Thursday, 19 December 2013

PDB


PROTEIN DATA BANK

INTRODUCTION
  • The Protein Data Bank (PDB) archive is the single worldwide repository of information about the 3D structures of large biological molecules, including proteins and nucleic acids.
  • These are the molecules of life that are found in all organisms including bacteria, yeast, plants, flies, other animals, and humans.
  • Obtain by X-ray crystallography (80%) or NMR spectroscopy (16%)
  • Submitted by biologists and biochemists from around the world.
For more information visit: Protein Data Bank


AMYLASE 



ClassificationAlpha Amylase
Structure Weight48016.77
MoleculeALPHA-1,4-GLUCAN-4-GLUCANOHYDROLASE
TypeProtein
Length425



TRYPSIN





ClassificationComplex (proteinase/inhibitor)
Structure Weight29892.08
MoleculeBETA-TRYPSIN
TypeProtein
Length223

PEPSIN 


ClassificationHydrolase (acid Proteinase)
Structure Weight34469.8
MoleculePEPSIN
TypeProtein
Length326

HTRA



ClassificationProtein Binding
Structure Weight14890.9
MoleculePutative serine protease
TypeProtein
Length134

CARBOXYPEPTIDASE



ClassificationCarboxypeptidase
Structure Weight138865.59
MoleculeCARBOXYPEPTIDASE A
TypeProtein
Length307

smiles :)

Simplified Molecular Input Line

Entry Specifications


INTRODUCTION OF SMILES

  • SMILES is a specification for unambiguously describing the structure of chemical molecules using short ASCII strings.
  • SMILES strings can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensional models of the molecules.

LAW OF SMILE


1) SMILES Bonds  

SINGLE*                    -
DOUBLE                    =
TRIPLE                      #
AROMATIC*              :

2) SMILES Branches

  • Represented by enclosure in parentheses
  • Can be nested or stacked
  • Examples:    
               1) OCC(C)C is iso-Butanol
                    2) OC(C)(C)C is tert-Butanol

3) SMILES Conventions
  • Avoid two consecutive left parentheses if possible
  • Strive for the fewest number of possible branches
  • Tautomeric bonds are not designated; enter the appropriate form

SMILES notation by using ChemSketch. :)





SMILESNameSMILESName
CCETHANE[OH3+]HYDRONIUM ION
C#NHYDROGEN CYANIDE[235U]URANIUM-235
O=C=OCARBON DIOXIDE[2H]O[2H]DEUTREIUM OXIDE

Click the link below for
1. SMILECAS Database Files

Thursday, 21 November 2013

Let's Educate Ourself About Internet

LET'S begin......:)




LESSON 1:What Was the “Victorian Internet”?
Telegraph


The Telegraph
•Invented in the 1840s.

•Signals sent over wires that were established over vast distances

•Used extensively by the U.S. Government during the American Civil War, 1861 - 1865
Morse Code was dots and dashes, or short signals and long signals







Famous Quote From
Sir Isaac Newton











LESSON 2:What Is the Internet?

Internet



A network of networks, joining many government, university and private computers together and providing an infrastructure for the use of E-mail, bulletin boards, file archives, hypertext documents, databases and other computational resources

The vast collection of computer networks which form and act as a single huge network for transport of data and messages across distances which can be anywhere from the same office to anywhere in the world.

Written by William F. Slater, III
1996
President of the Chicago Chapter of the Internet Society




The largest network of networks in the world.
Uses TCP/IP protocols and packet switching .
Runs on any communications substrate.                                                                                                                   
 Dr. Vinton Cerf,
Co-Creator of TCP/IP






LESSON 3:History of the Internet...







Click this link to Explore on Internet History...


LESSON 4:Internet Growth Trends


YearsInformation
1997111 hosts on Internet
1981213 hosts
1983562 hosts
19841,000 hosts
19865,000 hosts
198710,000 hosts
1989100,000 hosts
19921,000,000 hosts
2001150 – 175 million hosts
2002over 200 million hosts
(2010- 2013)about 80% of the planet will be on the Internet

LESSON 5: IP Addressing

•An IP address is a unique global address for a network interface
•Exceptions:
–Dynamically assigned IP addresses (à DHCP, Lab 7)
–IP addresses in private networks (à NAT, Lab 7)

•An IP address:
        - is a 32 bit long identifier
        - encodes a network number (network prefixand a host number 

Network prefix and host number
  •         The network prefix identifies a network and the host number identifies a specific host (actually,interface on the network).

network prefix host number




New To XML ???



What is XML ?

  • XML stands for EXtensible Markup Language
  • XML is a markup language much like HTML
  • XML was designed to carry data, not to display data
  • XML tags are not predefined. You must define your own tags
  • XML is designed to be self-descriptive
  • XML is a W3C Recommendation

The Difference Between XML and HTML



XMLHTML
designed to transport and store data, with focus on what data isdesigned to display data, with focus on how data looks
carrying informationdisplaying information

Invent Your Own Tags With XML


  • 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.

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.

What XML can do ?


 1) XML Separates Data from HTML

If you need to display dynamic data in your HTML document, it will take a lot of work to edit the HTML each time the data changes.
With XML, data can be stored in separate XML files. This way you can concentrate on using HTML/CSS for display and layout, and be sure that changes in the underlying data will not require any changes to the HTML

2) 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.

3)XML Simplifies Data Transport

One of the most time-consuming challenges for developers is to exchange data between incompatible systems over the Internet.
Exchanging data as XML greatly reduces this complexity, since the data can be read by different incompatible applications.

4)XML Simplifies Platform Changes

Upgrading to new systems (hardware or software platforms), is always time consuming. Large amounts of data must be converted and incompatible data is often lost.
XML data is stored in text format. This makes it easier to expand or upgrade to new operating systems, new applications, or new browsers, without losing data.

5)XML Makes Your Data More Available

Different applications can access your data, not only in HTML pages, but also from XML data sources.
With XML, your data can be available to all kinds of "reading machines" (Handheld computers, voice machines, news feeds, etc), and make it more available for blind people, or people with other disabilities


XML Tree


DOCUMENTATION

<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>


TREE




TABLE


tofromheadingbody
ToveJaniReminderDon't forget me this weekend!


XML Syntax Rules

All XML Elements Must Have a Closing Tag

In HTML, some elements do not have to have a closing tag:
<p>This is a paragraph.
<br>
In XML, it is illegal to omit the closing tag. All elements must have a closing tag:
<p>This is a paragraph.</p>

<br />


XML Tags are Case Sensitive

XML tags are case sensitive. The tag <Letter> is different from the tag <letter>.
Opening and closing tags must be written with the same case:

<Message>This is incorrect</message>

<message>This is correct</message>


XML Elements Must be Properly Nested

In HTML, you might see improperly nested elements:

<b><i>This text is bold and italic</b></i>
In XML, all elements must be properly nested within each other:
<b><i>This text is bold and italic</i></b>


XML Documents Must Have a Root Element

XML documents must contain one element that is the parent of all other elements. This element is called the rootelement.

<root>
  <child>
    <subchild>.....</subchild>
  </child>
</root>


XML Attribute Values Must be Quoted

XML elements can have attributes in name/value pairs just like in HTML.
In XML, the attribute values must always be quoted.
Study the two XML documents below. The first one is incorrect, the second is correct:

<note date=12/11/2007>
  <to>Tove</to>
  <from>Jani</from>
</note>

<note date="12/11/2007">
  <to>Tove</to>
  <from>Jani</from>
</note>


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:

&lt;<less than
&gt;>greater than
&amp;&ampersand 
&apos;'apostrophe
&quot;"quotation mark


XML Attributes

XML Attributes Must be Quoted

Attribute values must always be quoted. Either single or double quotes can be used. For a person's sex, the person element can be written like this:

<person sex="female">

or like this:

<person sex='female'>

If the attribute value itself contains double quotes you can use single quotes, like in this example:

<gangster name='George "Shotgun" Ziegler'>

or you can use character entities:

<gangster name="George &quot;Shotgun&quot; Ziegler">


XML Elements vs. Attributes

Take a look at these examples:

<person sex="female">
  <firstname>Anna</firstname>
  <lastname>Smith</lastname>
</person>

<person>
  <sex>female</sex>
  <firstname>Anna</firstname>
  <lastname>Smith</lastname>
</person>

In the first example sex is an attribute. In the last, sex is an element. Both examples provide the same information.
There are no rules about when to use attributes or when to use elements. Attributes are handy in HTML. In XML my advice is to avoid them. Use elements instead.


For more information, click this :)


Thank You !!


Tuesday, 19 November 2013

Lets Learn HTML

WHAT IS HTML?

Webpages are written in HTML - a simple scripting language.

HTML is short for HyperText Markup Language.

•      Hypertext is simply a piece of text that works as a link.
•      Markup Language is a way of writing layout information within documents.

Basically an HTML document is a plain text file that contains text and nothing else.

When a browser opens an HTML file, the browser will look for HTML codes in the text and use them to change the layout, insert images, or create links to other pages.

Since HTML documents are just text files they can be written in even the simplest text editor.

Some of the most popular HTML editors, such as FrontPage or Dreamweaver will let you create pages more or less as you write documents in Word or whatever text editor you're using.

All you need to do is type in the code, then save the document, making sure to put an .html extension or an .htm extension to the file (for instance "mypage.html").

For more information: http://www.w3schools.com/html/

LESSON 1: PAGE STRUCTURE

All normal webpages consist of a head and a body



  • The head is used for text and tags that do not show directly on the page.
  • The body is used for text and tags that are shown directly on the page.
The most basic code - the code you will use for any page you make, is shown below:

Figure 1.




LESSON 2: HOW TO MAKE A LINK

The tags used to produce links are the <a> and </a>

The <a> tells where the link should start and the </a> indicates where the link ends.

Everything between these two will work as a link.

The target of the link is added to the <a> tag using 
the href="http://www.whateverpage.com" setting.

The example below shows how to make the word here work as a link to yahoo.

Figure 2

LESSON 3: BULLETED LISTS

This page shows how to make different kinds of bulleted lists.

You have the following bullet options:
  • disc

  • circle

  • square
Look at these examples to see the detailed syntax.

Figure 3.
LESSON 4: NUMBERED LISTS

This page shows how to make different kinds of numbered lists.

You have the following number options:
  • Plain numbers

  • Capital Letters

  • Small Letters

  • Capital Roman Numbers

  • Small Roman Numbers


Figure 5


LESSON 5: HTML IMAGE

To reduce download times as much as possible two of the best image compressing formats used on the web are:



GIFJPG
256 colorsUnlimited colors
Can handle transparent areasCan't handle transparent areas
This format is not good at compressing photographsExcellent for compressing photographs and complex images
In general, it is excellent for banners, buttons and clipartIn general, it is not good for banners, buttons and clipart.

Table: Differences between GIF and JPG image.


LESSON 6: INSERTING HTML IMAGE

Here is the HTML code used to insert the image on this webpage:




Figure 6

LESSON 7: BASIC TABLES USING HTML

Tables are defined with the <table> tag.

To insert a table on your page you simply add these tags where you want the table to occur:


Figure 7
ROWS:

To add rows to your table use the <tr> and </tr> tags.

Example:
<table>
<tr></tr>
<tr></tr>
</table> 


It doesn't make sense to write the above lines in itself, cause you can't write content outside of table cells.

If you do write things outside of cells it will appear right above the table.

COLUMNS:

You can divide rows into columns with <td> and </td> tags:

Example:
<table>
<tr> <td>This is row one, left side.</td> <td>This is row one, right side.</td> </tr>
<tr> <td>This is row two, left side.</td> <td>This is row two, right side.</td> </tr>
</table>


Result:
This is row one, left side.This is row one, right side.
This is row two, left side.This is row two, right side.