Scientific web programming with PHP and MySQL

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Scientific web programming with PHP and MySQL

• Yves Sucaet
• Michael Zimmermann

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What to expect?

• Learn 5 new languages
• HTML, PHP, SQL, CSS and JavaScript
• Write dynamic web pages
• Turn web pages into web applications
• What is a database and why should you care?
• Lots of best practices
• dos and dont of web development
• Make your advisors happy!

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(No Transcript)
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Different technologies
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Reviewing the basics HTML

• CERN (Geneva) Tim Berners Lee
• Different versions 1, 2, 3, 3.2, 4, XHTML
• You can see HTML by choosing View Source

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Structure of an HTML document
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HTML tables
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How does the Web work?

• Your web browser
• Your client application
• Surfing to a website
• Connecting to a server
• A physical other computer
• This computer is called a web server
• Only when you contact it with a webbrowser!
• Special language HTTP

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HTTP vs. HTML

• HTML is what everybody knows
• Hyper Text Markup Language
• Used to define the layout of a website
• It's what you when you do View Source
  in your webbrowser
• HTTP provides a communication protocol
• If HTML is a letter, then HTTP is the USPS mail
• The web browser sends a request to the web server
  using HTTP (request)
• The web server sends HTTP back (response), which
  may or may not contain an HTML document

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The Internet ! WWW

• Not everything on the Internet is WWW
• Different applications require different
  protocols
• Email, File transfer, Gopher... (defined in RFCs)
• How does your computer know which is which?
• Different port-numbers different functions
• Port 80 HTTP
• Port 21 FTP (File transfer)
• Port 25 SMTP (Email)
• Ports are configurable!

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What is a web server? 1

• It's a piece of hardware
• When you type http//www.iastate.edu, a computer
  in Ames is contacted
• When you type http//www.stuff.co.nz, a computer
  in New Zealand does your bidding!
• It is the physical machine that serves you the
  websites that you request
• When you request a website, this corresponds to a
  physical file on the computer's hard disk
• Your own computer can function as a web server!

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What is a web server? 2

• It's a piece of software
• Connecting a computer to the Internet does not
  make it a web server
• You need to install software that can interpret
  the incoming HTTP requests from webbrowsers all
  around the world
• Xitami, Apache, IIS, Tomcat...
• You have a webserver on your computer that turns
  it into a webserver
• http//127.0.0.1 is always the local server.

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Markup languages

• HTML is a programming language
• It's static HTML by itself doesn't anything
• When you open HTML-documents locally, they appear
  in your web browser the way you intended
• HTML is easy
• Other markup languages SGML, LATEX, PCL

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Programming languages

• PHP is a programming language (scripting)
• It's dynamic PHP does a lot of things
• no laundry or dishes they're still working on
  that one
• When you open PHP-documents locally, they look
  like gibberish you need a web server to process
• PHP is still easy (not a easy as HTML though)
• Other languages JavaScript, Python, Ruby, Perl

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Your first PHP script
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Your first PHP script
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The reason why you have Xitami

• After saving the file, open it locally in your
  browser (use File Open)
• Chances are this doesn't even work
• If it does, it doesn't look like you intended
• PHP scripts need to be processed first!
• This is where the Xitami web server comes in
• Make sure you save the file in the
  c\xitami\webpages (Xitami) or c\inetpub\wwwroot
  (IIS) folder
• Then, surf to http//127.0.0.1/firstreal.php
• Now the page displays as you intend it.
• Use View Source to see the result no more
  echo

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Before we continue

• NetBeans can improve your speed a lot!

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A quick tour of NetBeans
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Looking at your scripts
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NetBeans is willing to help
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Now onto some science

• Central dogma of molecular biology
• DNA ? RNA ? protein

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Chemistry meets PHP

• DNA, RNA and proteins encode information
• Information can be represented as text
• Text can be treated as data
• Data can be stored by computers
• Programming languages can manipulate the data
• Retrieve, search, display, transform etc
• The web is the ultimate platform
• Flexible, scalable, multi-threading, multi-OS,

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Presenting molecular data

• Simply PHP
• More advanced data formats
• FASTA multiple sequences
• PDB 3D protein structures
• SBML, BioPax biochemical pathways

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Output
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Where to from here?

• Exercises on covered material
• Afternoon control structures
• Choices If then else, select case
• Loops for, while
• Tuesday
• HTML forms
• Working with files
• Wednesday Databases

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Questions

• http//lab.bcb.iastate.edu/training/webdev/nmsu