1. Master’s course Bioinformatics Data Analysis and Tools Lecture 6: Internet Basics Centre for Integrative Bioinformatics

2. Bioinformatics & Internet The Internet plays an increasingly important role in bioinformatics: On-line databases, with –Publications (e.g. ) –biological information (e.g. ) On-line bioinformatics tools, e.g. Communication with other scientists, as bioinformatics is inherently interdisciplinary.

3. Bioinformatics & Internet Advantages of using the Internet: Cheap Publicly available Computational intensive tools can be run on powerful dedicated servers On-line databases can easily be kept up-to-date

4. A network of connected computers. Any two computers (hosts) on the Internet are able to communicate by means of a language: the TCP/IP protocol (IP = Internet Protocol). Each host has a unique address: the IP address. What is the Internet?

5. How do computers communicate? The client-server model: 1.A client (the local host) initiates a request, e.g. asks the server to send some document. 2.The server (the remote host) responds to requests for a service, e.g. by sending the requested document. Request Client host Server host Response The Internet (TCP/IP) The Internet (TCP/IP)

6. The client A client is a program run by some user and which uses a connection to the Internet (= talks to some server). The communication between client and server is always initiated by the client. Only talks to one server at a time. Example: A web browser, e.g. MS Internet Explorer

7. The server A server is a program that runs on a shared computer and which continuously ‘listens’ for requests by any client. Can talk to several clients at the same time. Requires powerful hardware and sophisticated software. Example: Web server for serving web pages.

8. The ‘visible’ part of the Internet. A huge collection of billions of webpages, interlinked by hyperlinks. Hyperlink: Link on a webpage, on which you can click in order to visit another webpage.Link You can ‘surf’ the WWW with a browser, e.g. Internet Explorer, FireFox, etc. World Wide Web

9. The WWW has it’s own communication language, on top of TCP/IP: HTTP (HyperText Transfer Protocol) HTTP adds information on the file that is send: –Type (e.g. HTML, GIF, text, PowerPoint, etc.) –Date of last modification –Status (e.g. ‘ok’, ‘file not found’, ‘no permission to view file’, etc.) World Wide Web

10. So, we know that the WWW is a huge collection of webpages, which can be viewed with a browser. But, how to make a webpage? Answer: by using HTML (=HyperText Markup Language). A HTML document contains the content and defines the looks of a webpage. Webpages

11. General structure of a HTML document: My first Webpage Hello world bold text Go to IBIVU See: http://www.w3.org/MarkUp/Guide for anhttp://www.w3.org/MarkUp/Guide HTML tutorial. HTML

13. Upto now, we have seen webpages with ‘static’ information. But, what if we would like to show information which is variable, depending on user input, time of day, etc.? Answer: write a program or a script which generates HTML. The contents of the HTML will depend on some variables (again: user input, time of day, etc.). Dynamic Webpages

14. PHP is a popular scripting language for dynamically generating web pages. The PHP code can be embedded in the HTML code. Advantages of PHP: –easy to use –Virtually anything is possible, for example also connections with databases Dynamic Webpages

15. A Friendly Webpage <?php $HourOfDay = date("G"); if ($HourOfDay < 12) { echo "Good Morning World!"; } else { echo "Good Afternoon World!"; } echo " The hour of the day is ". $HourOfDay; ?> PHP example

17. Ok, but now we want to generate a HTML page based on user input. For example, the user gives a protein sequence, and we want to return a HTML page with protein sequences that may be homologues. (Sounds familiar? ) Solution: 1. User fills in a form on a webpage. 2. By clicking ‘submit’, the user input will be send to the server. 3. PHP on the server can ‘read’ this input, and generate HTML based on this input. This will be send to the user. PHP with user input

18. Webpage with a form: My Blast Please enter the protein sequence: HTML form

20. Results of your Blast search These are your results: <?php // Get user input $prot_sequence = $HTTP_GET_VARS[“sequence”]; // Find possible homologues $homologues = blast_algorithm($prot_sequence); // Embed the resulting sequences into this page echo " $homologues"; ?> PHP with user input

21. The Internet is a network of connected computers. The Internet is important for Bioinformaticians, as it is a cheap, easy to use medium for publishing, integrating and obtaining biological information. –Databases –Bioinformatics tools HTML is the language to build webpages PHP is a language to make webpages dynamic Summary