Computer in Science
Sunday, April 13, 2014
Internet History
XML
What is XML ?
- 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 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
Differences Between HTML and XML
XML
|
HTML
|
Transport and store data
|
Display Data only
|
Focus on what data is
|
Focus on how data looks
|
Carry information
|
Display information
|
A framework for defining markup languages.
|
A markup language itself
|
Case sensitive
|
Case insensitive
|
Dynamic
|
Static
|
Neither a programming language nor a presentation language
|
A presentation language
|
XML TREE
Wednesday, March 5, 2014
Protein Data Bank
Biologists and biochemists use sequence databases, structure databases, literature databases, etc. The database we will learn here is called the Protein Database (PDB). The PDB has all known 3D structures of proteins, DNAs and RNAs. To find the PDB on the web, type ‘PDB’ into google, and go to the first link returned, which is http://www.rcsb.org/pdb/home/home.do
You need to download the protein structures (i.e., the PDB files) that you are going to study, to your own computer. Each structure is in a pdb file with a name that does not carry much information (for example 1H97.pdb). A PDB file is a simple text file with the xyz coordinates of all the atoms in the protein (one protein has lots and lots of atoms).
Search for the protein that you want to study, for example, Neuraminidase
Scroll down to find the specific protein
Download the file by clicking PDB File(text)
The data format that PDB use is macromolecular crystallographic information file (mmCIF). It been introduced in the late 1990's. As the result,PDB has been very useful for every kind of human being,especially scientist,lecturers and students. These are 5 examples of the proteins that have been downloaded:
1) Neuraminidase
2) ClpP
3) HtrA
4) Trypsin
5) Subtilisin
Name | Neuraminidase | ClpP | HtrA | Trypsin | Subtilisin |
---|---|---|---|---|---|
Molecule Name
|
der Influenza-Neuraminidase-Teil 2
|
Escherichia coli |
Putative serine protease
|
Erythrina Trypsin Inhibator
|
Serine endopeptidase
|
Classification
|
Hydrolase
|
Hydrolase
|
Protein binding
|
Proteinase Inhibator
|
Protease
|
Type
|
Protein
|
Protein
|
Protein
|
Protein
|
Protein
|
Length
|
388
|
193
|
134
|
172
|
269
|
Now, what software or program shall we use to open such file? This is when Rasmol comes into rescue!
What is RasMol ?
RasMol is a program for molecular graphics visualisation originally developed by Roger Sayle. This site is provided for the convenience of users of RasMol and developers of open source versions of Rasmol. It is a free program which displays molecular structure.
RasMol was designed for viewing protein structures -- molecules so large that one would not make an ordinary molecular model by hand. However, it can also be used for small molecules. Using RasMol for small molecules is particularly useful if you do not have a set of models. If you do have models, it may be good to learn to use RasMol with small molecules, and even compare the RasMol model with the "physical" models.
To get started with RasMol :
1. Open file of RasMol: File/Open from within RasMol. From within Netscape, click on a RasMol viewable molecule (a .pdb file). (RasMol should automatically start and load in the molecule.)
Wednesday, February 19, 2014
chemsketch
Chemsketch is a most powerful program and easiest tool for drawing chemical structures, reactions, schematic diagrams and designing other chemistry-related reports and presentations. From April 1999 onward, Advanced Chemistry Development, Inc., (ACD/Labs) has been making ChemSketch available as freeware through the “Free Stuff” link at our Web site and it should be installed in its own separate folder... Thanks to them made it free. (before this you need to purchase it). Now we offer ACD/ChemSketch 8.0 for free! (newest version is ACD/Chemsketch 12.0). Make sure get the latest one..!!
All of the limitations on Freeware and also the Frequently Asked Questions (FAQs) can be found on web site at http://www.acdlabs.com/products/chem_dsn_lab/chemsketch/tech.html.you are encourage to visit the ChemSketch newsgroup at the address mentioned in the next section where you can post your questions or share tips.
The core capabilities of this program :-
-Drawing of Molecular Structure
-Structure Search
-Chemistry
-Reporting
-Enhanced Graphics
-Convenient Interface Design
Friday, February 14, 2014
Html
This is a paragraph.
<p> = start tag
</p> = end tag
What we learn today is the basic of how to create HTML code.
Step 1: open a application named NOTEPAD.
Step 2: write the code.
Step 3: save the document as HTML document.
Step 4: Open the folder where you save the code and click on the document you just saved.
Then a window will appear.The code that you create will show what should appear on the window.for example,if you type the code below you will see a table appears on the window.
For example:
<html>
<body>
<table border="1" style="width:300px">
<tr>
<td>Jill</td>
<td>Smith</td> <td>50</td>
</tr>
<tr>
<td>Eve</td>
<td>Jackson</td>
<td>94</td>
</tr>
</table>
</body>
</html>
The outcome will be:
Jill | Smith | 50 |
Eve | Jackson | 94 |
Try it yourself :)
For further infos on this, try http://www.w3schools.com/html/html_tables.asp
Goodluck!
Wednesday, February 5, 2014
Concept in Physics
1. A physical quantity is a quantity that can be measured.
2. A physical quantity can be divided into base quantity and derived quantity.
Base Quantities
1. Base quantities are the quantities that are conventionally accepted as functionally
independent of one another.
2. It is a quantity that cannot be defined in term of other physical quantity.
3. The base quantities and its units are as in the table below:
Quantity | Name of Unit | Unit symbol |
---|---|---|
Length | metre | m |
Mass | kilogram | kg |
Time | second | s |
Electic current | ampere | A |
Temperature | Kelvin | K |
Derived Quantities
A derived quantity is a Physics quantity that is not a base quantity. It is the quantities which derived from the base quantities through multiplying and/or dividing them.
For example:
Derived Unit
The derived unit is a combination of base units through multiplying and/or dividing them.
Prefixes
Prefixes are the preceding factor used to represent very small and very large physical quantities in SI units.
Click these links! Check them out:
http://physics.nist.gov/cuu/Units/units.html
http://physics.nist.gov/Pubs/SP811/sec04.html