XML

Assalamualaikum...
Hello Beautiful Readers !
How your life today?*smile
We hope all of you will be showered of HIS blessing.

X.M.L 
At first you open up this blog and see our title today, we sure that you are very very excited to know what is actually the meaning behind of this simple three letter. Right?*blinking

Okay, Let me tell you a story about this amazing code.

XML is stands for Extensible Markup Language. This XML is a general-purpose markup language.
It is classified as an extensible language because it allows its users to define their own tags.
The word extensible  is refers to the system that can be modified by changing or adding features. Plus, it was designed to describe data.

What is the purpose of this system?
Okay, the question of purpose is very common. For your information, everything exist in this world are not useless, of course there are something special behind it, same goes to this system.*smile
The primary purpose of this system created is to facilitate the sharing of data across different information systems, particularly via the Internet.

It is same html and xml?
Since our last post is all about html, we assume that this question will appear on your head. If you think so, we would like to say sorry, you are wrong. Actually, html and xml are pretty much different.
Let us tell you what makes this two system are too much different. :)

SYSTEM	HTML	XML
DIFFERENCES	designed to display data with focus on how data looks is a presentation language   is case insensitive	designed to be a software and hardware independent tool used to transport and store data, with focus on what data is. neither a programming language nor a presentation language  case sensitive

So how? can you see the differences clearly now?*smile
We hope so.

Now we want to show you how xml is looks like.

here xml looks like

Okay,that's all from us today. If you want to know mora about xml, you may click

PDB

Assalamualaikum everyone..

Have you ever heard about PDB?? I'm sure that pretty much of you never heard about it right??

So, let me explain to you about it.. =)

PDB is the short form from Protein Data Bank. For those who love biology, you must be very excited to learn about PDB right?

PDB is a repository for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. As we know, long time ago, scientists have determined the atomic structures of thousands of the biomolecular components of cells. These structures allow us to understand cell biology at the atomic level. The secrets of protein synthesis have been revealed, starting with the structure of DNA half a century ago, revealing the atomic basis of genetic information, to the recent structures of working ribosomes, caught in the act of translating this information into new proteins. The enzymes of glycolysis, citric acid cycle, and electron transport have all been studied and their structures have been determined.

So, PDB is important to many important biological questions, and also allow scientists to pose many new ones as it is a key resource in areas of structural biology, such as structural genomics. The PDB data is typically obtained by X-ray crystallography or NMR Spectroscopy. Then, it was submitted by biologist and biochemist from all aroud the world, as it is freely accesible to everyone on the internet via the website of its member organisations.The PDB is overseen by an organization called the wwPDB ( Worldwide Protein Data Bank ).

So, you might be wondering what is the important of PDB right?

Function	Explanation
To discover new drugs	When we know the structure of a protein, we can attempt to design small drug molecules to bind to it and block its function. The power of this approach has been shown in the battle against HIV and AIDS. Many of the anti-HIV drugs that are currently saving lives were discovered with the help of knowing the structures of HIV proteins (Figure 1)                                                             Figure 1
Reveals the atomic details of life	For instance, structures of oxy and deoxy hemoglobin revealed the atomic basis of allostery for control of oxygen binding, and structures of sickle cell hemoglobin revealed the atomic basis of a disease-causing mutation (Figure 2). With an atomic structure, it has been possible to explore the detailed mechanism of enzymes, and understand how they stabilize transition states. Atomic structures have revealed the complex motions of motor proteins and the basis of immune system function.                                                             Figure 2
For scientists to design new molecular machines	Biomolecular structures have also opened up a new discipline of biomolecular engineering and bionanotechnology. With understanding comes control, and researchers are currently modifying existing biomolecules for new functions, or even designing entirely new biomolecules. For instance, scientists are designing and building nanoscale structures with DNA (Figure 3)                                                                 Figure 3

             

The PDB is an exciting database to explore, but since it includes actual data from scientists, one needs to be a bit careful. PDB structure files include a few idiosyncracies that are related to the complex processes used to solve the structures. For instance, X-ray crystallographers will do almost anything to get their molecules to crystallize, so the structures may have pieces missing or sulfur atoms replaced by selenium. The file may also include only part of a whole molecule, as in the case of symmetrical molecules solved by crystallography, or many copies of the same molecule, as in the multiple models often generated in NMR spectroscopy. If you run into these challenges when you're exploring, you can consult the "Understanding PDB Data" pages at the RCSB PDB. It describes the experimental details of structure determination, how they are manifested in PDB files, and how to deal with them when exploring atomic structures.

Hope you have fun!

Internet History and Growth

Assalamualaikum wbt and I hope all of you are in the best of health.

It seems not right if we just learn lessons and lessons without having any slightest idea about the invention of the internet; why it was created, for originally what purpose and how it is being developed from the early years until today's modern era of 21st century.

The development of our communication system has gone long way since the era of what they called as "Victorian Internet", which is the invention of telegraph. We used to associate the invention of the telegraph with Samuel Morse, but actually, the credit of inventing this communication system generally fall to two sets of researchers, Sir William Cooke and Sir Charles Wheatstone in England, and Samuel Morse, Leonard Gale and Alfred Vail in the U.S. Mainly, the telegraph signals are sent through wires. In order to sent the signals through the telegraph wires, in the 1830s, Morse and Vail created a system code which is known as Morse Code. The code assigned letters which are commonly use (such as 'E') with simpler codes and letters which are rarely being used in English (such as "Q") with more complicated and long codes. This telegraph system was being used widely and extensively by the U.S Government during the American Civil War (1861-1865). 

Samuel Morse (1791-1872)

That was a very long time ago, and the functions of the telegraphs was already being replaced by the invention of telephone by Alexander Graham Bell in 1876.

However, the telephones are also using cable wire to send signals to each other. During American Cold War (click here to read more about the Cold War), they realised that they were facing another set of problems. How could the US authorities can successfully communicate with each other after a nuclear war? This is because, even how well the communication system is armoured and protected, its switches and wires are often vulnerable to the attacks of atomic bombs. This would obviously, destroy the communication system that they possessed. 

This eventually lead to the formation of the ARPANET in 1969. ARPANET stands for Advanced Research Projects Agency Network. In 1969 also, ARPANET began to deliver a message from one computer to another. The message was simple. It was only the word 'LOGIN' but it crashed the ARPA network. The second computer which were located in Stanford only received the first two letters of the message. 

The network grew steadily years after years. More networks being added into the system such as the University of Hawaii's ALOHAnet and the network at the London University College. As more computer networks being added, it became a bigger challenge for the developers to integrate all of the network into one single, main network, which we now called the Internet. 

Fortunately, by the end of 1970s, a computer scientist proposed a solution for this problem. His solution is by developing a way by all computers in the computers' mini-network to communicate to each other. He named his invention as TCP, which means Transmission Control Protocol, which later, he added another two letters, IP (Internet Protocol). Hence, nowadays we refer this protocol as TCP/IP

This effective protocol has transformed the Internet into a worldwide network. The researchers and scientists used this network as a platform to send files and data from one computer to another. It was not until 1989, that a computer programmer in Switzerland Tim Berners-Lee introduced the World Wide Web. This is an Internet that functions not only to send files and data to each other but also as a big network of "web" that contains a lot of information which are available for anyone who wants to retrieve it. That is the internet that we know today.

Years	Event
1969	ARPANET
1972	TCP/IP
1989	WWW created

We have a lot to be grateful for to these people, who have worked tirelessly to invent the Internet which has proved itself to be greatly useful for us. We can now search for information simply by typing away what we want to find on the Internet and millions of answers are there for us to choose from according to the relevance of the matter. Everything is really on our finger tips, we no longer need to stay hours and days and the library, skimming and scanning books. 

However, one must remembers that not all of the information that are being put up on the Internet is true and reliable. It is our job to not blindly believe any of them without doing some research to verify. 

The existence of the Internet is supposedly to help, neither to destroy us, nor to take away our 'life'. Stay connected and up to date is good, but when the things are necessary.   

Hypertext Markup Language (HTML)

Assalamualaikum wbt and good day to all.

Hypertext Markup Language or more widely known as HTML easily can be described as the computer language that we use to design and build a web page. It consists of various specific notations which each of them carry their own function. Therefore, it is crucial for this language to be typed out precisely correct or else, the desired effect would not appear on the web page. We called such error as syntax error.

There are many types of interface programs that we can use to edit and generate the HTML. However, for a beginner, it is recommended to simply use the Notepad that is available in almost every Windows-based computers.

In order for the HTML to work, instead of saving the Notepad file in .txt, we have to save it in .html.

Basically, all HTML coding start with <html>  followed by <body> and end with </body> followed by </html>.

When we click open the html file, it would look exactly like this.

Notice that the heading is in a bigger font compared to the content. There are six codes for the heading, ranging from <h1> to <h6>. The bigger the number, the smaller the font, Hence <h6> has the smallest font for the heading. The same concept also applied to the content, However, instead of <h1>, we use letter p as in <p1> and so on.

The HTML is responsible on the appearance, layout and the content of your webpage or in other words, how your webpage is going to look like. Therefore, obviously there are a lot of things that the HTML is capable of doing, basically everything that a webpage should contains!

Nevertheless, in this post, we are only going to show the HTML of some common, basic things first. Common and basic they may seem to be, we still should also pay close attention to this lesson as these are the things that would form the solid foundation of our HTML knowledge.

1. List

There are various types of lists that can be generated using HTML. Among of them are ordered list, unordered list and nested list. The ordered lists use numbers or letters to indicate the enumeration of the list, while the unordered lists use disc-shaped or square-shaped bullets.

Ordered list uses <ol> and unordered list uses <ul>. The nested list is the combination of various lists; all ordered lists, all unordered lists or a mixture of both ordered and unordered lists.

The result is :-

2. Hypertext link

For those that are familiar to blogging, you should know that every time we want to put a link from our blog to other website, we simply click on the link button on the compose editor pad. HTML is the one that makes it functions that way.

We can put links to the other section of the very post by putting a section name preceded by #

 which would come out as

By right, if you really type out the paragraphs until the Chapter 4 is out of the available view on your monitor, by clicking 'see also Chapter 4', it would scrolled by itself directly to Chapter 4.

We also can put a link to section in URL. This can be done by using relative or absolute URL, followed by # and then the section name. Relative URL is a filename or a relative path to a filename. Absolute URL is the complete URL beginning with the 'http://'.

3. Image

We can also put images on our webpage using HTML. The HTML for a static image and a moving image is exactly the same.

Well, obviously the moving image would not move in the screenshot...Just want to show how it would look like :)

4. Last but never the least : Table

Yes, you can create various types of tables; with cellpadding, without cellpadding, with and without border.

In order to have a table with border attribute, you have specify the border in the html.

And if I paste this html into the HTML editor of this blogspot,

Jill	Smith	50
Eve	Jackson	94

Taraaa, the table appears in this post!

Or you can also create a table with cellpadding and without cellpadding using this following HTML.

So, your webpage would appear like this,

Now you noticed the difference of a table with cellpadding and the one that is without, aren't you?

In this modern era of technology, it is highly essential for us to have at least some knowledge in computing. The development of technologies nowadays is very rapid and fast-paced. We should not let ourselves lacking behind and choose to wallow in self-ignorant about the importance of this knowledge. Furthermore, almost all businesses these days use websites in order to provide a better service the customers. Hence, there is always a high demand for a person who is good in IT. If you are willing to spare some times to learn, you can eventually make money out of it! This is your big chance!

Thus, since our lesson is very limited, we recommend you to this website to know everything you want to know about HTML and various other computing lessons.

Happy learning!

CHEMistry SKETCHing

Hello there! Eh, Assalamualaikum..hello guys!! 

In the previous post, we have already talked about SMILES. How was it? Did you find it interesting? Sure it was! To those who are or were learning Chemistry, you might have been so familiar in using the abbreviations of the molecules' names. However, never did we know that it is actually being called SMILES! That was new, wasn't it? Well at least to us, it was.

We hope you have opened up our links that we put there and read them all. If you really did, then you must have noticed that we have mentioned that one of the module editor is ChemSketch. Yup, you are right. This post is dedicated for ChemSketch.

First of all, what is ChemSketch ? The name is self-explanatory, isn't it? No it is not? Haha, fear not! Here we come to rescue! ChemSketch is a chemically intelligent drawing interface that allows you to draw almost any chemical structure including organics, organometallics, polymers, and Markush structures.Wow! This is terrific!!

You can use it to produce professional looking structures and diagrams for reports and publications. Hence, this is a really useful tool and an essential skills for us to learn. This is because it would no doubt help us to perform better in our study and also in our future career. It would come in handy if you successfully mastered on how to handle this software. Besides, taking into consideration this current technology era, it would be great to put that in your resume, isn't it? You have better chances to be hired!

It features these following awesome tasks:

1. It can draw and view structures in 2D, or render in 3D to view from any angle

2.Draw reactions and reaction schemes

3. Calculate reactant quantities

4.Generate structures from InChI and SMILES (as we introduced) strings

5.Generate IUPAC systematic names for molecules of up to 50 atoms and 3 ring structures

6.Additional Resources,you may import and export structure files in a variety of standard file formats 

There are a lot of features in ChemSketch. It would be impossible to teach you everything about it in one simple post! However, to get you started, we would explain to you about the two modes that we are using in ChemSketch. They are Structure and Draw mode. You would find yourself always switching between these two modes in order to draw or construct a particular chemical molecules.

Structure	Draw
Generates structural parts of the file such as atoms and bonds	Allows you to enhance the structure with arrows, boxes and the non-structure drawings
Panels open for construction of structures	Panels open for text formatting and drawing

Explaining ChemSketch with mere words can be very confusing. Therefore, we have a better idea! We would let our reliable, useful friend Mr Youtube to teach you further and better. Well, he can move his pictures around and can talk to you directly, hence you would be easier to understand. :)

Come on, click this below link!
ChemSketch Tutorial

Learning ChemSketch; nobody said it is going to be easy, but we are telling you it going to worth it!

Download ChemSketch and try yourself!

SMILES

“You'll find that life is still worthwhile, if you just smile.” 

― Charles Chaplin

When we say about "SMILES", people might imagine one of this faces :

It does not matter which kind of smiley faces you are thinking right now, we want to introduce you to a new type of  "SMILES". 

Our main character today is the SMILES that stands for the Simplified Molecular Input Line Entry Specification. It is a specification for unambiguously describing the structure of chemical molecule using short ASCII strings. Now, you might be wondering what is the meaning of ASCII right? ASCII is the short form from American Standard Code for Information Interchange. 

Click here if you want to know more information about ASCII from wikipedia.

From graph-based definition, SMILES is a string obtained by printing the symbol nodes encountered in a depth-first tree traversal of a chemical graph. The chemical graph is first trimmed to remove to remove hydrogen atoms and cycles are broken into to turn it into a spanning tree. Where cycles have been broken, numeric suffix labels are included to indicate the connected nodes. Parentheses are used to indicate points of branching on the tree.

Name	SMILES
ethane	CC
carbon dioxide	O=C=O
hydrogen cyanide	C#N
triethylamine	CCN(CC)CC
acetic acid	CC(=O)O
cyclohexane	C1CCCCC1
benzene	c1ccccc1
hydronium ion	[OH3+]
deuterium oxide	[2H]O[2H]
uranium-235	[235U]
E-difluoroethene	F/C=C/F
Z-difluoroethene	F/C=C\F
L-alanine	N[C@@H](C)C(=O)O
D-alanine	N[C@H](C)C(=O)O

               Some examples of SMILES and its name

SMILES strings can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensional models of the molecules. Examples of molecule editors are ACD/ChemSketch, Accelrys Draw, and Vimol . Two-dimensional editors generate output used as illustrations or for querying chemical databases while three-dimensional molecule editors are used to build molecular models, usually as part of molecular modelling software packages.

SMILES is widely used and computationally efficient as it simple yet comprehensive chemical nomenclature. It uses symbols and a set of intuitive rules. It also uses hydrogen-suppressed molecular graphs (HSMG).

Some of the uses of SMILES are:

• Keys for database access
• Mechanism for researchers to exchange chemical information
• Entry system for chemical data
• Part of languages for artificial intelligence or expert systems in chemistry 

So, what we can get by using this SMILES? For example, apart from writing ethane as C2H6, we write it as CC by using SMILES. It is simple right? As you can see, it removed its hydrogen atom. SMILES makes our life easier and simpler in presenting the molecule. =)

Although SMILES seems simple, SMILES differs in several fundamental ways from most chemical nomenclatures and other chemical formats. It is useful to review a few fundamental concepts before digging into the specifics of the SMILES language. 

This post is just a brief view about SMILES. There is a lot of other things about SMILES that we did not discuss yet with you. So, lets try to know and study more about this interesting SMILES. Your effort will not be wasted!

You can view and get more information about SMILES at SMILES.info. Hope you enjoy it!

Our Journey Starts Here!!!

" A journey of a thousand miles begins with a single step." - Lao Tzu

It is not easy for someone to actually take the first step to start the journey. It sometimes, requires a whole lot of courage and determination because this journey is uncertain. You never know where it ends, when it would end and even, whether it really would end.

However, we have to remember that in this earth, we are all caliphs of Allah, which bear big responsibilities in order to make this world a better place and to prepare ourselves for the Hereafter. With that in mind, we take our first step; our journey in IIUM Kuantan started on 2nd September when we all registered as first degree students.

As soon as we stepped our foot pass this huge, beautiful gate. we are officially belong to the IIUM Kuantan's community. We were very excited because finally, we would start a new life as degree students, which differ so much from our life during our matriculation years.

Being located at Bandar Indera Mahkota, which is more or less ten minutes from Teluk Chempedak beach, this place is serenely peaceful and beautiful. Hence, this place is more than conducive for the students.

The three of us are taking the same course, that is Bachelor in Mathematical Sciences, also famously known here as CTS (Computational Theoretical Sciences). The reason why we chose this course as our first degree is because we found that Mathematics subject is very challenging and interesting. Not to mention, when we graduated, there will be a huge selection of careers for us to involve in.

Minor	Concentration	Job
Business	Statistics	Manager, Project Admin, Business Process Specialist, Teacher
Education	Financial Mathematics	Teacher, Lecturer, Academic Trainee, Internal Audit Executive
ICT	Computational Mathematics	Senior Solution Development Engineer, IT Programming

Some of the careers you can involve in after you graduated with a Mathematics degree

There is quite a huge numbers of students in our class, which makes it very fun because we can get to know and mingle around each other. The classes also become happening. When we said Mathematics, you might think we are crazy to be willing to deal with numbers and theorems and formulas every day, but wait! Believe it or not, we have the least amounts of classes per day. So, more time to lazy around each day. :)

Most people might have this misconception that Mathematics is all about numbers and calculations. While that is partly true, the most scariest part of Mathematics is when you open the textbook, you suddenly found yourself facing with a lot of words which take not a little effort to be understood. This is because, we need to understand a certain theory or formula about Mathematics from its very root. Thus, it teaches us to think critically and creatively as to solve the Mathematical problems given.

Studying a Mathematics degree in IIUM is different from a normal university. Why are we saying this? First, IIUM is a teaching university which means you will have classes mostly in classrooms. We found this is a good thing because it enables us to understand a certain topic better and deeper.
Secondly, no matter what courses you are enrolling in, you would always found yourselves learning more about Islam in the classroom. This is very interesting as you can strengthen your Islamic values while learning a worldly knowledge. Third, IIUM study plan trains their students in a holistic way which would transform you to be all-rounder people as soon as you graduated.

Sounds intriguing, right! Come and join us, experience it yourself!

To those who interested to enroll in IIUM, be it our beloved Kuantan campus or Gombak campus, you are more than welcomed to go to .IIUM Website.