FRESHIES

Wednesday, November 6, 2013

XML , IP and SMILES

XML

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

The design of XML is to emphasize the simplicity for the Internet users.It is a textual data format with strong support via Unicode for the languages of the world. Although the design of XML focuses on documents, it is widely used for the representation of arbitrary data structures, for example in web services.

The following is the example of XML

<note>
<to>Aminah</to>
<from>Aisyah</from>
<heading> Message</heading>
<body> I'll call you later after this afternoon. Don't forget to clean up the dishes..</body>
</note>

To know more about XML, you can refer it here http://www.w3schools.com/xml/xml_whatis.asp

INTERNET PROTOCOL

Internet Protocol (IP) is the principal communications protocol in the Internet protocol suite for relaying datagrams across network boundaries. Its routing function enables internetworking, and essentially establishes the Internet.

Internet Protocol is comprised of four binary octets, making it a 32-bit address.
It is difficult for humans to read in binary format, because IP are often
converted to “dotted decimal format”. To convert the 32-bit binary address to dotted decimal format, divide the address into four 8-bit octets and then convert each octet to a
decimal number. Each octet in the IP address will have one of 256 values (0 through 255)

Example of IP address in dotted decimal form:

192.48.29.253

When convert into 32-digit octet, we will get:

Decimal	Octet
192	11000000
48	00110000
29	00011101
253	11111101

One the person who contributed to development of IP is:


Vint Cerf

SMILES (Simplified Molecular Input Line Entry System).

It is a format system to simplify the structure of the molecular formula to enter the system.
SMILES is a specification for unambiguously describing the structure of chemical molecules using short ASCII strings.

Example:

Structures	SMILES
Straight Chain (1-propene)	C-C=C
Branched chain (2-methylpropane)	CC(C)C
Aliphatic (cyclohexane)	C│CCCCC│

This is one of the example of brached chain alkane that can be described using SMILES:


2-methylbutane . SMILES : CC(C)CC

Thursday, October 3, 2013

Protein Data Bank

The Protein Data Bank is the picture of the 3-D structural data of the large biological molecules, such as protein and nucleic acid. It describe proteins and other biological molecules by using method such as X-ray crystallography, NMR Spectroscopy and cryo-electron microscopy. The data is submitted for the use of the scientist and it is accessible by the internet around the world.

The PDB currently contain 29956 structures. Structures deposited by the Protein Data Bank at the Research Collaboratory for Structural Bioinformatics (RCSB) are written in standard format. There are also short description used written in standard format. The data contained in the archive include atomic coordinates, bibliographic citations, primary and secondary structure, information, and crystallographic structure factors and NMR experimental data.

Structures are available for many of the proteins and nucleic acids involved in the central processes of life, so you can go to the PDB archive to find structures for ribosomes, oncogenes, drug targets, and even whole viruses. However, it can be a challenge to find the information that you need, since the PDB archives so many different structures. You will often find multiple structures for a given molecule, or partial structures, or structures that have been modified or inactivated from their native form.

The examples of protein data bank that we can obtain are:

Structure of subtilisin

Structure of Lon A

Structure of dipeptidase

Struture of carboxypeptidase

Structure of DegP

These images can be obtained by first downloading the files from RCSB Protein Data Bank. All information about the protein are also available. The downloaded files can be opened with RasWin program (RasWin is only for windows users) to view the image of the protein structure. In addition, the downloaded files can be saved as BMP, GIF, EPSF, PPM or RAST by exporting the files to any intended format.

Protein	Main Function
Subtilisin	Protein digesting enzyme
Lon A	Degradation of denatured polypeptides
Dipeptidase	Enzymes secreted by enterocytes into small intestine
Carboxypeptidase	Hydrolize a peptide bond of carboxyterminal
DegP Peptidase	Chaperone in the bacterial envelope

Friday, September 27, 2013

How to Create A Webpage Using HTML

HTML , or HyperText Markup Language is a universal coding system that is being used worldwide for many purposes, from creating a personal web page to establishing a company web site .
Since we cannot use our own language to start a web page , codes of HTML are used to build and design the web page. Some of the functions of HTML in a website are:

Format text as title/heading
Arrange graphics on web pages
Link different websites

Besides, there are certain elements that we will usually see in HTML codes, which consist of start tag (also known as opening tag) and end tag (closing tag) such as:

<h1> (the start tag for heading)
</h1> (end tag for heading)
<p> (opening of a paragraph)
</p> (closing of paragraph)
<a href="link to any web page"> (start tag for link to other pages)
</a> (end tag for link)

Anything between the start tag and the end tag of every elements will be displayed as contents of the website, according to their respective formats.

For example, if we want to create a table in our website , we can use HTML codes as well.
The code for a table is <table>
These are the codes we need to create a table with two columns and two rows:

<table border="1">
<tr>
<td>A</td>
<td>B</td>
</tr>
<tr>
<td>a</td>
<td>b</td>
</tr>
</table>

and here is the table that we would get:

Column A	Column B
any content related to A	any content related to B

Next:

How to create link using html

First of all, open the notepad and type the

<html>

<body>

and

<p>

The tags to produce links are the <a>and </a>. Then type <a>

The <a>tells where the links 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 belowshows how to make the word here work as a link to yahoo.

Click <a href="http://www.yahoo.com">here</a> to go to yahoo.

You simply:

Specify the target in the <a href=" ">.

Then add the text that should work as a link.

Finally add an </a> tag to indicate where the link ends.

If you want to continue to write further more about the links, you can add <h2>Chapter </h2> and

<p> This chapter explains......</p>

At the end type

<body>

and

<html>

to close the html text.

How to create images using html

In HTML, images are defined with the <img> tag.

The <img> tag is empty, which means that it contains attributes only, and has no closing tag.

To display an image on a page, you need to use the src attribute. Src stands for "source".

The value of the src attribute is the URL of the image you want to display.

The steps of creating images using HTML are as below,

<html>

<body>

<p>

An image:

<img src="image.gif" alt="smiley face"

width="32" height="32" />

</p>

<p>

A moving image:

<img src="image2.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

The image will appeare according to the text above.

Finally , after finishing the content for the website , the final code is

</body>
</html>

Thursday, September 26, 2013

My First Day In IIum Kuantan

My first day in IIUM Kuantan was not really the best day of my life , if I was to be asked about it . Being a direct intake student , I already know that this would be a completely new world for me . So I was quite excited about meeting new people and getting new friends here in Kuantan. However, upon arrival , I was shocked to see that there was no new student to be registered that day , except me and a few friends that I met in Gombak Campus . By the way , I used to study In Gombak Campus last semester and was transferred here this semester. How could that be? What happened was actually there are two types of admission to IIUM :

Types of admission	Explanation
CFS	For students who undergo their foundation studies in IIUM Petaling Jaya
Direct Intake	Local students who did not go to IIUM Petaling Jaya for foundation studies , as well as international students from various countries who want to pursue undergraduate studies in IIUM. Direct intake students make an online application for admission to the university

All direct intake students are required to sit for entrance tests which will determine whether they will be allowed to start their first year in the university or not. Those who pass the entrance test will proceed to their first year session , but for those who did not pass the entrance test will be registered to pre-sessional program. So my first semester in IIUM was spent as a pre-sessional student , and luckily enough I passsed all the subject to be allowed to begin my first year in IIUM Kuantan.

Despite all the confusions and everything that happened during the registration day in Kuantan , it is a relief that I was given a room which has been occupied by three lovely new students , who are now my new friends. Apart of the many things I saw here, there is one that caught my attention when I first entered the campus area:

OCD , IIUM KUANTAN

This is the Office of the Campus Director of IIUM Kuantan. It looks quite similar to the Rectory Building in IIUM Gombak , with the stairs and all.

The rest of the day was spent with my new friends, tidying up the room and talking to each other.
Since it was quite a tiring day for me , I went to bed early , knowing that I am now a part of the big family of IIUM. I hope this is the beginning of a beautiful journey that I will never forget.