Extensible Markup Language (XML)

XML- Extensible Markup Language

- was designed to describe data and focus what data is.
- XML's design goals 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.
- is a markup language much like HTML.
- tags are not predefined.

1) XML syntax



2) XML tree




3) XML table

Computational method:

Method	Molecular mechanics	Semi empirical	Ab initio
Speed	Very fast speed	Fast speed	Slow speed
Accuracy	Parameter restriction	Good accuracy	Very good accuracy

PDB-PROTEIN DATA BANK

PDB- 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. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. These molecules are visualized, downloaded, and analyzed by users who range from students to specialized scientists.

from http://www.pdb.org/pdb/home/home.do

example of pdb:



thank you...happy PDB-ing... ;))))

SMILES

SMILES- simplified molecular input line entry system

Tutorial 1:


tutorial 2:

tutorial 3:




thank you..SMILES SOKMO dehh... :)

EXCEL (REGRESSION)

1) Beer's law plot data

2) Titration of 50 mL of 0.1 M HCl with 0.1 M NaOH
3) Percentage of runners injured in Boston Marathon


4) No. of new housing starts (in thousand) for 1990 through 1997

thank you..regress your head straight! ;)))

|CHEMSKETCH|

what is chemsketch?
chemsketch is a commonly used chemical drawing program for 2D and 3D structures, copyright of Advanced Chemistry Development, Inc. The program has certain additional features including calculation of molecular weight, calculation of percentages of elements present, IUPAC name generation, and viewing in RasMol.

here are some of the "sketch-es" or drawing made during the previous class.





thank you..sketch yourself now! ;D

MAPLE

as copied from our 1st note:
"Interactions between the mathematical and biological sciences have been increasing rapidly in recent years. Both traditional topics, such as population and disease modeling, and new ones, such as those in genomics arising from the accumulation of DNA sequence data, have made biomathematics an exciting field. The best predictions of numerous individuals and committees have suggested that the area will continue to be one of great growth." Mathematical Models in Biology by Allman and Rhodes

therefore, we need to study KOS1110:computer in science.. ;((

for this particular subject, we used MAPLE 12 software as a tool in this learning process.

what is MAPLE?pls read by your self HERE..

based on the notes given, this subject is mostly dealt with add maths and computer (which,honestly out of my interest at all..sorry).


for a start, still remember such equation?if u do,certainly you can go for MAPLE..hehheee.

through the weeks, you will learn how to solve add maths equation using MAPLE and lastly, learning MAPLE programming.

week no.	topic(s)
week 1	Basic Operations on Numbers, Expressions and Functions
week 2	Graphing Functions, Expressions, and Equations
week 3	Data Types: sequences, sets, lists, table, array, and data conversions
week 4	MAPLE programming

tq for viewing..happy study MAPLE..enjoice!

computer aided drug design [CADD]

well, for a start madam has asked us to find few terms related to this particular subject..here they are...>>>

1) bioinformatics - application of information technology and computer science to the field of molecular biology.

e.g: mapping and analyzing DNA and protein sequences, aligning different DNA and protein sequences to compare them and creating and viewing 3-D models of protein structures.

2) bioinformatics tools -the software programs for the saving, retrieving, and analysis of biological data and extracting the information from them.

e.g:
>> the basic local alignment tool [BLAST] for comparing gene and protein sequences against others in public databases.

>>FASTA - a database search tool used to compare a nucleotide or peptide sequence to a sequence database.

3) protein data bank [PDB] - a repository for the 3-D structural data of large biological molecules, such as protein and nucleic acids.

unfortunately, couldn't find anything regarding NCBI.. ;(

hope these may be helpful to others...
adios~