Extensible Markup Language

Extensible Markup Language (XML) is a set of rules in encoding document in machine readable form. XML's design goal emphasize simplicity, generality and usability over the internet. Although the design of XML focuses on documents, it is widely used for the representation of arbitrary data structures, for example in web services.

Many application programming interfaces (APIs) have been developed that software developers use to process XML data, and several schema system exist to aid in the definition of XML-based languages.
As of 2009^[update], hundreds of XML-based languages have been developed^, including RSS, Atom, SOAP, and XHTML. XML-based formats have become the default for most office-productivity tools, including Microsoft Office (Office Open XML), OpenOffice.org (OpenDocument), and Apple's iWork. 

Here I will show a simple problem in how the XML is used.

Below will be the XML Table.

Computational Method.

Molecular Mechanic	Semi Empirical	Ab Initio
Very Fast Speed	Fast Speed	Low Speed
Restriction Parameters	Good accuracy	Very Good Accuracy
Very Good Protein Modelling	Good Protein Modelling	Best Protein Modelling

From the XML Table we can change it into XML Documentation as shown below. Here I use Microsoft Word to write it.

We also can change it into XML Tree. Here I use Microsoft Power Point.

 

 We can used XML to store and transport data and use HTML to display it. So when there are any changes in the data, we just need to change it in XML and refresh the HTML to display the new changes. Thus, it is more convenient to use XML rather than HTML in storing and make changes in data.

Protein Data Bank

PROTEIN DATA BANK (PDB)

Protein Data Bank (PDB) is a repository for 3-D biological macromolecular structure such as proteins and nucleic acid. 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. The PDB is overseen by an organization called the Worldwide Protein Data Bank, wwPDB. The PDB database is updated weekly every Tuesday. Up until 21 September 2010, there are 68421 structures that exist in the PDB. Table below show the experimental method to show the structures.

Experimental Method	Proteins	Nucleic Acids	Protein/Nucleic Acid complexes	Other	Total
X-ray diffraction	55480	1231	2605	17	59333
NMR	7512	925	162	7	8606
Electron microscopy	214	17	77	0	308
Hybrid	24	1	1	1	27
Other	126	4	4	13	147
Total:	63356	2178	2849	38	68421

One example that we can take from the Pdb database is the structure of LexA protein. We can search for it in the search box at the top of the page as shown below.

Next, we click at the first type of LexA proteins that come out in the search. Here we can see the description of the LexA protein with it scientific name.

 

We also can download the structure from this page and by using Raswin, we can alter the colour and shape of the structures. For example, below I use the stick for display and group for colour.

 

There are other type of display and colour that we can choose by using Raswin. Anybody who would like to download this program can click here. 

Simplified Molecular Input Line Entry Specifications (SMILES)

Continue from the previous post, here we will discuss about Structure mode. Below is the screen for the structure mode in ChemSketch.

The structure mode can be used to draw molecules. Below is the tutorial that I have done regarding to this problem.

Apart from can be used to draw molecules, it also come with SMILES notation. To see more example of SMILES you can click here.

Below also some of the example of SMILES.

Ethanol	CCO
Acetic acid	CC(=O)O
Cyclohexane	C1CCCCC1
Pyridine	c1cnccc1
Trans-2-butene	C/C=C/C
L-alanine	N[C@@H](C)C(=O)O
Sodium chloride	[Na+].[Cl-]
Displacement reaction	C=CCBr>>C=CCI

ChemSketch

ACD/ChemSketch is a chemical drawing software package from Advanced Chemistry Development Inc.
It is design to be used alone or integrated with other applications. ChemSketch is used to draw Chemical structures, reactions and schematic diagrams. it also can be used to design chemistry-related report and presentations. ChemSketch have two mode which is Structure and Draw.  There are also other type of ACD labs that is available. It is listed in the table below with its category.

Java Web Start 6.0	Freeware
ChemLab 2.5	Shareware
Microsoft Photodraw 2.0	Commercial
Genetic Pro 3.0	Shareware

Here, we will discuss about the Draw mode. Below is the layout of the ChemSketch for Draw mode and its toolbar.

Draw mode is mainly used to draw graphical objects. The object that we can draw using this application is;

• Energy Diagram
• Many types of orbitals.
• Apparatus
• DNA-strand
• Lipids

From Tutorial that I have done below is how we use ChemSketch to draw energy diagram.

Below is how orbitals look like when we used ChemSketch to draw it.

Below is how we draw apparatus using ChemSketch.

Next one is how DNA-strand is drawn using this application.

Lastly is the drawing of lipids in ChemSketch,

 

So, anybody who want to learn more about this application can go to this page.

Excel

Microsoft Office Excel is a spreadsheet application featuring calculation, graphing tools, pivot tables and a macro programming language.It is written and distributed by Microsoft for Microsoft Windows and Mac OS X. Below is the layout of Microsoft Excel.

Since 1993 until now, there are currently 5 version of Microsoft Excel. It is shown in table below.

Excel 2.0	1993
Excel 5.0	1995
Excel 2000	2000
Excel 2007	2007
Excel 2010	2010

For students that always need to calculate thing in their studies, by knowing how to use Microsoft Excel is a big help for them. This is because they can easily calculate they problem with it. Students also can created many type of graph that is very useful in presenting the data for the question. Below is an example on how students can use Excel in analysing the problem.

Below is also another example in how students can use Excel in solving problem.

There are other features that can help student in solving their mathematical problem. If anyone want to learn more about it, you can click here for Excel 2003 and here for Excel 2007.