designing XML

Hello there….back again with today’s assignment of Extensible Markup Language(XML)...

XML  was designated to describe data and focus on what data is. It is much similar to HTML actually but is definitely not a replacement of HTML.

Goals of XML:

-to transport and store data, with focus on what data is

-to display data with focus on how data looks

Comparison between HTML and XML:

HTML is about displaying information while XML is about carrying information..

XML tree

XML documentation
<?xml version="1.0" encoding="ISO-8859-1">

<university>

<faculty category="MEDICINE">

<department>Pathology</department>

<students>32 students</students>

<staff>40 staffs</staff>

<location>HTTA</location>

</faculty>

<faculty category="SCIENCE">

<department>Bio Medicine</department>

<students>100 students</students>

<staff>50 staffs</staff>

<location>Gombak</location>

</faculty>

</university>

XML table

Faculty	MEDICINE	SCIENCE
Department	Pathology	Bio Medicine
Students	32 students	100 students
Staff	40 staffs	50 staffs
Location	HTTA	Gombak

For more information about XML, check out its wikipedia HERE...

Thats all for today I guess, my last class of kos1110...:)

Till then,

signing out for now...heee..

SCATTER PLOT??

Now its about Scatter Plot in exel...
Click HERE for more information regarding scatter plot...
First part is about the Beers' Law Scatter Plot and Linear Regression...
This is a graph of absorbance versus concentration...begin by entering data for the graph in first two columns in the spreadsheet...below is an example..

Conc. (m)	Absorbance
Data	Data

Below is the completed graph...

Next is regarding Titration Data Plotting...
This data is of a strong acid-strong base concentration...With this titration, a strong base(NaOH) of known concentration is added to a strong acid..the equivalence point can be found with a color indicator in the curve or through a pH titration curve(the blue line in the graph)...

Column A	Column B
mL of 0.1M NaOH added	pH of the 0.1M HCL/0.1M NaOH mixture

Below is the completed graph...

Below are the picture of the completed graph from my tutorial...

This graph is about finding the line of best fit

This graph is about quadratic regression..

Thats all for now....really tired....
signing out for now...

Beautiful Drawing...

Today my post is about CHEMSKETCH...
Basically chemsketch is about drawing chemical structures, and to view them as three dimensional (3D) models.
However, in order to draw these structures we must first download the chemsketch software which can be obtained by clicking HERE .

For my assignment I did a few drawings which consists the drawing of of enegy of reaction diagram, different kinds of orbitals, vacuum distillation apparatus, two chain DNA strand and lipid and micelles.

The energy diagram is about drawing a graph of curve using mode polyline. Then, modufy the curve and add the axis. Below is the picture of a completed energy diagram...

  The picture of the word chemistry was a challenge of writing the word by using the same method of drawing the curve...It was tough but I guess I managed to pull through it..

Next was drawing different kinds of orbitals such as p-orbital, d-orbital and pi-orbital. This was drawn by using polygon tool from the draw mode..d- orbital is two p-orbital where one of it is rotated 90 degrees and being put on top of the other. ..pi-orbital was drawn by using eclipse tool and the converted to polyline. The nodes was compressed, a copy was made, flip top to bottom. and both was align together..Below are the pictures of the orbitals..

p/s: the top one is p-orbital, on the right is d-orbital and below is pi-orbital...

Third was drawing vacuum...it was merely pasting pictures of apparatus together to form a vacuum, including some editing of the nodes and rotating...below is the picture of a labelled vacuum distillation apparatus...

Next is the drawing of DNA strand by using polyline...this was quite difficult in sense of drawing a perfect curved DNA strand. It is a combination of two strands of DNA which overlaps each other and some parts of the strands having shades and being moved to the back to produce a 3D picture...below is the picture of two-chain DNA strand..
Strand 1                                                

Style	Color	Shade
Shade	White	-30%

Strand 2

Style	Color	Shade
Shade	White	-95%

Finally is the drawing of lipids and micelles by using eclipse tool from the drawing mode...the circle was colored black. The tail of lipids was drawn by using polyline, editing the nodes, converting to curve and smoothing it....twelve lipid structure was drawn and rotated into a circle to produce a micelles picture.. below is the picture of a lipid and micelles...

Thats alll about chemsketch....
signing out for now...

Protein Data Bank (PDB)

Here I am once again....

Today I am going to talk about the great Protein Data Bank...shortform PDB..

Definition: The Protein Data Bank (PDB) is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acid.

This PDB is a member of the worldwide Protein Data Bank(wwPDB).

PDB has its special webpage which can be viewed by users to search for annotations relating to sequence, structure and function. These molecules are visualized, downloaded, and analyzed by users who range from students to specialized scientists. 

The PDB database is updated weekly (on Tuesday). As of Tuesday Oct !2, 2010 at 5pm PDT there are 68562 Structures

Click HERE to view the official webpage of PDB.

For today's assignment I have to talk about Crystal structure of Bacillus subtilis Lon-N terminal domain

To search for this structure at the PDB webpage, firsly we would have to write the word" lonA" at the search box, where it gives to different kinds of structure which are 3M65 and 3M6A..I choose the first structure to talk about which is 3M65..reacearch about this structure was done by the author Duman,R.E. and Lowe, J.Y.

Here is a picture of the structure whereby the structure is in the form of ribbon and color being temperature..

Primary citation about this lonA structure:
Lon ATP- dependent proteases are key components of the protein quality control systems of bacterial cell and eukaryotic organelles. Eubacterial Lon proteases contain a N- terminal domain an ATPase domain, and a protease domain all in one polypeptide chain. The N-terminal domain is thought to be involved in substrate recognition, the ATPase domain in substrate unfolding and translocation into the protease chamber, and the protease domain in the hydrolysisof polypeptides into small peptide fragments.

Molecular structure:

Classification	Structure Weight	Molecule
Hydrolase	48027.40	ATP-dependent protease La 1

Thats all from me about Bacillus subtilis...
sigining out for now.......

SMILES....

Simplified Molecular Input Line Entry System(SMILES) was our assignment for today.

We learned to draw molecular structure in chemsketch...it was quite difficult but then became fun once I know how to do it.

What is SMILES...

  "Is a specification unambiguously describing the structure of chemical molecules using short ASCII strings"

In drawing a molecular structure it is important to have bonds which shows the connection of one molecule to another..here are a few examples of symbols representing bonds.. 

Single	-
Double	=
Triple	#

With this I attach my completed assignment for viewing...not sure if its right or not..

Tutorial 1

 

 

Tutorial 2

Tutorial 3

Tutorial 4

Below every structure is the condensed molecular formula of the structure which was determined by the computer. only for the first tutorial I did it manually. Computer really makes life easy..hee

Below is a link to Wikipedia.for more information regarding SMILES..

 CLICK
That's all for now...signing out..