XML

Extensible Markup Language (XML) is a set of rules for encoding documents in machine-readable form. It is defined in the XML 1.0 Specification produced by the W3C, and several other related specifications, all gratis open standards

XML's design goals emphasize simplicity, generality, and usability over the Internet. It is a textual data format with strong support viaUnicode for the languages of the world. 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 systems exist to aid in the definition of XML-based languages.

XML Table

Computational Method  

Molecular  Mechanics	Semi Empirical	Ab Initio
Very fast speed	Fast speed	Slow speed
Restriction parameters	Good accuracy	Very good accuracy
Very good protein	Good protein	Best protein
Modelling	Modelling	Modelling

XML Documentation

<computational table>
<method category="Molecular Mechanics">
<speed>very fast speed</speed>
<accuracy>restriction parameters</accuracy>
<protein modelling>very good protein modelling</protein modelling>
</method>
<method category="Semi Empirical">
<speed>fast speed</speed>
<accuracy>good accuracy</accuracy>
<protein modelling>good protein modelling</protein modelling>
</method>
<method category="Ab Initio">
<speed>slow speed</speed>
<accuracy>very good accuracy</accuracy>
<protein modelling>best protein modelling</protein modelling>
</method>
</computational table>

XML Tree

For more example and tutorial on XML,click here.

protein data bank!

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

The PDB is a key resource in areas of structural biology, such as structural genomics. Most major scientific journals, and some funding agencies, such as the NIH in the USA, now require scientists to submit their structure data to the PDB. If the contents of the PDB are thought of as primary data, then there are hundreds of derived (i.e., secondary) databases that categorize the data differently. For example, both SCOP and CATH categorize structures according to type of structure and assumed evolutionary relations; GO categorize structures based on genes.

FILE FORMAT

The file format initially used by the PDB was called the PDB file format. This original format was restricted by the width of computer punch cards to 80 characters per line. Around 1996, the "macromolecular Crystallographic Information file" format, mmCIF, started to be phased in. An XML version of this format, called PDBML, was described in 2005. The structure files can be downloaded in any of these three formats. In fact, individual files are easily downloaded into graphics packages using web addresses:

• For PDB format files, use, e.g., http://www.pdb.org/pdb/files/4hhb.pdb.gz
• For PDBML (XML) files, use, e.g., http://www.pdb.org/pdb/files/4hhb.xml.gz

For more information about this topic,click here.

SMILES =)

The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of chemical molecules using short ASCII strings. SMILES strings can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensional models of the molecules.

In July 2006, the IUPAC introduced the InChI as a standard for formula representation. SMILES is generally considered to have the advantage of being slightly more human-readable than InChI; it also has a wide base of software support with extensive theoretical (e.g., graph theory) backing.

Example of some reaction in SMILES:

Reaction SMILES	Name
[I-].[Na+].C=CCBr>>[Na+].[Br-].C=CCI	displacement reaction
(C(=O)O).(OCC)>>(C(=O)OCC).(O)	intermolecular esterification

for more example of reaction SMILES,click here.

Chemsketch

ChemSketch is designed to be used on its own for drawing chemical structures, reactions, schematic diagrams or integrated with other ACD applications and as the front end to our software. Able to import Windows Metafile, MDL MOL, CS ChemDraw, or ISIS/Sketch BIN file. Export Bitmap, TIFF, Metafile, MOL, Paintbrush, ISIS/Sketch, GIF , and ChemDraw. Fully loaded with useful pre-drawn structures including lab equipment, DNA/RNA building kit, amino acids etc. Structures can be 2D "cleaned" as well as 3D optimized using ACD's powerful algorithm. Publish a professional quality report from within ChemSketch or drag drop structures/text into MS applications i.e. MS Word.

 The ChemBasic language, which is integrated with ACD/ChemSketch chemistry drawing software, is intended to be a tool for

• manipulating chemical structures, both 2D- and 3D;
• customizing ACD/Labs software, through direct access to its embedded functionality;
• developing add-ons to ACD/Labs chemistry software.

Improvement in Chemsketch through Version

Version 10.0 to 11.0	Interface changes Improvement in Structural Representation IUPAC International Chemical Identifier (InCHl) improvement
Version 9.0 to 10.0	Expanded ACD/Dictionary
Version 8.0 to 9.0	Support of InChI Identifier. Advancements in Markush structure representation. Increased size of ACD/Dictionary. Ability to create animated graphical images from ACD/3D Viewer.

to download Chemsketch and Chembasic for free,click here.

Microsoft Excel

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 and a macro programming language called VBA (Visual Basic for Application). 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.

Versions of Microsoft Excel:

Windows	1990 Excel 3.0 1992 Excel 4.0 1993 Excel 5.0  1995 Excel for Windows 95 (version 7.0)  1997 Excel 97  1999 Excel 2000 (version 9.0) 2001 Excel 2002 (version 10)  2003 Excel 2003 (version 11)  2007 Excel 2007 (version 12)  2010 Excel 2010 (version 14)
Macintosh	1985 Excel 1.0 1988 Excel 1.5 1989 Excel 2.2 1990 Excel 3.0 1992 Excel 4.0 1993 Excel 5.0 1998 Excel 8.0 2000 Excel 9.0 2001 Excel 10.0 2004 Excel 11.0  2008 Excel 12.0 2010 Excel 14.0
OS/2	1989 Excel 2.2 1990 Excel 2.3 1991 Excel 3.0

Microsoft Excel has the basic features of all spreadsheets using a grid of cells arranged in numbered rows and letter-named columns to organize data manipulations like arithmetic operations. It has a battery of supplied functions to answer statistical, engineering and financial needs. In addition, it can display data as line graphs, histograms and charts, and with a very limited three-dimensional graphical display. It allows sectioning of data to view its dependencies on various factors from different perspectives. And it has a programming aspect, Visual Basic for Applications, allowing the user to employ a wide variety of numerical methods, for example, for solving differential equations of mathematical physics and then reporting the results back to the spreadsheet.

It also has a variety of interactive features allowing user interfaces that can completely hide the spreadsheet from the user, so the spreadsheet presents itself as a so-called application, or decision support system (DSS), via a custom-designed user interface, for example, a stock analyzer or in general, as a design tool that asks the user questions and provides answers and reports^. In a more elaborate realization, an Excel application can automatically poll external databases and measuring instruments using an update schedule,analyze the results, make a Word report or Power Point slide show, and e-mail these presentations on a regular basis to a list of participants.

to download latest version of Microsoft Excel 2010,click here.

maple!

Maple is a procedural programming language. It also includes a number of functional programming

constructs.

Maple is interactive and the programming language is interpreted. Maple is not suitable

for running numerically intensive programs because of the interpreter overhead. Though it

is suitable for high-precision numerical calculations and as a tool for generating numerical

codes.

With Maple you can create powerful interactive documents. The Maple environment

lets you start solving problems right away by entering expressions

in 2-D Math and solving these expressions using point-and-click interfaces.

You can combine text and math in the same line, add tables to organize the

content of your work, or insert images, sketch regions, and spreadsheets.

You can visualize and animate problems in two and three dimensions, format

text for academic papers, or books, and insert hyperlinks to other Maple

files, Web sites, or email addresses. You can embed and program graphical

user interface components, as well as devise custom solutions using the

Maple programming language.

To start Maple on:

Windows	From the Start menu, select All Programs → Maple 12 →Maple 12. Alternatively: Double-click the Maple desktop icon
Macintosh	1. From the Finder, select Applications and Maple 12. 2. Double-click Maple 12
UNIX	Enter the full path, for example, /usr/local/maple/bin/xmaple Alternatively: 1. Add the Maple directory (for example, /usr/local/maple/bin) to your command search path. 2. Enter xmaple.

A MAPLE command is a statement of a calculation followed by a semicolon (the result is displayed on the screen) or a colon (the result is stored but not displayed). Following are some commands followed by the displayed results. Enter the commands on your worksheet and verify the given results.
for example:

• [> 4+5;9
  
• [> 6^2;36
  

there are a lot more you can do in maple as it provide interface for solving mostly all problems in mathematics field especially. To learn more,here i provides you with some useful links for introduction of maple programs. 

link 1

link 2

link 3

link 4

thank YOU!
=D