obtained by X-ray crystallography or NMR spectroscopy and submitted by biologists and biochemists from around the world, are freely accessible on the Internet via the websites of its member organisations (PDBe, PDBj, and RCSB). The PDB is a key resource in areas of structural biology, such as structural genomic.

The example of Protein Data Bank(PDB) in 3-D structure.

THE STRUCTURE OF CLPP AT 2.3 ANGSTROM RESOLUTION SUGGESTS A MODEL FOR ATP-DEPENDENT PROTEOLYSIS

Authors	Wang, J.
Classification	Peptidase
Type	protein
Display mode	Ribbons
Colour	Chain

THE GEOMETRY OF THE REACTIVE SITE AND OF THE PEPTIDE GROUPS IN TRYPSIN, TRYPSINOGEN AND ITS COMPLEXES WITH INHIBITORS

Authors	Huber,R.
Classification	Complex (protienase/inhibitor)
Type	Protein
Display mode	Strands
Colour	Group

S146A MUTANT OF THERMOMYCES (HUMICOLA) LANUGINOSA LIPASE COMPLEX WITH OLEIC ACID

Authors	Brzozowski,A.M.
Classification	Lipase
Type	Protein
Display mode	Spacefill
Colour	Temperature

The structure of human pancreatic alpha-amylase at 1.8 angstroms resolution and comparisons with related enzymes

Authors	Luo,Y.
Classification	Hydrolase (o Glycosyl)
Type	Protein
Display mode	Backbone
Colour	Structure

Desired Character	HTML Required
<	<
>	>
&	&
"	"
Non-breaking Space	&nbsp