XML

XML is a meta-language for describing markup languages. In other words, XML provides a facility to define tags and the structural relationships between them. XML is different with HTML as XML was designed to transport and store data, with focus on what data is. Meanwhile, HTML was designed to display data, with focus on how data looks. XML is often used to simplify data storage.

Below are the exercise that I did:

XML Tree

:

XML Table

Medicine	Science
Pathology	Bio Medicine
32 Students	100 Students
40 Staff	50 Staff
HTAA	Gombak

XML Documentations
<University>
<Faculty category="Medicine">
<Department>Pathology</Department>
<Students>32 Students</Students>
<Staff>40 Staffs</Staff>
<Location>HTAA</Location>
</Faculty>

<Faculty category="Science">
<Department>Bio Medicine</Department>
<Students>100 Students</Students>
<Staff>50 Staffs</Staff>
<Location>Gombak</Location>
</Faculty>
</University>



To know more about XML, please click here
Or you can click here to have some XML tutorial.

Excel

Microsoft Excel is a spreadsheet application which can be use to calculate and distribute data, create chart and graph. It has function to calculate mathematical equations, statistics, engineering and financial equation. It allowed user to insert the mathematical equation and Microsoft Excel will help user to calculate the answer. This function is called Visual Basic for Applications.

Microsoft Excel can generate chart and histogram. The chart can be embedded in the same spreadsheet or as a separate object. Below are the example of the chart that I have created with the help from Microsoft Excel.

Concentration vs Absorbance Graph

Acid-Base titration chart

Temperature vs Percentage of Injured Chart

Housing vs Year Chart

From the above pictures, we can see Microsft Excel is really helpful to us if we want to generate chart from the data given. By using Microsoft Chart, can also calculate and predict the data. For example, in Housing vs Chart above, I want to predict the number of house in year 2001. By using Visual Basic for Applications, I inserted the mathematical formula and Microsoft Excel help me to calculate the answer.

Microsoft Excel	Microsoft Word
Can generate chart easily	Require several steps to generate chart
Can calculate answer for Mathematics questions	Cannot calculate answer for mathematics questions
Have Visual Basic Applications	Do not have Visual Basic Applications

If you want to know more about Microsoft Excel, please click here.

Interested to learn how to use Microsft Excel, please click here.

Chem Sketch

ACD Chem Sketch is a software that allowed us to draw any chemical structure including organic and inorganic, polymer and even laboratory apparatus. In Chem Sketch, we can choose to either use the "structure" or "draw". In "structure", we can draw many chemical structure like the one that have been said in post SMILES before. In "draw", we can draw many diagrams including DNA protein and even laboratory apparatus.

We can use Chem Sketch to draw energy diagram.

Example of orbitals

The best part of Chem Sketch; drawing laboratory apparatus

DNA strand can be draw too!

The beautiful lipid structure!

Chemsketch	What we can do?
Draw	Draw energy diagram, orbitals, laboratory apparatus.
Structure	Draw chemical structure

Chem Sketch is really helpful to us!


Get to know more about Chem Sketch by clicking here.

Want a tutorial on how to draw chemical structure? Please click here.

Protein Data Bank

The protein Data Bank contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies. These are the molecules that are found in living things such as bacteria, yeast, fungi and even human. The data are obtained from  X-ray crystallography or NMR spectroscopy. X-Ray crystallography is a method of determining the arrangement of atom in a structure. The data typically sent by scientists all over the world are freely accessible by public. We can use this Protein Data Bank to help us to understand the genomic microbiology.

RasMol is a computer program written for molecular graphics visualization intended. RasMol can be used to depict and explore the macromolecules structure in the Protein Data Bank. By using RasMol, we can view the structure of the molecules using several types of display and colours. As an example, the protein below is being view by using cartoon display.

From the Protein Data Bank, we can get information about the compound of the protein and some additional explanation about the protein. We also can know the author of the structure and the date of the structure is released.  For the above picture, the author of the protein is Duman R.E and Lowe J.Y and it is being published on 30tth June 2010. The above picture shows lon ATP dependent protease. This structure play important role in controlling the protein quality. 

This is lon ATP view by using ball and stick display

To know more about...	Please click the link
Protein Data Bank	Here
RasMol	Here

SMILES

SMILES (Simplified Molecular Input Line Entry System) is a line notation (a typographical method using printable characters) for entering and representing molecules and reactions.

SMILES supports all elements in the periodic table. An atom is represented using its respective atomic symbol. Upper case letters refer to non-aromatic atoms; lower case letters refer to aromatic atoms.

c1ccccc1  is Benzene (aromatic compounds) 

C1CCCCC1 is Cyclohexane (aliphatic or non-aromatic compound)

 

Slide 2

Single, double, triple, and aromatic bonds are represented by the symbols -, =, #, and :, respectively.

single	-
double	=

Slide 3

Configuration around double bonds is specified by the characters / and \ which are "directional bonds" and can be thought of as kinds of single or aromatic (eg. default) bonds.

Slide 4

Slide One SMILES notation
C=CC\C=C\O
CCN(CC)CC
CC(C)C(=O)O
CC(C)C(CCC)C(CCC)C=C

Want to know more about SMILES?

• Click here
• Or here 

Happy SMILING!

MAPLE

Today, I'm going to write about Maple.

 This is not the maple i want to write.

Maple is a mathematics software program that involved Math and calculations. We are obliged to learn Maple as this program will help us in our work someday.

 

A snapshot of Maple

For the first week, we learn the Introduction of Maple. We are being taught on how to use Maple and how to write simple Mathematics equation using Maple. In maple, we cannot write the product expression as simply as 2 x 4. The product symbol (x) have to be replaced with the star symbol (*) and the semicolon symbol (;) is being used if we want to show the answer.

For the next class, things get harder as we, Biotech students did not know much about Mathematics or Calculus, and Dr Salihi keep asking us "This is Form 5 AddMath questions, don't tell me you have forget it." Unfortunately, many of us have forget it.

We learn how to solve inequalities, integration and function questions and how to derive a graph from the function. Well, it is not easy as it sounds because besides struggling to remember what we have learn back in Matriculation years, we have to remember many new things like the word "evalf" is used if we want to evaluate the answer and the word "solve" is used if we want, well, to solve the question.

Here are some words use in Maple and the definition of the words in the real life.

Word in Maple	Definition
evalf	evaluate the answer (to how many decimal points)
solve	solve the question
proc	procedures
restart	clear Maple memory

You can learn more about Maple by clicking here and here.

If you wish to download Maple free trial, please click here.