PDB PROTEIN DATA BANK

ASSALAMUALAIKUM

PDB PROTEIN DATA BANK

Actually we are shocked during this lecture because we have no idea about this topic.Well,as you all know,we all from CTS department where we learn only about mathematics.And suddenly,madam taught us about biology.We are totally CONFUSED!!!!!!!!!!!!!

So,lets learn together about this topic..

First of all,what is PDB PROTEIN DATA BANK?

 A repository for 3D biological macromolecular structure.It includes proteins,nucleic acids and viruses.

What about the history ?

PROTEIN DATA BANK was founded in 1971 by Brookhaven National Laboratory,New York.First set of data were entered on punched cards.Then,with magnetic tapes.It is transfered to the Research Collaborators for structural Bioinformatics(RCSB) in 1998.

Here we provide you some example of enzyme image :

1.AMYLASE

2.LIPASE

3.PEPSIN

4.SUCRASE

5.TRYPSIN

We used rasmol application to view this image after download the file at rscb ..You all can try by click here.

Here we provide all the specification of design of molecules:

DISPLAY	COLOURS
Wireframe	Monochrome
Backbone	CPK
Sticks	Shapely
Spacefill	Group
Ball & Stick	Chain
Ribbons	Temperature
Strands	Structure
Cartoons	User

So,thats all from us about this topic and this semester..Enjoy our blog...muahhhxxxx 

byeeeeee uollssss !!!!!

XML..

Assalamualaikum.. 

we meet again..

For the previous post, we have share with you about HTML. Today, we would like to share with you about XML..

Table of Contents

1)	Introduction
2)	XML tree
3)	XML Syntax Error

Introduction to XML.

=>Extensible Markup Language (XML) is a markup language that defines a set of rules for encoding documents in a format which is both human-readable and machine-readable.

=>XML was designed to describe data or carry data, not to display data.

=>XML tags are not predefined. You must define your own tags. It is also designed to be self-descriptive.
=>XML Does not do anything
=> its just a plain text
=> XML is not a replacement for HTML but it is a complement to HTML.

How Can XML be Used?

XML is used in many aspects of web development, often to simplify data storage and sharing.

• XML Separates Data from HTML

• XML Simplifies Data Sharing

• XML Simplifies Data Transport

• XML Simplifies Platform Changes

• XML Makes Your Data More Available

Internet Languages Written in XML

Several Internet languages are written in XML. Here are some examples:

• XHTML 
• XML Schema
• SVG
• WSDL
• RSS

Click HERE to know more about XML.




XML DOCUMENTATION and TREE

But not this tree.. :)

XML documents must contain a root element. This element is "the parent" of all other elements. The elements in an XML document form a document tree. The tree starts at the root and branches to the lowest level of the tree.

example of XML TREE

<inventory>




<drink>


<lemonade>





<price>$2.50</price>




<amount>20</amount>


<price>$1.50</price>




</lemonade><pop>


</drink>

<amount>10</amount>
</pop><snack>


<amount>60</amount>

<chips>
<price>$4.50</price>
</chips>


</inventory>



</snack>

XML Syntax Rules

Here are some syntax error that must be avoid while doing xml code.

1. All XML Elements Must Have a Closing Tag

2. XML Tags are Case Sensitive

3. XML Elements Must be Properly Nested

4. XML Documents Must Have a Root Element

5. XML Attribute Values Must be Quoted

6. 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

Here we provide some tutorial on XML;

• www.w3schools.com/xml/
• http://ww.youtube.com/watch?v=yUw-aTOwAw8

That's all from us

Thank You.. :)

SMILES

Assalamualiakum :)

Today we want to talk about SMILES but not this smile

SMILES here means the simplified molecular-input line-entry system (SMILES) which is a specification in form of a line notation for describing the structure of chemical species 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 molecule.

There are two types of SMILES which are Canonical SMILES and Isomeric SMILES. Canonical SMILES includes rules for ensuring that each distinct chemical molecule has a single unique SMILES representation while Isomeric SMILES includes extensions to support the specification of isotopes chirality and configuration about double bond.

Here are some examples of SMILES

To learn more about SMILES, click here

Thats all from us. Thank you

Bye uolls!

INTERNET NETWORKING

Assalamualaikum :)

We meet again..

Did you enjoy and get better understanding about our post last time??

If you enjoy it, come and visit us often.

Dont forget to invite you friend too..

Orait,

Can i ask you some question..

Have you ever wondered how you could open our blog? But we are far away from you all.

Is there a magic happen to you?? 

hey,, stop thinking that. its nonsense.. hahaha..

So, let us explain to you..

Actually, there are some networking that connect us with you which is internet networking..

Introduction to Internet.

         The Internet is a global network connecting millions of computers. More than 100 countries are linked into exchanges of data, news and opinions. According to Internet World Stats, as of December 31, 2011 there was an estimated 2,267,233,742 Internet users worldwide. The number of Internet users represents 32.7 percent of the world's population.
         Unlike online services, which are centrally controlled, the Internet is decentralized by design. Each Internet computer, called a host, is independent. Its operators can choose which Internet services to use and which local services to make available to the global Internet community. Remarkably, this anarchy by design works exceedingly well. There are a variety of ways to access the Internet. Most online services offer access to some Internet services. It is also possible to gain access through a commercial Internet Service Provider (ISP).

Click HERE to know more about internet.

Who Owns the Internet?

No one actually owns the Internet, and no single person or organization controls the Internet in its entirety. The Internet is more of a concept than an actual tangible entity, and it relies on a physical infrastructure that connects networks to other networks.






The Universal Resource Locator (URL)
->Each page of information on the web has a unique address called the URL at which it can be found

Other explanation on URL

-Here are the Protocols that may appear in URL's

Protocol Name	Use
ftp://	File Transfer
http://	Hypertext
https://	Hypertext Secure
Mailto:	Sending email
News:	Requesting news
telnet://	Remote login

-Much of the power of browsers is that they are multiprotocol. That is , they can retrieve and render information from a variety of servers and sources.

For more information about URL, Just click here..


Internet Suite Protocol
>Actually, there are many problem on internet networking while creating URL such as HETEROGENEITY AND SCALLING. Now, its all solve by the appearance of TCP/IP.

>The Internet protocol suite is the computer networking model and set of communications protocols used on the Internet and similar computer networks. It is commonly known as TCP/IP, because its most important protocols, the Transmission Control Protocol (TCP) and the Internet Protocol (IP), were the first networking protocols defined in this standard.
>TCP/IP provides end-to-end connectivity specifying how data should be packetized, addressed, transmitted, routed and received at the destination.

For more information, Click HERE..

Advantages of the Internet.

There are many advantage of internet networking such as:  

 1) Faster Communication

  2) Abundant Information Resources

  3) Inexhaustible Education

  4) Entertainment for Everyone

  5) Social Networking and Staying Connected

  6) Online Services and E-commerce

Disadvantages of the Internet.

Despite of all the advantage, there are also many disadvantage of internet such as:

  1)Theft of Personal Information 

  2)Spamming

  3)Malware Threats

  4)Age-inappropriate Content

  5)Social Isolation, Obesity, and Depression

=>Here we provide an INTERESTING video about history of internet.

=>Just Click HERE     

=>Let's watch.. Enjoy it..

Okey, thats all from us..

Thank you..

HTML

Assalamualaikum..

Every tuesday we are having a computer in science class at Orchid Lab.And today we are going to share about what we learn on that class.The title is HTML.

HTML

Do you know what is HTML?Where is HTML look like?And what it benefit us as a user?Where we can learn more about HTML?

So let we share with you..

But before that.......

Smile like this.....hahahaha

Okay,lets talk about HTML...

What is html?

HTML is a markup language for describing web documents (web pages).

• HTML stands for Hyper Text Markup Language
• A markup language is a set of markup tags
• HTML documents are described by HTML tags
• Each HTML tag describes different document content

What is HTML look like?

By the way,we forgot to tell you that HTML creates by using notepad application.Here we attached some example of the code and outcome.

The code..

The outcome..

What it benefits us as a user?

• We can make a list
• We can attach an image and a moving image
• We can make a table whether it fit or not fit to the word
• We can paste the URL and user can click the URL to go to the related page

LIST

<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">

<html xmlns="http://www.w3.org/1999/xhtml">

<head>

<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />

<title>Example on building nested HTML lists</title>

</head>

<body>

<h1>Example on building nested HTML lists</h1>

<ul>

<li>List Item 1</li>

<li>List Item 2

<ul>

<li>Sub Item 1</li>

<li>Sub Item 2</li>

<li>Sub Item 3</li>

<li>Sub Item 4</li>

<li>Sub Item 5</li>

</ul>

</li>

<li>List Item 3</li>

<li>List Item 4</li>

<li>List Item 5</li>

<li>List Item 6</li>

<li>List Item 7</li>

<li>List Item 8</li>

<li>List Item 9</li>

<li>List Item 10</li>

</ul>

</body>

</html>

IMAGE AND MOVING IMAGE

<html>

<body>

<p>

An image:

<img src="http://upload.wikimedia.org/wikipedia/commons/thumb/8/85/Smiley.svg/2000px-Smiley.svg.png" alt="Smiley face" width="32" height="32" />

</p>

<p>

A moving image:

<img src="http://i789.photobucket.com/albums/yy180/countfifty/hackanm.gif" alt="Computer man"width="48" height="48" />

</p>

<p>

Note that the syntax of inserting a moving image is no different from a non-moving image

</p> 

</body>

</html>

An image: 
A moving image: 
Note that the syntax of inserting a moving image is no different from a non-moving image

TABLE

<html>
<body>
<h4>KULIYYAH OF SCIENCE<h/4>
<table border="1">
<tr>
<td>No</td>
<td>Department</td>
<td>HOD</td>
<td>Image</td>
<td>Url</td>
</tr>
<tr>
<td>1</td>
<td>MARINE</td>
<td>DR. NORMAWATY</td>
<td><img src="http://wwwsst.ums.edu.my/data/image/marine%20science/Norma.jpg" alt="DR. NORMAWATY" width="32" height="32" /></td>
<td><a href="http://www.iium.edu.my/science/departments/marine-science/about-marine-science">MARINE</a></td>
</tr>
<tr>
<td>2</td>
<td>PHYSICS</td>
<td>JESNI BIN SHAMSUL SHAARI</td>
<td><img src="http://www.iium.edu.my/sites/default/files/staff_img/3844.jpg" alt="JESNI BIN SHAMSUL SHAARI" width="32" height="32" /></td>
<td><a href="http://www.iium.edu.my/science/departments-1">PHYSICS</a></td></td>
</tr>
<tr>
<td>3</td>
<td>CHEMISTRY</td>
<td>WAN KHARTINI BINTI WAN ABDUL KHODIR</td>
<td><img src="http://www.iium.edu.my/sites/default/files/staff_img/6822.jpg" alt="WAN KHARTINI BINTI WAN ABDUL KHODIR" width="32" height="32" /></td>
<td><a href="http://www.iium.edu.my/science/departments-0">CHEMISTRY</a></td>
</tr>
<tr>
<td>4</td>
<td>CTS</td>
<td>DR PAH CHIN HEE</td>
<td><img src="http://www.iium.edu.my/sites/default/files/staff_img/5826.jpg" alt="CTS" width="32" height="32" /></td>
<td><a href="http://www.iium.edu.my/science/departments/about-cts">CTS</a></td>
</tr>
<tr>
<td>5</td>
<td>BIOTECH</td>
<td>TENGKU HAZIYAMIN BIN TENGKU ABDUL HAMID</td>
<td><img src="http://www.iium.edu.my/sites/default/files/staff_img/4261.jpg" alt="TENGKU HAZIYAMIN BIN TENGKU ABDUL HAMID" width="32" height="32" /></td>
<td><a href="http://www.iium.edu.my/science/departments/about-biotechnology">BIOTECH</a></td>
</tr>
<tr>
<td>6</td>
<td>PLANTSCIENCE</td>
<td>MOHD SHUKOR BIN NORDIN</td>
<td><img src="http://www.iium.edu.my/sites/default/files/staff_img/6887.jpg" alt="MOHD SHUKOR BIN NORDIN" width="32" height="32" /></td>
<td><a href="http://www.iium.edu.my/science/departments-2">PLANT SCIENCE</a></td>
</tr>
</table>
</body>

</html>

KULIYYAH OF SCIENCE

No	Department	HOD	Image	Url
1	MARINE	DR. NORMAWATY		MARINE
2	PHYSICS	JESNI BIN SHAMSUL SHAARI		PHYSICS
3	CHEMISTRY	WAN KHARTINI BINTI WAN ABDUL KHODIR		CHEMISTRY
4	CTS	DR PAH CHIN HEE		CTS
5	BIOTECH	TENGKU HAZIYAMIN BIN TENGKU ABDUL HAMID		BIOTECH
6	PLANTSCIENCE	MOHD SHUKOR BIN NORDIN		PLANT SCIENCE

What is the structure of HTML?

Below is a visualization of an HTML page structure:

<html>

<head>

<title>Page title</title>

</head>

<body>

<h1>This is a heading</h1>

<p>This is a paragraph.</p>

<p>This is another paragraph.</p>

</body>

</html>

Where we can learn more about HTML?

Just click this URL

• http://www.w3schools.com/html/html_intro.asp
• https://www.youtube.com/watch?v=v4oN4DuR7YU

Okay,that is all about HTML..We hope you all get better understanding about it..

So,time to we take a nap...zzzzzzzz

ehhhh....byeeee bloggerzzz....

CHEMSKETCH

Assalamualaikum:)

What we have learned today is about another software called ACD/ChemSketch.

1. ChemSketch is a free download for educational use. It can be used to produce structures of organic molecules, names of organic molecules as well as Lewis structures, 3D structures, space filling models or ball and stick models, among other things.This software is efficient as it is able to draw the molecular structures in chemistry, make it more simpler to draw and design the structure. 

To start use ChemSketch, first you have to download the software from http://chemsketch.en.softonic.com/

1. 
   

1. Here we provide you some interface of the software,

Figure 1

Figure 2

Figure 3

Figure 1 shows the first interface of the software as you begin. 

The software consists of two mode,

Structure and Draw. There are similarities and differences between them. Generally, the Structure mode generates structural parts of the file such as atoms and bonds and the Draw mode allows you to enhance them with arrows, boxes, and non-structure drawings. 

In both modes, there are drop down dialog boxes and panels in which you make stylistic choices among different fonts, line widths, etc. 

As you explore the toolbar buttons, point to a button and in a moment a tool tip will appear. This is one of the best ways to learn the tools buttons and their functions.

When you are using Help, open the window on Mouse Commands. Each tool seems to behave slightly differently depending on whether you single or double-click, drag, etc. It is good to be aware of the possibilities.

Tools

The two images below show the Structure and Drawing Modes windows. In addition to the buttons in both modes, there are tool panels that apply formatting to your structure and drawing. Access the panels from the Tools menu in both modes.

There are some tutorial that can guide you as reference to use this software. Here we provide you some links that may benefits you.

  1)www.youtube.com/watch?v=izRQwA0MNDY

2)www.youtube.com/watch?v=CHlJuAcyTv8

                                     

  By using the ChemSketch program, we can also provide a table to ease the user.At first, the user have to 

type the input needed to construct the table.Then, the user

just have to drag the input one by one into their own column and row.Each of the table 

will fit according to their own input automatically.

Example of table we used in ChemSketch:

MAPLE PROGRAMMING

Assalamualaikum :)

Today we want to share with you about maple programming.

MAPLE PROGRAMMING

MAPLE is a powerful mathematical software package. It can be used to obtain both symbolic and numerical solutions of problems in arithmetic, algebra, and calculus and to generate plots of the solutions it generates.

Based on history,Maple is a commercial computer algebra system developed and sold commercially by Maplesoft, a software company based in Waterloo, Ontario, Canada. The current major version is version 18, which was released in March 2014.

It was first developed in 1980 by the Symbolic Computition Group at the University of Waterloo. In 1988, Maplesoft (then known as Waterloo Maple Inc.) was founded to commercialize the technology.

MAPLE SYNTAX AND OPERATIONS

Commands.
A MAPLE command is a statement of a calculation followed by a semicolon (the result is displayed on the screen) or a colon (the result is stored but not displayed). Following are some commands followed by the displayed results. Enter the commands on your worksheet and verify the given results. When you get to "Save the file," select "Save" under the "File" menu or type CTRL-S.

• [> 4+5;9
• [> 6^2;36
• [> 3*4 + 7;19
• [> 3*(4+7);33
  
• Save the file

If you don't include a semicolon or colon at the end of a command, MAPLE will interpret the next command line as a continuation of the previous command.


Arithmetic operations
The symbols +, -, *, /, and ^ (or **) denote addition, subtraction, multiplication, division, and exponentiation (4^2 = 4**2 = 4² = 16). When a string of operations are specified in a command, MAPLE first does exponentiations, then multiplications and divisions, then additions and subtractions. To change the order, use parentheses.

Editing commands.
If you make a mistake in a command (like forgetting a semicolon) or want to change a command, you can go back and edit the command with the cursor and mouse as you would a word-processor text.

Operating on the last result.
Use a quotation mark (") to refer to the result of the last calculation, and a double quotation mark ("") to refer to the next-to-last result. For example,

• [> 5*2;10
• [> 7 + ";17
• [> " * "";170

Exact arithmetic and floating-point arithmetic
MAPLE calculates fractions (exact arithmetic) unless you specify that you want decimals (floating-point arithmetic) with the evalf function ("evalf" stands for "evaluate using floating-point arithmetic"):

• [> 25/27 + 3/51;452
  459
• [> evalf(25/27 + 3/51,3); ( or [> evalf(",3); )0.985
• Save the file

The second argument in the evalf command (the 3 following the comma) specifies the number of significant figures you want in the result. If you omit this command, you will get ten significant figures.

On-line help
You can get help with MAPLE syntax by using the HELP menu, as described previously. If you have a question about a particular command, you can quickly get help by typing a question mark followed by the command name (no semicolon). For example,

• [> ? evalfwill open a window containing information about what the evalf function does and how to use it.
• Close the help window. Click on the little box at the upper left of the window and select Close.

You can download the maple software here:

http://en.softonic.com/s/maple-17-software-free-download

Here we provide you some illustration about the software:

For more understanding,you may refer to :

And you also may refer to here :

http://fit.hcmup.edu.vn/~longab/GiaoTrinh/Maple/TLTK/maple-by-example-third-edition.9780120885268.28692.pdf

Here are some basic example of maple programming :

QUESTIONS	RESULTS
> y := (1+x)∧3: > simplify(y∧(1/3)) assuming x<-1;	1 + x
>sqrt(-1);	1
>a:= (x-y-z)*(x+y+z);	a := (x − y − z)(x + y + z);

Okay,thats all from us .

Thank you.. :)