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Bioinformatics Web Development
A beginner's course for Biologists and Bioinformatics students
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Introduction
Chapter 1: Internet and Networks
1-1: Data transmission on the Internet
1-2: The TCP/IP family of Internet protocols
1-3: Networking Basics
1-4: A 101 practical guide to setting up a small home or office Local Area Network with a SOHO router
Chapter 2: Linux
2-1: Installing Ubuntu Linux
2-2: The Linux Filesystem
2-3: Basic Linux Shell Commands
2-4: Installing and using Open SSH Server for remote connections
2-5: Installing a LAMP (Linux, Apache PHP, MySQL) Server
2-6: Apache Web Server Configuration
2-7: Setting up an Ubuntu Linux Web Server – Reference Summary
Chapter 3: HTML and CSS
3-1: Hosts, Domains and URLs
3-2: Uploading local files to a remote server
3-3: Code Text Editors
3-4: A minimal HTML page
3-5: Text Markup with HTML
3-6: Styling your webpages or website with CSS
3-7: CSS Basic Concepts
3-8: Introducing HTML5 footer, header, nav, article, section and aside elements
3-9: Styling common HTML tags with CSS
3-10: Website Page Layouts
3-11: Creating and managing web forms
Chapter 4: The PHP programming language
4-1: Dynamic web pages with PHP – A simple (yet useful) example
4-2: PHP basics – statements, variables, strings
4-3: PHP basics – arrays
4-4: PHP basics – predefined variables
4-5: PHP basics – conditional statements
4-6: PHP basics – built-in functions and manipulation of sequences
4-7: PHP basics – more on sequences manipulation with predefined functions
4-8: Using regular expressions in PHP – metacharacters and preg_match() basics
4-9: Regular expressions in PHP – retrieving matches with preg_match()
4-10: Regular expressions in PHP – retrieving all matches, even overlapping, with preg_match_all()
4-11: Regular expressions in PHP – Retrieving matches position with the PREG_OFFSET_CAPTURE flag
4-12: PHP programming language basics – Writing and using your own functions
Chapter 5: Web applications
5-1: The color sequence web application
5-2: The reverse-complement web application
5-3: The T-Score web application – background information
5-4: The T-Score web application – Web scraping of the scoring matrix data
5-5: The T-Score web application – Scoring and ranking peptides for MHC binding
5-6: The T-Score web application – Web form and data processing
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