DEVELOPMENT APPLICATION TO BIOINFORMATICS-III Vicky Khanna 200960013 M-Tech Bioinformatics
WHY DO WE NEED WEB APPLICATIONS? ? ? Parsing the NCBI Files to extract a particular pattern. Removal of Hetro. Atoms from RCSB files for Drug Discovery Analysis. Automated Search and parsing for a particular gene or gene sequence from Meta-Databases like KEGG, NCBIGenbank, BRENDA etc.
WEB TECHNOLOGIES World Wide Web is based on Client-Server technology One of the most popular and dominant client server technologies today 3
CONSTITUENTS OF WORLD WIDE WEB Web Browsers Web Content Web Site URL – Uniform Resource Locator HTTP – Hyper Text Transfer Protocol HTML – Hyper Text Markup Language Gateway to Non-Web Resources 4
OVERVIEW File System Web Server HTML Pages GIF/JPG Images etc Web Gateway Database Non-Web Content (Dynamic Content) 5
WEB CONTENT - TYPES OF CONTENT Static Content Dynamic Content resides in a file Author determines the content at the time of creation Each request will return exactly the same data (Content doesn’t change) Example: HTML files, gif/jpeg files Disadvantage: Not possible to implement applications Created on the fly by a web server upon a request to reflect the current info Content may vary for each request Example: A typical web application (Banking etc) Disadvantage: More processing power required on the server Active Content Server returns a run-able copy of the program Browser executes the program locally on the client machine May need continuous information feed Examples: Java Applets, Active-X controls for IE Disadvantage: Possible Security risks 6
WEB TECHNOLOGIES The Web Application employs various technologies in different layers. Client Side Scripting Web browser HTML, XHTML, CSS Scripting Languages Server Side Scripting ASP, ASP. NET ( Microsoft Technology) Servlet and JSP ( Java Technology) Web Services XML, DTD, Schema, XML DOM, SOAP, WSDL 7
COMMON GATEWAY INTERFACE (CGI) A general framework for creating server side web applications. The first mechanism for creating dynamic web site. Instead of returning a static web document, web server returns results of a program. CGI programs can be written in languages like C/C++, Perl, Java, etc. 8
CGI OVERVIEW For example Browser sends the parameter: Genename=chaperone. Web server passes the request to a C: Perl program C: Perl Program returns HTML that says, Total. Genes=36896 ! Genename=chaperone Web Browser Total. Genes=36896 9
PERL – CGI PROGRAMMING CONTD Name. pl Client sends a HTTP request encoded with the data to be passed to the server (shiv, 27 etc) Perl interpreter executes the corresponding perl script and gives back the HTML document. Web server receives the request and understands that this request is for a dynamic page and invokes the perl interpreter by passing the parameters 10 Web server collects the HTML document from the perl and sends It to the browser.
PERL – CGI PROGRAMMING CONTD HTML form & CGI Script <html><body> <form action=“name. pl" method="POST"> Your Name: <input type="text" name="name"> Age : <input type="text" name="age"> <input type="submit" value="Send"> </form> </body></html> use CGI; print header; print "<HTML> <BODY>"; print "<H 1> Hi ". param('name'). "!</H 1><BR>"; print "<H 2> You are ". param('age'). " years old!</H 2><BR>"; print "</BODY></HTML>"; 11
WORKING OF A CGI APPLICATION 7. Invoke getinfo. exe under cgi-bin, passes params thru env variable/stdin 3. Cannot resolve locally? Resolve from other DNS… 2. Translate DNS 4. Returns IP name to IP address Address 202. 68. 33. 49 getinfo. exe the u thr ct r e nn ve Co ser st 5. to ue eq n/w PR e TT ns po d. H n es Se P R TML ly 6. T HT s H al nd ntain amic e o n. S 10 ich c ed dy wh erat n ge ML e HT pos om 9. C dout t on s 1. User Submits form; URL http: //abcbooks. co. in/cgibin/getinfo. exe? title=Web+Servers 12 8. Query DB for Data
PERL – DBI & DBD Database Driver Have libraries for connecting to various databases Examples DBD-Oracle DBD-Mysql DBD-CSV DBD-ODBC DBI Database Interface module DBI modules do not have vendor libraries to access database It locates the corresponding DBD module for interacting with database 13
PERL – DBI & DBD - Oracle Perl Script DBD - Mysql DBI Module Oracle Mysql DBD – CSV 14 CSV Form at
PERL – DBI & DBD Connecting to Oracle Database # !c: perlbinperl. exe use DBI; use DBI: : Oracle; # Connecting to database $DBHandle=DBI->connect(“dbi: Oracle: test: 172. 17. 36. 166: 3306” , ”vicky”, ”password”)or die($DBI: : errstr); # Database Operations # Disconnecting $DBHandle->disconnect(); Connecting to Mysql Database use DBI; use DBI: : mysql(: sql_types); $DBHandle=DBI->connect(“dbi: mysql: test: 172. 17. 36. 166: 3306, ”vicky”, ”password”)or die(“Error=> DBI: : errstr); 15
PERL – DBI & DBD Executing Insert statements #!/usr/bin/perl $Fname=“Vicky"; $Roll=200960013; use DBI qw(: sql_types); $DBHandle=DBI->connect("DBI: mysql: test: 10. 3. 4. 59: 3306", "root", ”password") or die($DBI: : errstr); $query="insert into table values("". $Fname. "", ". $Roll. ")"; $queryhandle=$DBHandle->prepare("$query"); $queryhandle->execute(); $DBHandle->disconnect(); 16
PERL – DBI & DBD Executing an Select Query #!/usr/bin/perl $Fname=“Vicky"; $Roll=200960013; #use param(“Fname”) in case of HTML use DBI qw(: sql_types); $DBHandle=DBI->connect("DBI: mysql: test: 10. 3. 4. 59: 3306", "root", ”password") or die($DBI: : errstr); $query 1="select * from table"; $queryhandle=$DBHandle->prepare("$query 1"); $queryhandle->execute(); $queryhandle->bind_columns($FName, $Roll); while($queryhandle->fetch()) { print $FName. " ". $Roll; print "n"; } $DBHandle->disconnect(); 17
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