Saturday, 22 December 2012

SMILES

yyeeaaahh..!!




Assalamualaikum...guys....!!
How are you ??..Alhamdulillah..praise be to Allah...

Haaaaaaaaaaaaaaaaaa......???..What the picture is about??..Mouth?..Nose?..Half-face??..no 'lah'...please open your mind okay..!!..hahaha..

Today,we gonna learn about SMILE?..What is smile?..Is it kind of face expression??..Okay,we gonna explain to you..The SMILES mentioned is actually an abbreviation of the Simplified Molecular-Input Line-Entry System,which is a specification in form of a line notation for describing the structure of chemical molecules using short ASCII strings.




In other words, SMILES is the formula used for sketching molecular structure in ChemSketch.

Did you forgot about the Chemsketch??..Okay,please review the older post or just click here to read about ChemSketch.




Some examples of SMILES :


Molecule Structure SMILES Formula
Dinitrogen N≡N N#N
Copper (II) Sulphate Cu2+ SO42- [Cu+2].[O-]S(=O)(=O)[O-]
Glucose (glucopyranose) (C6H12O6) Molecular structure of glucopyranose OC[C@@H](O1)[C@@H](O)[C@H](O)[C@@H](O)[C@@H](O)1
Vanillin Molecular structure of vanillin O=Cc1ccc(O)c(OC)c1
Melatonin (C13H16N2O2) Molecular structure of melatonin CC(=O)NCCC1=CNc2c1cc(OC)cc2


 If you want to learn more about SMILES, just click on this to find the website that provide the tutorial on using this great tool on Chemsketch.


Okay,that's all for today.....thank you guys.....







Monday, 29 October 2012


Introduction to XML


Assalamualaikum....guys!!!..
Are you there???...hahaha

Okay,let's continue our lesson guys......never give to seek the knowledge,okay..!!.


Today,we gonna learn about XML XMLis another language of computer rather than HTML. XML is Extensible Markup Language. It was designed to describe data and focus what data is. It is more similar to HTML but, it is difference.


What is XML?

  • XML stands for EXtensible Markup Language
  • XML is a markup language much like HTML
  • XML was designed to carry data, not to display data
  • XML tags are not predefined. You must define your own tags
  • 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 was designed to transport and store data, with focus on what data is
  • HTML was designed to display data, with focus on how data looks
HTML is about displaying information, while XML is about carrying 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.




Okay,guys....we need rest.!!..see you soon...





Monday, 15 October 2012


What is HTML?

Assalamualaikum.....guys!!..

Great news..!!..Great news..!!!.....today we gonna learn interesting topic...very intersting.
We gonna create OUR OWN WEB PAGES or even OUR OWN WEBSITES....hahahaha

Okay..first,we have t know what is HTML?..hotmail??..aiiyoo...no 'lah'..hahaha

HTML is an abbreviation of "HyperText Mark-up Language".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


In other word,HTML is the "mother tongue" of your browser.

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.




You are now ready to learn the essence of HTML: elements.
Elements give structure to a HTML document and tells the browser how you want your website to be presented. Generally elements consists of a start tag, some content, and an end tag.

"Tags"?

Tags are labels you use to mark up the begining and end of an element.
All tags have the same format: they begin with a less-than sign "<" and end with a greater-than sign ">".

Generally speaking, there are two kinds of tags - opening tags: <html> and closing tags: </html>. The only difference between an opening tag and a closing tag is the forward slash "/". You label content by putting it between an opening tag and a closing tag.

Here some examples..

Okay, the element em emphasis text. All text between the opening tag <em> and the closing tag </em> is emphasised in the browser. ("em" is short for "emphasis".)
Example 1:
 
 <em>Emphasised text.</em>
 
 
Will look like this in the browser:
Emphasised text.
The elements h1h2h3h4h5 and h6 is used to make headings (h stands for "heading"), where h1 is the first level and normally the largest text, h2 is the second level and normally slightly smaller text, and h6 is the sixth and last in the hierarchy of headings and normally the smallest text.


Example 2:
 
 <h1>This is a heading</h1>
 <h2>This is a subheading</h2>
 
 
Will look like this in the browser:

This is a heading

This is a subheading

So, I always need an opening tag and a closing tag?

As they say, there's an exception to every rule and in HTML the exception is that there are a few elements which both open and close in the same tag. These so-called empty elements are not connected to a specific passage in the text but rather are isolated labels, for example, a line break which looks like this: <br />.

Should tags be typed in uppercase or lowercase?

Most browsers might not care if you type your tags in upper, lower or mixed cases. <HTML>, <html> or <HtMl> will normally give the same result. However, the correct way is to type tags in lowercase. So get into the habit of writing your tags in lowercase.

Where do I put all these tags?

You type your tags in an HTML document. A website contains one or more HTML documents. When you surf the Web, you merely open different HTML documents.






More example...



<html>
<body>
<h4>Disc bullets list:</h4>
<ul type="disc">
 <li>Apples</li>
 <li>Bananas</li>
 <li>Lemons</li>
 <li>Oranges</li>
</ul>  
<h4>Letters list:</h4>
<ol type="A">
 <li>Apples</li>
 <li>Bananas</li>
 <li>Lemons</li>                        

                            
 <li>Oranges</li>
</ol> 
<h4>A nested List:</h4>
<ul>
  <li>Coffee</li>
  <li>Tea
    <ul>
    <li>Black tea</li>
    <li>Green tea</li>
    </ul>
  </li>
  <li>Milk</li>
</ul>
</body>
</html>
















okay..that's all for today...we will meet again..see you soon!! thank you...









Monday, 8 October 2012

Protein Data Bank...........
A Storage of Macromolecular Structure



Assalamualaikum...hi,guys..!!

  Praise be To Allah we are able to meet again..Today,we would like to introduce you something related to bank...BANK???????...yes..it is about a bank..a place to keep money safe,right??..haha..but not for this bank,this bank only for keeping or saving macromolecular structure..need more explanation??

  Okay,then,we will explain..this bank is known as Protein Data Bank (PDB)
.The Protein Data Bank (PDB) is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids. (See also crystallographic database). The data, typically obtained by X-ray crystallography or NMR spectroscopy and submitted by biologists and biochemists from around the world, are freely accessible on the Internet via the websites of its member organisations (PDBe, PDBj, and RCSB). The PDB is overseen by an organization called the Worldwide Protein Data Bank, wwPDB.


Then,we proceed to the next topic which is Rasmol...Haaaaaaaaaa????
What is Rasmol??

  RasMol is quite related to PDB. RasMol is a computer program written for molecular graphics visualization intended and used primarily for the depiction and exploration of biological macromolecule structures, such as those found in the Protein Data Bank. It was originally developed by Roger Sayle in the early 90s.


Let's see some example here :

Molecule Name PBD ID Structure in RasMol
ClpP 1YG6
ClpP is a self-compartmentalized proteolytic assembly comprised of two, stacked, heptameric rings that, when associated with its cognate hexameric ATPase (ClpA or ClpX), form the ClpAP and ClpXP ATP-dependent protease, respectively. The symmetry mismatch is an absolute feature of this large energy-dependent protease and also of the proteasome, which shares a similar barrel-shaped architecture, but how it is accommodated within the complex has yet to be understood, despite recent structural investigations, due in part to the conformational lability of the N-termini.
HtrA 2L97
High-temperature requirement A (HtrA), a highly conserved family of serine protease, plays crucial roles in protein quality control in prokaryotes and eukaryotes. The HtrA protein contains a C-terminal PDZ domain that mediates the proteolytic activity.
Thermolysin 3FLF
Thermolysin is a thermostable neutral metalloproteinase enzyme produced by the gram-positive bacteria Bacillus thermoproteolyticus. It requires one zinc ion for enzyme activity and four calcium ions for structural stability.Thermolysin specifically catalyzes the hydrolysis of peptide bonds containing hydrophobic amino acids.
Trypsin 4PTI
Trypsin 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.
LEXA 1JHF
LexA is a repressor enzyme 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.


To view and setting the PDB file (the structure picture), you should have RasMol application. The application can be downloaded here.














Monday, 1 October 2012


Chemsketch....The Beauty of Molecules


Assalamualaikum..hi guys!!..

Okay,guys...we gonna tell you some interesting topic here...focus okay!!..hahaha


Today,we had learned about chemsketch.Do you know what the chemsketch is?? Chemsketch is a softwear that help us especially scientist to draw chemical structures, reactions, schematic diagrams and designing other chemistry-related reports and presentations.

Moreover,we as students of biotechnology easy to understand about what we had learned during theoritical class.In this class,we learned chemsketch from beginning till the end by the awesome support from our beloved lecturer.By the way,you can see our result from what we had learned today.Hopefully you enjoy it!!!


The structure of DNA







If you are a student who is currently studying any bio-chemistry related subjects, you will come to love this software for its amazing functions, doing things that would be hard to be done manually by hand. This program can plot graphs, sketch formulas, chemically speaking, draw many types of orbitals, and even draw the apparatus that are usually found in a chemistry laboratory.



















With little reading on the manual, you can even draw simple organic structures such as lipids. Once you’ve done lipid, you can do an even bigger structure such as micelles. We would gladly provide you with the link to the website for the manual. Click on this manual for the link.







There’s even a mathematical function in this program where it can calculate many things for the formula of any molecule you draw. Composition and density are some of the things this program can calculate based entirely on your drawing.



.



If you want to know more, you can visit this website to learn more about this amazing software. Thats all for this time..see you later..assalamualaikum~~~^_^


Assalamualaikum w.b.t.

Ouch....this blog is quite outdated..!!..sorry guys,we totally busy for a past few weeks...eh..!! maybe??... or just pretending to be busy..hahaha..

Okay..let's start our sharing moments......just new experiences studying in IIUM Kuantan..waahhh....wahh..
For this semester, we are taking computer-related subject which is Computer in Science ( KOS 1110). Since its a new subject which offer basic modelling and programming lessons,its quite hard for us to understand the term and topic given..but practices make perfect,right??...haha..

Want to know the content of the subject??...so,please be curious person first..hahaha...we gonna tell you some of our lessons in class @ computer lab...0ooppss..!!..First of all.we would like to introduce you our beloved lecturers,special thanks to both of them..hehe..Thanks Dr.Linda and Dr. Salihi.

Okay,then..let's enjoy..............................................


Monday, 24 September 2012

Our First Day in International Islamic University Malaysia Kuantan Campus.


 FIRST STEP IN IIUM


Assalamualaikum w.b.t. everyone.

Nice to meet you...

   This is our first time writing a blog. so, we hope all of you enjoy reading our blog. 
Today we like to tell you about our first day in International Islamic University Malaysia(IIUM) Kuantan Campus.




   After three months holiday, on 4th September 2012 we have registered for undergraduate at IIUM Kuantan. We feel very grateful because have been choosing to further our study at IIUM Kuantan. IIUM Kuantan is located at Bandar Indera Mahkota, Kuantan. There are many beautiful scenery around here such as lake, and a very beautiful mosque.  

IIUM mosque
Harian Metro paper



   After registration, we begin our Ta’aruf week at 2 p.m. Some of the activities during Ta’aruf week are briefing by all Kuliyyahs, Bai’ah ceremony and Islamic Cultural Night. For us, Islamic Cultural Night is the most memorable activity because we can see the talent from all the new students. All performances were very fun and enjoyable.  


During ta’aruf week we also had been introduced to the IIUM song. We sang the song whole-hearted. The lyrics are very inspiring each of us to become a good students and a good Muslim.




This is the official website of IIUM. Feel free to visit. :)


This is the list of Kuliyyah And courses provided by IIUM Kuantan. 

KuliyyahCourses
MedicineMedicine
DentistryDentistry
PharmacyPharmacy
SciencesBiotechnology
Computer and Theoretical Science
Allied Health SciencesDietetics
Audiology
Optometry
Biomedical Science
Radiotherapy and Diagnostic Imaging
Physiotherapy

NursingNursing 

After we complete our registration we are officially one of the members of IIUM Kuantan. We are so nervous to start our life here. As we know degree life is not easy. But we will strengthen our heart to survive our life here.

That's all from us. Thank you. :D