Thursday, 31 October 2013

The XML Language

Howdy! What a pleasent today. Aside from this day being an election day for IIUM Kuantan next SRC Lineup, I would like to post an introduce to all of you a little bit about XML. From reading this post, perhaps; we could answer several questions like what is XML? How can XML be used? What is its syntax, elements, attributes and validation.

A Brief Introduction to XML

What is XML? Just as how HTML actually means HyperText Markup Language, XML means Extensible Markup Language. Both HTML and XML are markup language and they are much alike, but they aren't the same. One obvious different between HTML and XML is tag, HTML has a predefined tags while XML doesn't. Even though both of them are markup languages, XML isn't a replacement for HTML.

Differences between HTML and XML

HTML tags are predefined, while XML tags are not predefined.
XML focuses on what data is, it is designed to store and transport data, while HTML is more on layout and interface with focus on displaying the data.
HTML is about displaying information, while XML is about carrying information

XML doesn't do anything, it itself is just a plain text

The sole reasons why XML was created was to structure, store, and transport information..

Following are one example of XML taken from kirupa.com

What does it mean by plain text? By plain text, it means that it is nothing special, it's just the same with what we write in our notepad, which means, software which could handle plain text document will always occur to support XML. Though, XML tags could be handled specially if the software is XML-aware. The nature of the application will determine the functional meaning of the XML tags.

So if XML is not a replacement for HTML, what is XML?

XML is not HTML, but XML is complement to HTML, which means that XML is used to interoperate with HTML, with XML functioning to transport data, and HTML functioning to display the data.

XML carries data without ever having specific dependence with hardware and software

XML Syntax Rules

All XML must have closing tag

"<message>...</message>" this is correct
"<message>... " this is incorrect

In XML, it is illegal to omit the closing tag
XML Elements must be nested

<i><o>...</o></i> this is correct
<i><o>...</i></o> this is incorrect

XML Elements must contain parent/root element

e.g.
<root>
<child>
<subchild>...</subchild>
</child>
</root>

XML attributes must be quoted

CHEMSKETCH

Assalamualaikum...

Hi everyone...I'm hoped that you all are in good health now so that we can face this beautiful with our brightest smile...And don't forget to be greatful to Allah SWT because of His Will we all can smile today :)

OK...Let's get started...Today I want to share about ChemSketch...Do you guys know what is ChemSketch? -ChemSketch is a software for quick and easy drawing molecules, reactions, schematic diagrams and designing other chemistry-related. So, this software can make our jobs easier and systematic. We also can produce professional looking structures and diagrams for reports and publications.

Among the features in this chemsketch software is:-

Draw and view structures in 2D, or render in 3D to view from any angle
Draw reactions and reaction schemes, and calculate reactant quantities
Generate structures from InChI and SMILES strings
Generate IUPAC systematic names for molecules of up to 50 atoms and 3 ring structures
Predict logP for individual structures
Search for structures in the built-in dictionary of over 165,000 systematic, trivial, and trade names.

This software is awesome right...I did not realize that software like this exist in this world until my beloved lecturer, Madam Haslinda, introduce us about this software...so, if you guys want to download this software you can click here.

Now I will show you how the software looks like. And I will show you what this software can do.

Blank Page

We can make graph

We can draw apparatus

We can make chemical structure

3D Structure

IUPAC Names

This is great. This software can make many more amazing things.

Now I will give you guys a brief information about the small button that located on top of the page:

Type	Code
	C- Carbon H- Hydrogen N- Nitrogen O- Oxygen F- Fluorine Na- Sodium Si- Silicon P- Phosphorus S- Sulphur Cl- Chlorine K- Potassium Br- Bromine I- Iodine
1 2 3	1-Select/Move 2- Rotate/Resize 3- 3D Rotation
	Benzene Cyclohexane Cyclopentane t-Butyl i-Propyl Acetyl Caboxyl Benzoyl Nitro Acetoxy Sulfo Phosphono
1 2 3	Draw Normal Draw Continuous Draw Chain
1 2 3 4	Up Stereo Bonds Down Stereo Bons Coordinating Bonds Undefined Stereo Bonds
	Lasso On/Off
1 2	Flip Top to Bottom Flip Left to Right
	Periodic Table

I hope this info could help you to understand more about this software. I will give you the way to understand chemsketch better. Try do it yourself. Make this as a challenge for us. There is no victory without efforts. Bye2..

Assalamualaikum

SIMPLIFIED MOLECULAR INPUT LINE ENTRY SPECIFICATION (SMILES)

Assalamualaikum everyone..:) in this peacful day, i would like to share what i had learn about SMILES in my last computer class.

Actually, SMILES stand for simplified molecular input line entry specification. This SMILES is a specification for unambiguously describing the structure of chemical molecules using short ASCII strings. And the SMILES string can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensional models of the molecules. The original SMILES specification was developed by Arthur Weininger and David Weininger in the late 1980s. This SMILES was:-

Widely used AND computationally efficient
Uses atomic symbols and a set of intuitive rules
Uses hydrogen-suppressed molecular graphs (HSMG)

More information visit here.

We know that some molecule have it isomer, then there is term Isomeric SMILE Srefers to the version of the SMILES specification that includes extensions to support the specification of isotopes, chirality, and configuration about double bonds. (A notable feature of these rules is that they allow rigorous partial specification of chirality.)

GRAPH-BASED DEFINITION

String SMILES can be obtained by printing the symbol nodes encountered in a depth-first tree traversal of a chemical graph in terms of a graph-based computational procedure,
The chemical graph is first trimmed to remove hydrogen atoms and cycles are broken to turn it into a spanning tree
Where cycles have been broken, numeric suffix lables are included to indicate the connected nodes
Points of branching on the tree can be indicated by using parentheses

SMILES BOND

Type	Symbol
Single	-
Double	=
Triple	#
Aromatic	:

CATOGARIES OF SMILES

Catagories	Name	Example
Branches	2-Butanol iso-Butanol	CC(O)CC OCC(C)C
Bond	Ethene 1,1-Dichloroethene	C=C ClC(Cl)=CCl
Other Atoms	Benzene Cyclohexane	c1ccccc1 C1CCCCC1
Charges	Proron Hydroxyl anion Ammonium cation	[H+] [OH- [NH4+]

SMILES Cyclic Structures

Break one single or one aromatic bond in each ring
Number in any order

Designate ring-breaking atoms by the same digit following the atomic symbol

Numbers indicate start and stop of ring
Same number indicates start and end of the ring, entered immediately following the start/end atoms
Only numbers 1 –9 are used
A number should appear only twice
Atom can be associated w. 2 consecutive numbers

Ex: Napthalene: c12ccccc1cccc2

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
A branch cannot begin a SMILES notation
A branch cannot immediately follow a double-or triple-bond symbol
Example: C=(CC)C is invalid, but C(=CC)C or C(CC)=C are valid SMILES

SMILES Fragments

Name	SMILES
Nitro	N(=O)(=O)
Sulfonic acid	S(=O)(=O)O
Cyanide/Nitrile	C#N
Azide	N=N#N

Example SMILES Metals

[Al] [As] [Au] [Be]
[Bi] [Cd] [Ca] [Fe]
[Hg] [K] [Li] [Mg]
[Na] [Ni] [Pt] [Sb]
[Sn] [Zn] [Zr]

Disconnected Structures

Tetramethyl ammonium bromide

Example: C[N+]C(C)C.[Br-]

Isomeric and Chiral SMILES

Isomeric configuration indicated by forward and backward slashes: / \
Examples:

trans-1,2-dibromoethene: Br/C=C/Br
cis-1,2-dibromoethene: Br/C=C\Br

Chirality indicated by the “@” symbol

Monday, 7 October 2013

INTERNET HISTORY AND GROWTH

Assalamualaikum... Nowadays, internet is part of life because we can get access on everything from the internet. Internet make our life easier but there are only certain people that concern about internet growth and history. So today we will talk about internet growth and history.

The first invention that had been created was telegraph. The creator who got the idea to invent this cool stuff is Baron Pavel L'vovitch Schilling, also known as Pavel Schilling. The telegraph was invented in 1840s then this telegraph was used extensively by the U.S. Government during the American Civil War, 1861 - 1865. The telegraph used morse code consisted of dots, dashes, short and long signal.

So up until now, we haven't yet define what is it exactly an Internet. Then what is its definition? The Internet.

The internet is a network of networks, joining many computers together and providing an infrastructure for the use of E-mail, bulletin boards, file archives, hypertext documents, databases and other computational resources.

Characteristics of the Internet?

 The largest network of networks in the world
 Uses TCP/IP protocols and packet switching
 Runs on any communications substrate

Brief history of the internet

 1968 - DARPA (Defense Advanced Research Projects Agency)
contracts with BBN (Bolt, Beranek & Newman) to create ARPAnet
 1970 - First five nodes:

UCLA
Stanford
UC Santa Barbara
U of Utah, and
BBN

 1974 - TCP specification by Vint Cerf
 1984 – On January 1, the Internet with its 1000 hosts
converts en masse to using TCP/IP for its messaging

Evolution of the Internet

Year	Achievement
1945	Memex Conceived
1948	A Mathematical Theory of Communication
1958	Silicon Chip
1962	First Vast Computer Network Envisioned
1964	Packet Switching Invented
1965	Hypertext Invented
1969	ARPANET
1972	TCP/IP Created
1984	Internet Named and Goes TCP/IP
1989	WWW Created
1993	Mosaic Created
1995	Age of e-Commerce Begin

click to enlarge

for an interactive view on the evolution of the web, click here

Tuesday, 1 October 2013

Protein Data Bank

A little introduction

Protein Data Bank is a storage site for information and 3d images of biological proteins related macromolecule. It is worldwide, and shared among students and researchers, uploaded into the site and downloadable. One of the site is RCSB Protein Data Bank. The downloaded macromolecules images are opened by using a software like RasWIN, we could get the software from here.

Samples of 5 proteins

LexA

"Repressor LexA or LexA is a repressor enzyme (EC 3.4.21.88) that represses SOS response genes coding for DNA polymerases required for repairing DNA damage. LexA is intimately linked to RecA in the biochemical cycle of DNA damage and repair. RecA binds to DNA-bound LexA causing LexA to cleave itself in a process called autoproteolysis." - Wikipedia.org

LEXA G85D MUTANT

"LexA repressor undergoes a self-cleavage reaction. In vivo, this reaction requires an activated form of RecA, but it occurs spontaneously in vitro at high pH. Accordingly, LexA must ... " Click For More

Type	Code
Molecule	LEXA REPRESSOR
Polymer	1 \| Type: Protein \| Length: 202
Chain	A, B
EC#	3.4.21.88
Mutation	G85D
Organism	Escheria coli
Gene Name	lexA exrA spr tsl umuA b4043 JW4003
UnitProtKB	Protein Feature View \| Search PDB \| P0A7C2

For more information, visit http://www.rcsb.org/pdb/explore/explore.do?structureId=1JHF

Trypsin

"Trypsin (EC 3.4.21.4) is a serine protease found in the digestive system of many vertebrates, where it hydrolyses proteins. Trypsin is produced in the pancreas as the inactive proenzyme trypsinogen. Trypsin cleaves peptide chains mainly at the carboxyl side of the amino acids lysine or arginine, except when either is followed by proline. It is used for numerous biotechnological processes. The process is commonly referred to as trypsin proteolysis or trypsinisation, and proteins that have been digested/treated with trypsin are said to have been trypsinized." - Wikipedia.org

ON THE DISORDERED ACTIVATION DOMAIN IN TRYPSINOGEN. CHEMICAL LABELLING AND LOW-TEMPERATURE CRYSTALLOGRAPHY

Type	Code
Molecule	Trypsin
Polymer	1 \| Type: Protein \| Length: 223
Chain	A
EC#	3.4.21.4
Mutation	N/A
Organism	Bos Taurus
Gene Name	N/A
UnitProtKB	Protein Feature View \| Search PDB \| P00760

For more information, visit http://www.rcsb.org/pdb/explore/explore.do?structureId=2PTN

HtrA

Crystal Structure of DegP (HtrA)

"Molecular chaperones and proteases monitor the folded state of other proteins. In addition to recognizing non-native conformations, these quality control factors distinguish ... " Click for more

Type	Code
Molecule	PROTEASE DO
Polymer	1 \| Type: Protein \| Length: 448
Chain	A, B
EC#	3.4.21.107
Mutation	S210A
Organism	Escherichia Coli
Gene Name	degP htrA ptd b0161 JW0157
UnitProtKB	Protein Feature View \| Search PDB \| P0C0V0

For more information, visit http://www.rcsb.org/pdb/explore/explore.do?structureId=1KY9

Pepsin

"Pepsin (from the Greek πέψη, pepsi, meaning digestion) is an enzyme whose zymogen (pepsinogen) is released by the chief cells in the stomach and that degrades food proteins into peptides. It was discovered in 1836 by Theodor Schwann who also coined its name from the Greek word pepsis, meaning digestion (peptein: to digest). It was the first enzyme to be discovered, and, in 1929, it became one of the first enzymes to be crystallized, by John H. Northrop. Pepsin is a digestive protease, a member of the aspartate protease family." - Wikipedia

CRYSTAL STRUCTURE OF ASCARIS PEPSIN INHIBITOR-3

"The three-dimensional structures of pepsin inhibitor-3 (PI-3) from Ascaris suum and of the complex between PI-3 and porcine pepsin at 1. 75 A and 2.45 A resolution, respectively, have revealed ... " Click for more

Type	Code
Molecule	MAJOR PEPSIN INHIBITOR PI-3
Polymer	1 \| Type: Protein \| Length: 149
Chain	A
EC#	N/A
Mutation	N/A
Organism	Ascaris Suum
Gene Name	N/A
UnitProtKB	Protein Feature View \| Search PDB \| P19400

For more information, visit http://www.rcsb.org/pdb/explore/explore.do?structureId=1F32

Amylase

"Amylase /ˈæmɪleɪz/ is an enzyme that catalyses the breakdown of starch into sugars. Amylase is present in the saliva of humans and some other mammals, where it begins the chemical process of digestion. Foods that contain much starch but little sugar, such as rice and potato, taste slightly sweet as they are chewed because amylase turns some of their starch into sugar in the mouth. The pancreas also makes amylase (alpha amylase) to hydrolyse dietary starch into disaccharides and trisaccharides which are converted by other enzymes to glucose to supply the body with energy. Plants and some bacteria also produce amylase. As diastase, amylase was the first enzyme to be discovered and isolated (by Anselme Payen in 1833). Specific amylase proteins are designated by different Greek letters. All amylases are glycoside hydrolases and act on α-1,4-glycosidic bonds." - Wikipedia

HUMAN SALIVARY AMYLASE

"Salivary alpha-amylase, a major component of human saliva, plays a role in the initial digestion of starch and may be involved in the colonization of bacteria involved ..." Click for more

Type	Code
Molecule	AMYLASE
Polymer	1 \| Type: Protein \| Length: 496
Chain	A
EC#	3.2.1.1
Mutation	1
Organism	Homo Sapiens
Gene Name	AMY1A AMY1 AMY1B AMY1C
UnitProtKB	Protein Feature View \| Search PDB \| P04745

or more information, visit http://www.rcsb.org/pdb/explore/explore.do?structureId=1SMD

Tuesday, 24 September 2013

HTML

Basically, HTML means Hypertext Markup Language. Unlike programming language, it's a language that's understood by internet browser e.g. Internet Explorer and Mozilla Firefox.

To create an html file, we need an editor such as the notepad. In the notepad, we need to type in the html code, or the source code for html file. The basic building of html code is

 <html>  
 <body>  
 </body>  
 </html>

Those are the codes that is needed to be typed first into the editor. In between the <body> and </body> tags, we could have our content. To make a header, we type words between the <h1> and </h1> tags, there are also h2, h3 and h4 each with different sizes, try and explore yourselves. To have a simple paragraph, we write between the tags <p> and </p>.

 <html>  
 <body>  
 <h1>My First Heading</h1>  
 <p>My First Paragraph</p>  
 </body>  
 </html>

Preview
=================================

My First Heading

My First Paragraph
=================================
Now you have a complete html file, you could save it as .html file by renaming the file with .html at the end of its name before saving. e.g. 1.html

Now, is there any other things besides heading and paragraph? Of course, in fact, there are plenty of things to do with HTML, but we will go basic by basic. We will start with what is important in a note, or perhaps, in a story.

The List

For now, I'll introduce to you three types of list, bullet list, ordered list, and nested list (list in which there is/are another list/s)

Bullet List

 <ul type="disc">  
      <li>Apples</li>  
      <li>Bananas</li>  
      <li>Lemons</li>  
      <li>Oranges</li>  
 </ul>

This is a source code for disc type bullet list, a disc type bullet list will show a bullet that is round, you could change the type to square to have a square bullet by renaming "disc" into "square". You could change the list by renaming the items between <li> and </li> tags, and you could even add up more lists by adding another <li> and </li> tags before the </ul> list

Preview
==================================

Apples
Bananas
Lemons
Oranges

==================================

Ordered List

An ordered list is used as a replacement for the bullet list to show a more ordered manner, such as if you are going to list things by using a until z instead of only having a black round bullet.

 <ol type="A">  
      <li>Apples</li>  
      <li>Bananas</li>  
      <li>Lemons</li>  
      <li>Oranges</li>  
 </ol>

Preview
===================================

Apples
Bananas
Lemons
Oranges

===================================
So you don't have to write A until Z by yourselves, it will happen automatically as you add more lists. Besides having an A to Z list, it also support numbered list, you just need to change the type from "A" to "1". Notice the different between the bullet list and ordered list, the tag for bullet list is <ul>, while the tag for ordered list is <ol>.

Nested List

Then, what about nested list, nested list is a list where we have another list inside the list.

 <ul>  
      <li>Coffee</li>  
      <li>Tea  
           <ul>  
           <li>Black Tea</li>  
           <li>Green Tea</li>  
           </ul>  
      </li>  
      <li>Milk</li>  
 </ul>

Basically, if you find another sets of <ul> </ul> or <ol> </ol> tags inside the list's source code, it means that there is another list inside the list. Notice the red text? That is another sets of <ul> </ul> tags inside the list's source code that is written in black.

Preview
=====================================

Coffee
Tea
- Black Tea
- Green Tea
Milk

=====================================

Next, after you have your note and list, for easy navigation; perhaps you need to hyperlink some of the words in your note to a certain site. So how should we do it? Here comes the part which we call as link. What is a link? A link is more like and address that is when we click on it, we will be directed into the page with the same address as the link. Normally, we will have our link behind word.

Link

 <a href="type website address">Type the word to represent the link</a>

The basic tag or code for link is <a href=" "> </a>

Example

 <a href="http://www.google.com/">Go to google</a>

Preview
==================================
Go to google
==================================

You can have your Link's code anywhere in the page, may it be in a list or not, under a condition that it is always inside the tag <body> and </body>

Image

Another important thing for a note is image, everyone like it visually. Instead of having only a journal full of words, why not we try to put pictures or images inside our page.

Basic code for picture are

 <img src="your image link">  
 With description  
 <img src="your image link" alt="description">  
 With description and size  
 <img src="your image link" alt="description" width="width size" height"height size"/>

It is your choice to have a description or not, or to have a fixed size or not. Sometime, you don't need a fixed designated size for picture, while sometime you don't, it depends on how you want the picture to be resized. If you want it in its original size, perhaps you don't have to resize it, but there is a time when the size of the picture is way too large that you need to resize it in any way, you are free to resize it by editing the width and height. By using the same code, you could have both passive or moving picture.

example

 An Image:  
 <img src="http://upload.wikimedia.org/wikipedia/commons/e/ec/Happy_smiley_face.png" alt="Nature" width="32" height"32"/>  
 A moving image:  
 <img src="http://heathersanimations.com/links/animal2link.gif" alt="Now a moving image" width="48" height="48"/>

Preview

=================================
An Image: Nature

A moving image:

==================================

I think that's enough for today, why don't we summarised what we have learned today.

Type	Code
Bullet List	<ul type="disc"> <li>item 1</li> <li>item 2</li> </ul> or <ul type="square"> <li>item 1</li> <li>item 2</li> </ul>
Ordered List	<ol type="A"> <li>item 1</li> <li>item 2</li> </ol> or <ol type="1"> <li>item 1</li> <li>item 2</li> </ol>
Link	<a href="link">any word</a>
Image	<img src="image link"/> or <img src="image link" alt="description"> or <img src="image link" alt="description" width="width size" height"height size"/>

Tuesday, 17 September 2013

Our First Day in IIUM Kuantan

We are three ex-Matriculation students from CFS IIUM Petaling Jaya named Amar Ridzwan from Besut, Terengganu, Affende Sazuki from Banting, Selangor , and Azizi Rosli from Puncak Alam, Kuala Selangor, Selangor.

Name	Description	Facebook	Twitter
Amar Ridzwan	Wearing spectacles Tall Cartoon lover	Amar Ridzwan	@amarridzwan
Azizi Rosli	Intermediate Height Cartoon Lover Like to surf the internet	AziziNET	@azizinet00
Affende Sazuki	A bit genius Loves Mathematics Happy go lucky	Muhammad Affende	@muhammadaffende

When we were in CFS IIUM, we thought that IIUM Kuantan is a boring place compared to its counterpart in Gombak. We never heard of IIUM Kuantan before we reached CFS IIUM in Petaling Jaya, we were like "What?! There is a campus in Kuantan? I never heard of it!".

Even worse was when we went to IIUM Kuantan during educational trip that had been organised by PRESSS which is one of the society in CFS IIUM to represent Physical Science student. It was really quiet back then, IIUM Kuantan. Perhaps, it was because the seniors weren't there due to semester break. We developed a negative mindset pertaining to the campus.

On 3rd of September, we registered here. It wasn't like what we thought, it was full of people, and the environment was truly different from what we saw during the trip. The committees were nice, they always smile, and they guided us during the registration day. It makes our registration process ran smoothly.

taken from http://ex-cfsiiumstudents.blogspot.com

One of the most worrying thing as a new student is the orientation. In IIUM, the orientation is called Ta'aruf Programme. To tell the truth, it was really demanding, it demanded our patience, and it was intolerable at first when it started exactly after the registration, but then we eventually get used to it. Just imagine a day or two full of protocols and briefings that we tried to concentrate on, but forgot a minute after.

Before the ta'aruf programme, we found out that there were two groups of hostels that are situated outside from the campus, the closer Tabari in IM7, and the further Tabari in IM2. A little frustated at first, but then we were very glad that even though we don't get to stay inside of the campus, we get to stay in the closer hostel in IM7, the hostel is closed to a lake which is beautiful, and in front of it is Sri Manja boutique hotel.

At first, we were with our family, then, it was very sad knowing the fact that we were going to separate and stay far from our family. If it isn't because we have our friends and dreams here, we may not be living here far from our family. We know that it was a great sacrifice, but we need to move on, to pursue our dream, our parents dream, to fulfill our duty as vicegerents and slave of Allah swt.

Who would have thought, that IIUM Kuantan is a fun place, despite the fact that our Kulliyyah is the furthest Kulliyyah in the campus. The architecture of the building, the masjid, the design, the trees surrounding it, and the seniors. IIUM Kuantan, being a symbol of islamicisation, who couldn't be proud being a chapter of it. We were blind back then during the trip, but the first day we were here as a student of IIUM Kuantan changed our views of our own campus.

Masjid Sultan Haji Ahmad Shah IIUM Kuantan

Admin Building, Kulliyyah of Science

Experience IIUM Kuantan, try to understand IIUM Kuantan, and you will know IIUM Kuantan is a fun place to be in. The fact that it is called quiet isn't true, it is not quiet, but calm.

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