SMILES :)

Assalamualaikum guys.. hopefully you smile and happy always..

let us smile together......

huh, why i asked you to smile and smile today? haha..
actually just want you to get the mood because today we will learn about SMILES.. But not smile in that picture ok..;)

SMILES is the short form of Simplified Molecular Input Line Entry System. This system uses atomic symbol and a set of intuitive rules. It also uses hydrogen-suppressed molecular graphs(HSMG). There are two types of smiles.

1) Canonical SMILES
2)Isomeric SMILES

Let us introduce you a few types of bonds of SMILES:

BOND
SINGLE	shows a single bond(-)
DOUBLE	shows a double bond(=)
TRIPLE	shows a triple bond
AROMATIC	can be omitted

There are a few SMILES charges that we need to know. There are:

[H+]       : proton

[OH-]     : hydroxyl anion

[OH3+]  : hydronium cation

[Fe++]    : iron(II) cation

[NH4+]   : ammonium cation


Please take note that the further Restrictions for SMILES are:
*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


How to draw the structure given???
Let us learn together..:)
If we want to draw this structure for example, we just can draw it by using the chemsketch application.
1) Open the chemsketch application
2) Choose the shape that we want to use / draw
3) Put the atom that we want to put ( in this case, Cl).

Here is another product that we can get...

So, to be more improve, you can practice by your own..
Remember, practice makes perfect!! :)

journey to PDB

">Assalamualaikum....
Today, we have learned two chapters. One of them is Protein Data Bank (PDB).
PDB is defined as a repository for 3-D biological macromolecular structure. It is founded in 1971 by Brookhaven National Laboratory in New York.

PDB first set of data were entered on punched cards. In 1998, it has been transferred to the research Collaborators for Structural Bioinformatics (RCSB).Currently, it holds 29 000 released structures.

Besides that, PDB is an important resource for research in the academic, pharmaceutical, and biotechnology sectors.
Will the molecule turns into a cancer cell?
Can these combinations of molecules cure common cold?
How does radiation effect the RNA and DNA?
These are types of application that can being solved when we use PDB.

 

The structure table above shows the things that can be defined by PDB.

No.	Type of proteins
1	Htra
2	subtilisin
3	collagenes
4	aminopeptidase
5	carboxypeptidae

The most interesting part when we learned PDB is this software can shows to us the image of the protein in different and attractive ways.This is the first time we explore such a beautiful protein structure.
Here,we serves to you some examples of the protein structures.

 carboxypeptidase

 aminopeptidase

 collageness

subtilisin

htra

See!!!How wonderful these structures right??

We had use this link protein data bank(PDB)  in order to download this all the structures.
Hope u will enjoyed  this topics same like us....;)

journey of Chemsketch

Wednesday comes again....
and the most interesting part is we will learn something new in Computer in Science subject.Today,we was being introduced with Chemsketch.This software is established to enable us draw chemical structures including oganics, organometallics, polymers, and Markush structures. It also includes features such as calculation of molecular properties (e.g., molecular weight, density, molar refractivity etc.), 2D and 3D structure cleaning and viewing, functionality for naming structures (fewer than 50 atoms and 3 rings), and prediction of logP.

structures that we can draw by using Chemsketch

  

To apply what we had learn and get used to this,we had been asked to practise some of the exercise of the Chem sketch in order to get used with the Chemsketch.The exercise that we have made is:

No	Tittle
1	Drawing of energy reaction diagram
2	Drawing different kinds of orbital
3	Drawing vacuum distillation apparatus
4	Drawing two chain DNA strands
5	Drawing a lipid and micelles

               To make our task more easier,we also get the additional information from this link http://www.acdlabs.com/resources/knowledgebase/faqs/chemsketch.php

What is XML??

Assalamualaikum...

Today, we are exited to show you what we had learnt today. Do you ever heard about XML?? Let's read and get something new with us...

XML stands for Extensible Markup Language. It is design to transport and store data. XML is important and it actually very easy to learn.

There are a few of characteristics of XML. XML are:

-Described format

-Structured format

-Can be validated

-Standard format

Last week, we learnt about HTML. Today, after we learnt about XML, we see that there are some differences between HTML and XML. Here is some differences between these two things :

XML						HTML
Used to tansport and store data						Used to display data with focus on how data look
Provides a framework for defining markup languages						Is markup language
Preseve white space						Not preserve white space
Used basically to transport data between application and database						Used for designing web-page

Besides that, we learn about XML Documentation, XML Table and XML tree.. Let's look what all this 3 are about?? We give you an example, so that you will be more understand, insya allah..

XML Documentation..

XML Table..

XML tree..

First..not this tree ok..

BUT...this XML tree:)

Hope you will get something today, Insya allah..

bye, see you next week..:)

the brief history of internet!

Assalamualaikum....

today we had learn about the history of internet and its development.Very interesting topics as we know when and how internet was introduced to us.As we know,internet has become an indeed integral part in our lives.With internet,the worlds is like at the tip of our fingers.Right from online banking, to shopping to online dating, the internet facilitates all, and since it has been such great boom to humanity.Due to that, we must try to know about its history and origin.

At the beginning,it was first developed by U.S Defense Advanced Rsearch Project Agency (DARPA) that started a research program called the Internetting project to develop communication protocols which would allow networked computers to communicate transparently across multiple, linked packet networks.  The system of networks which emerged from the research is what we know as the Internet. The system of protocols which was developed during this project is the TCP/IP

 Protocol Suite, after the two initial protocols developed: Transmission Control Protocol (TCP) and Internet Protocol (IP).Starting for the time,internet had being developed until now.Since its creation in 1983, the Internet has grown exponentially in terms of numbers of networks connected to it. By 1985, 100 networks, both public domain and commercial utilizing TCP/IP protocol suite became available. By 1987, the number had grown to two hundred; in 1989, it exceeded five hundred and by the end of 1991, the Internet had grown to include some 5,000 networks in over 36 countries, serving over 700,000 host computers used by over 4,000,000 people. Over the years, there has been wave of commercialization of the Internet. Originally, commercial efforts mainly comprised vendors providing the basic networking products, and service providers offering the connectivity and basic Internet services. The Internet has now become almost a "commodity" service, and much of the latest attention has been on the use of this global information infrastructure for support of other commercial services. This has been tremendously accelerated by the widespread and rapid adoption of browsers and the World Wide Web technology, allowing users easy access to information linked throughout the globe. New products developments in technology are readily accessible as downloads that are providing increasingly sophisticated information services on top of the basic Internet data communications.

Year	Events
1983	The Internet was created
1985	TCP/IP protocol suite became available
1987	The number of networks increase to 200
1989	It exceeded 500 networks
1991	The internet had grown to 5000 networks

The table shows that,the internet users around the worlds was increased.In order to get more clearer information about the topics,we also get through on http://www.walthowe.com/navnet/history.html .

the second journey..html..:)

very wonderful day we think!hmmmmmmmmmmm.....

first time learnt about html.....

first impression about html.......not very easy but fun....!!!

First of all, do you know what is HTML?
Ohh, it is short form of Hyper-text Mark-up Language.

We started to create web pages. Then, we learnt the other information that can be displayed in a web browser. This function is to:
*read HTML documents
*compose them into visible or audible web pages. The browser does not display the HTML tags, but uses the tags to interpret the content of the pages.

Here, some of the ways how to use the HTML.
1) Open the notepad
2) Write the command that has been given by madam.
3) Save the works in the documents by using .txt and .html files. (for example table.txt and the second one is table.html)
4) After that, we can open the Html by double click in the html files and the applications appear..

After learn and practice all the HTML application, for us, it looked easy to learn and understanding. By using this HTML, all things and information such as picture, table and others can be formatted. For us, it is new for us and it is very interesting. We enjoy it, alhamdulillah..:)

This is what we learnt today,,:)

No	Tittle
1	Intro
2	List
3	Link
4	Images
5	Table

JOURNEY OF MAPLE

Maple? What is this? We never heard that before. It sound interesting and make us eager to learn it more.

‘’Assalamualaikum class. Sorry, I’m late today.” The first sentence that we heard from our maple lecture, Bro.Aziz.  after introduce ourselves, bro Aziz introduce us about maple, but we didn’t  understand it!! Won that day, we just follow what he asked us to do. After many weeks go along with maple, Alhamdulillah, today we can introduce to you what is maple about. Hopefully you enjoy it!! 

From our humble understanding, Maple is a very powerful   computer algebra system.  It is used by students, educators, mathematicians, statisticians, scientists, and engineers for doing numerical and symbolic computation.So,for those who planning to be researcher,Maple will be the most important subject to be taken . Maple has  many strengths as that will give us many benefits. Among of them are: 

(1) it can do exact integer computation,

(2) it can do numerical computation to any (well, almost) number of specified digits,

 (3) it can do symbolic computation,

(4) it comes with many built-in functions and packages for doing a wide variety of mathematical tasks,

 (5) it has facilities for doing two- and three-dimensional plotting and animation,

(6) it has a worksheet-based interface,

 (7) it has facilities for making technical documents, and

8) mapleis a simple programming language, which means that users can easily write their own functions and packages.
For your information, this is some of the subtopics that we had learn in maple.

our table!!!!

No	Tittle
1	Basic Algebraic Operations on Expression
2	Graphing Functions, Expressions and Equations
3	Using Graph and Table to Predict Limits
4	Implicit Differentiation
5	Tangent Lines

To get information, we also use this link to get a clear view of maple..

www.maplesoft.com/

that's all.. :)