XML

Assalamualikum wr, wbt..,
What is XML ? here the link...

* 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
* XML is a W3C Recommendation

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

MY ASSIGNMENT ........>>>>>>

1. XML TREE

2. XML DOCUMENTATION

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


< INTERNATIONAL ISLAMIC UNIVERSITY MALAYSIA >

< UNIVERSITY >

< FACULTY > Sciences < /FACULTY >
< DEPARTMENT > Biotechnology < /DEPARTMENT >
< STUDENT > 58 < /STUDENT >
< STAFF > NA < /STAFF >

< LOCATION > Longitude 103'18'18.85E Latitude 3'51'21.97'N < /LOCATION >

< FACULTY > Medicine < /FACULTY >
< DEPARTMENT > Medicine < /DEPARTMENT >
< STUDENT > 123 < /STUDENT >
< STAFF > NA < /STAFF >
< LOCATION > Longitude 103'18'14.36E Latitude 3'50'33.85'N < /LOCATION >



< /UNIVERSITY >

< /INTERNATIONAL ISLAMIC UNIVERSITY MALAYSIA >







3. XML TABLE

SCIENCES	MEDICINE
BIOTECHNOLOGY	MEDICINE
58	123
NA	NA
Longitude 103'18'18.85E Latitude 3'51'21.97'N	Longitude 103'18'14.36E Latitude 3'50'33.85'N

tq

EXCEL

Assalamualaikum wr, wbt.......,

Microsoft Excel (full name Microsoft Office Excel) is a spreadsheet application written and distributed by Microsoft for Microsoft Windows and Mac OS X. It features calculation, graphing tools, pivot tables and a macro programming language called VBA (Visual Basic for Applications). It has been a very widely applied spreadsheet for these platforms, especially since version 5 in 1993. Excel forms part of Microsoft Office. The current versions are Microsoft Office Excel 2010 for Windows and 2008 for Mac.

http://en.wikipedia.org/wiki/Microsoft_Excel

On that day, i have learned to scatter plot using EXCEL. So, below what i have done on my tutorial...,

 Part 1 - Beer's Law Scatter Plot and Linear Regression

&

Part 2 - Titration Data Plotting

 

KOS1110	COMPUTER IN SCIENCE
TIME	2.00PM - 5.00PM
VENUE	ORKID LAB

CHEMSKETCH

ACD/ChemSketch is a chemically intelligent drawing interface that allows TO draw almost any chemical structure including organics, organometallics, polymers, and Markush structures. Use it to produce professional looking structures and diagrams for reports and publications.

Features

• Draw and view structures in 2D, or render in 3D to view from any angle
• Draw reactions and reaction schemes, and calculate reactant quantities
• Generate structures from InChI and SMILES strings
• Generate IUPAC systematic names for molecules of up to 50 atoms and 3 ring structures
• Predict logP for individual structures
• Search for structures in the built-in dictionary of over 165,000 systematic, trivial, and trade names

Benefits

• Visualize chemical structures in 2D or 3D to gain more insight into spatial configurations, and relationships to molecular properties
• Create professional reports, working with structures, text, and graphics simultaneously

ACD/ChemSketch also allows to check other tautomeric forms for your drawn structure. Consideration of tautomeric forms is very important for structure searching, predictions (such as physicochemical properties, i.e., pK_a), and interpretation (i.e., of NMR, MS, and other analytical data). 

http://www.acdlabs.com/products/draw_nom/draw/chemsketch/ 

 

Above picture is what i have done using the manual of CHEMSKETCH


That's All....... THANK YOU...........

KOS1110	COMPUTER IN SCIENCE
TIME	2.00PM - 5.00PM
VENUE	ORKID LAB

Protein Data Bank (PDB)

Assalamualaikum wr, wbt..,

Today"s lecture is about PDB (Protein Data Bank). Actually it is a resource for scientist for studying biological macromolecules. It  is an interesting topic to be learned.The PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies. The RCSB PDB also provides a variety of tools and resources. We can perform simple and advanced searches based on annotations relating to sequence, structure and function. These molecules can be visualized, downloaded, and analyzed.

Below, there is link for us to know the detail about PDB.......

http://www.pdb.org/pdb/home/home.do 

http://en.wikipedia.org/wiki/Protein_Data_Bank

For example, the picture showed the structure of Lon ATP-dependent Proteases  that we can get from PDB website. The explanation about the enzyme is written the table below. ( actually it is just COPY & PASTE.... huhu). By the way, is just an example.. So take it easy...........

Lon ATP-dependent proteases

Lon ATP-dependent proteases are key components of the protein quality control systems of bacterial cells and eukaryotic organelles. Eubacterial Lon proteases contain an 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 hydrolysis of polypeptides into small peptide fragments. Like other AAA+ ATPases and self-compartmentalising proteases, Lon functions as an oligomeric complex, although the subunit stoichiometry is currently unclear. Here, we present crystal structures of truncated versions of Lon protease from Bacillus subtilis (BsLon), which reveal previously unknown architectural features of Lon complexes. Our analytical ultracentrifugation and electron microscopy show different oligomerisation of Lon proteases from two different bacterial species, Aquifex aeolicus and B. subtilis. The structure of BsLon-AP shows a hexameric complex consisting of a small part of the N-terminal domain, the ATPase, and protease domains. The structure shows the approximate arrangement of the three functional domains of Lon. It also reveals a resemblance between the architecture of Lon proteases and the bacterial proteasome-like protease HslUV. Our second structure, BsLon-N, represents the first 209 amino acids of the N-terminal domain of BsLon and consists of a globular domain, similar in structure to the E. coli Lon N-terminal domain, and an additional four-helix bundle, which is part of a predicted coiled-coil region. An unexpected dimeric interaction between BsLon-N monomers reveals the possibility that Lon complexes may be stabilised by coiled-coil interactions between neighbouring N-terminal domains. Together, BsLon-N and BsLon-AP are 36 amino acids short of offering a complete picture of a full-length Lon protease.

tHAT'S ALL, THANK YOU.....


WASSALAM

SMILES

Assalamualaikum wr, wbt...,

Let's continue our lecture in computer in science .., Today i learned about SMILES.

SMILE (Simplified Molecular Input Line Entry Specification) is a specification for unambiguously describing the structure of chemical molecules using short ASCll strings. SMILES strings can be imported by most molecule editors for conversion back into 2D drawings or 3D models of the molecules. (actually i just copied my lecturer notes..., huhuhu)

What i can say, from SMILES we can draw numerous molecules in chemistry such as alkanes, alkenes, alkynes, aromatic compound and many more.  It is widely used by scientist and chemist and computationally efficient (perhaps >-<).....

 http://en.wikipedia.or/wiki/Simplified_molecular_input_line_entry_specification

So, below this is my tutorial for today class...,

THAT'S ALL FOR TODAY CLASS.........., SEE YAAA !!!!! 

STRUCTURE	SMILE NOTATION
	C=CC\C=C\O

	CCN(CC)CC
	CC(C)C(=O)O

	CC(C)C(CCC)C(CCC)C=C
	C1CCCCC1

	CC1=CC(Br)CCC1
	C1CN(CCC1)C2CCCCO2

	c1ccco1
	O=C1C=CN=CN1

	c1ccccn1
	O=n1ccccc1

	[O-][n+]1ccccc1
	O=C1C=CC=CN1

	Cn1cccc1
	c1cccn1

	Cn1cccc1
	C[C@H]=C\C=C\F

C\C=C\C=C\F