DYNAMIC DUO KOS1110

Friday 25 October 2013

I voted for Girls' Generation's "I Got a Boy" to win Video of the Year a...

Sunday 23 December 2012

Protein Data Bank

What is Protein Data Bank?

A repository for 3-D biological macromolecular structure.
It is obtained by using crystallography or NMR spectroscopy.
Founded in 1971 by Brookhaven National Laboratory, New York

-PDB is an important resource for research in the academic, pharmaceutical, and biotechnology sectors
Format is save in mmCIF(macromolecular Crystallograhic Information File)

The dictionary definition language (DDL) is structured in a way that data files that conform to this syntax can be readily loaded into a database

Software tools...

pdb-extract
ADIT
PDB Validation Suite

Data Query....

Compound Information	Myoglobin,Lysozyme
Number of chains	1-5
Secondary structure content	Present of alpha min 80%

Example of protein data bank content.

NAME	EXPLANATION
Structure of ClpP in complex with ADEP1	Clp-family proteins are prototypes for studying the mechanism of ATP-dependent proteases because the proteolytic activity of the ClpP core is tightly regulated by activating Clp-ATPases. The structures of Bacillus subtilis ClpP alone and in complex with ADEP1 and ADEP2.

NAME	EXPLANATION
TRYPSIN INHIBITOR (T1) FROM NICOTIANA ALATA	The three-dimensional structures of a series of 6-kDa trypsin inhibitors isolated from the stigma of the ornamental tobacco Nicotiana alata have been determined by 1H NMR spectroscopy combined with simulated annealing calculations

What is XML?

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

The Difference Between XML and HTML

XML is not a replacement for HTML.

XML and HTML were designed with different goals:

XML/th>	HTML/th>
Design to transport & store data	Design to display data
"Focus on what the data about"	"Focus on how data looks"
Carrying information	Display information

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 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>

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.

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.

HTML

What is HTML?

HTML is a language for describing web pages.

HTML stands for Hyper Text Markup Language
HTML is a markup language
A markup language is a set of markup tags
The tags describe document content
HTML documents contain HTML tags and plain text
HTML documents are also called web pages

HTML code example:

<!DOCTYPE html>

<html>

<body>

<h1>My First Heading</h1>

<p>My first paragraph.</p>

</body>

</html>

Web Browsers

The purpose of a web browser (such as Google Chrome, Internet Explorer, Firefox, Safari) is to read HTML documents and display them as web pages. The browser does not display the HTML tags, but uses the tags to interpret the content of the page:

HTML Page Structure

Below is a visualization of an HTML page structure:

<html>

<body>

<h1>This a Heading</h1>

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

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

</body>

</html>

HTML Versions

Since the early days of the web, there have been many versions of HTML:

Version	Year
HTML	1991
HTML+	1993
HTML 2.0	1995
HTML 3.2	1997
HTML 4.01	1999
XHTML 1.0	2000
HTML 5	2012
XHTML 5	2013

SMILES

SMILES as a simple yet comprehensive chemical language in which molecules and reactions can be specified using ASCII characters representing atom and bond symbols. SMILES contains the same information as is found in an extended connection table but with several advantages. A SMILES string is human understandable, very compact, and if canonicalized represents a unique string that can be used as a universal identifier for a specific chemical structure. In addition, a chemically correct and comprehensible depiction can be made from any SMILES string symbolizing either a molecule or reaction.

Some simple SMILES examples:

Ethanol CCO

Acetic acid CC(=O)O

Cyclohexane C1CCCCC1

Pyridine c1cnccc1

Trans-2-butene C/C=C/C

L-alanine N[C@@H](C)C(=O)O

Sodium chloride [Na+].[Cl-]

Displacement reaction C=CCBr>>C=CCI

Application on some molecules

Molecule	Structure	SMILES Formula
Dinitrogen	N≡N	N#N
Methyl isocyanate (MIC)	CH₃–N=C=O	CN=C=O
Copper(II) sulfate	Cu²⁺ SO4^2-	[Cu+2].[O-]S(=O)(=O)[O-]
Œnanthotoxin (C₁₇H₂₂O₂)		CCC[C@@H](O)CC\C=C\C=C\C#CC#C\C=C\CO
Pyrethrin II (C₂₂H₂₈O₅)		COC(=O)C(\C)=C\C1C(C)(C)[C@H]1C(=O)O[C@@H]2C(C)=C(C(=O)C2)CC=CC=C
Aflatoxin B1 (C₁₇H₁₂O₆)		O1C=C[C@H]([C@H]1O2)c3c2cc(OC)c4c3OC(=O)C5=C4CCC(=O)5
Glucose (glucopyranose) (C₆H₁₂O₆)		OC[C@@H](O1)[C@@H](O)[C@H](O)[C@@H](O)[C@@H](O)1

ChemSketch

ACD/ChemSketch is the intelligent,interactive all-purpose chemical drawing and graphics package from ACD/Labs developed to assist chemists quickly and easily draw molecular structures, reactions, and schematic diagrams, calculate chemical properties, and design professional reports and presentations.

Features	Descriptions
Draw	structures in 2D and 3D, reactions and rection schemes
Generate	structures from InChl and SMILES strings, IUPAC systematic names for molecules of up to 50 atoms entry rings structures
Search	search logP for industrial structures, structures in the built-in dictionary of over 165 000 systematic, trivial, and trade names

Below are some images as example:

Monday 24 September 2012

Welcome To Garden Of Knowledge And Virtue!!!!

Assalamualaikum everyone!
What a beautiful day we have today, and hopefully for the whole week!
Today I am very excited to tell you about my first ever experience in IIUM Kuantan.
We were ordered to register ourselves at IIUM Kuantan Campus on September the 4th of 2012.
After finishing the registration process and moving into the respective mahallah, we were immediately proceeded to the taaruf session.

*Masjid Sultan Haji Ahmad Shah*

http://www.iium.edu.my/

(click for more info) :D

This time I bring you posts about Taaruf Week in IIUM Kuantan which I was involved in September 2012.

Like most Taaruf Week, all students (from CFS mainly) will sign up a week earlier before lectures begin. You'll be surprised that the Taaruf Week in IIUM Kuantan only lasted for THREE days!

Differed with Taaruf Week in CFS IIUM, IIUM Gombak's Taaruf Week also held during the same week.
By the way, I want to bring you the post about the activities and everything that I have experienced during the Week of Taaruf.

Registration

For September 2012 Intake, the place of registration is at the Office of Campus Director (OCD). Starting at 8.30 am till 12.00 pm, you should dress neatly; wearing a dark pants for the boys and baju kurung for the girls.

*The OCD bulding*

Bring all the documents and hard copies requested. Maybe there will be additional forms to be filled. There are several counter we must go through ;the finance counter, the mahallah registration counter, and taaruf kit counter.

Then we can continue moving into our respective mahallah, for most sciences student, they were required to stay at At-Tabari 1 and 2 while other students were spread into other mahallah.

*Mahallah atTabari*

Briefing by the Student Committee and Departments

The first session (at 2 p.m.) we are officially a student of IIUM Kuantan. Location for September 2012 Intake is at the Grand Hall, OCD.

During this session, the committee will explain a bit about the Taaruf Week and what we are going to experience in the next three days, as well as briefing by the departments, like security, library, ITD, and others.

Kuliyyah Briefing

*Kuliyyah of Sciences building*

For this session, the students were divided according to their respective Kulliyyah as each Kuliyyah has a dean and deputy dean respectively. The students of Kuliyyah of Sciences were directed to the main auditorium in the Kuliyyah of Sciences building (which is the most remote kuliyyah in IIUM Kuantan, if you wish to go there by walking, you'll die immediately)

The Dean explained everything about our Kuliyyah and introduced us the administration and lecturers. Then we were enlightened about our courses plan and our future in this Kuliyyah.

Baiah Session and Closing Ceremony

Begin with the arrival of Rector of IIUM, Deans of Kuliyyah, Deputy Deans, and lectures. Then proceeded with the Asmaulhusna recitation, singing the National anthem, IIUM official anthem and quranic recitation by the selected students.

Then the Rector of IIUM, Prof. Dato' Sri Dr Zaleha Kamaruddin take place at the podium and delivered a wonderful speech about values ,ethics,vision and mission the IIUM holds.

Right after that, all the new students giving out their baiah in front of the Rector, Deans and lecturers in a sassy way.

The baiah basically ensuring that all the students giving out their best performance in every aspect of their life and also making a promise to the IIUM, themselves and to their parents on being the best of the best in their life and also in their academic grades.
After that we were presented with multimedia created by the taaruf committee and dismissed.

The subject that the new student of Kuliyyah of Sciences take this semester

Table

Name	Ic Number
Muhammad Yazeed bin Mustapa	921017016997
Khairuzzaman bin Mohamad Baharoraji	920305016567

Group 1 KOS1110

Dynamic Group:

Khairuzzaman Mohamad Baharoraji 1214513
Muhammad Yazeed Mustapa 1215995