User Tools

Site Tools


start

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

start [2013/01/29 21:26]
cellbiol [A beginner's course for Biologists]
start [2013/03/02 11:15] (current)
cellbiol
Line 1: Line 1:
 +~~NOCACHE~~  ​
 +====== Web Development for Bioinformatics ====== ​
  
-====== Welcome to the Web Development ​for Bioinformatics ​Web Book ======  +===== A Beginners Course ​for Biology and Bioinformatics ​Students ​=====
- +
-===== A beginner'​s course for Biologists ​=====+
  
 //**By Andrea Cabibbo, Ph.D.**// //**By Andrea Cabibbo, Ph.D.**//
  
 +This online book is a 101 web development and programming course mainly aimed at Biology students that are planning to direct their career toward Bioinformatics and/or to deploy web sites, web applications or web-based resources for their research projects. ​
 +
 +It can also serve as source of ideas, slides, teaching material for teachers and lecturers in the field of web development and/or Bioinformatics. For this purpose, images are always provided in full size.
 +
 +Bioinformatics researchers or programmers that have been "away from the web" for a while, might quickly get a handle on the recent trends in basic web development tools such as HTML5, CSS2 and 3, PHP and more by jumping straight to [[chapter_3_-_your_first_webpage_-_learning_html_and_css:​introduction|chapter 3]]. 
 +
 +The basics of the Internet, Linux Systems management, web servers installation and configuration,​ web development,​ programming including the principles of Object Oriented Programming (OOP) are covered, assuming no previous knowledge about these topics. To this end, great care was taken in never leaving logical gaps in the development flow of the treated arguments. Should you spot any gaps, thanks for pointing them out by using the discussion tools present at the bottom of each page or sending us an e-mail.
 +
 +We should maybe mention that although you will learn many things from this book, there are important topics that are not covered. ​
 +
 +Usage and interaction with databases, quite an important aspect in Bioinformatics programming,​ is considered out of the scope of this edition of the book. Unfortunately our "from scratch"​ approach makes it difficult to cover everything, we will however consider to include such a topic in a future edition.
 +
 +CGI, the way Perl, Python, Ruby and other languages interact with web data, is not addressed explicitly, as we use PHP as our working language. Since PHP is natively a web programming language, it has an extremely gentle learning curve that makes it excellent for learning the basic concepts of programming from scratch and being immediately productive, which are among the main objectives of this course. Once programming basics are learned in PHP, adding another programming language "to your toolbox"​ will be relatively easy.
  
-This online book covers ​the basics ​of Bioinformatics Web Development. It is a 101 Bioinformatics Web Development course mainly aimed at Biology students that are planning to direct their career toward Bioinformatics+Finally, during this course you will probably learn more about web development than about Bioinformatics itself, that is still an important presence in particular throughout ​the second part of the book where we discuss programming and web applications
  
-The basics of the Internet, Linux System management, ​web development, programming ​and the principles ​of Object Oriented Programming, are includedassuming no previous knowledge about these topics+Many have reasoned along the lines "do we need specific ​web development ​frameworks for Bioinformatics" ​and the short answer is generally no ([[http://​www.biostars.org/​p/​7097/​|link]]). There is an extremely rich variety ​of programming languagesweb development frameworks (Ruby on Rails is very popular lately), tools for general web development that are perfectly fit to handle Bioinformatics dataBioinformatics web servers and applications,​ Bioinformatics and Biological web databases. We do have extensive Bioinformatics specific libraries anyway (bioperl, biopython, bioruby, biophp) that can be used in the deployment of web Bioinformatics applications.
  
-These notions are then used to build some simple yet complete ​Bioinformatics ​applicationsthat are intended as scaffolds ​to be used as a starting point to build more complex ​applications ​in the specific field of interest ​of the student+The duty of the Bioinformatics student is to acquire solid basis in web development,​ become familiar with the available general technologies and then combine them with his knowledge about the various ​Bioinformatics ​methods and algorithms, to develop great Bioinformatics web projects and applications. In this book we focus on the first part of this process, while constantly keeping an eye on the second part
  
-Rather than focusing on specific Bioinformatics tools, or trying to cover all the available tools, we provide the basic informatics/​computing knowledge oriented toward Bioinformatics web development that will put the student in the condition to either use existing software libraries (you have to understand what a library is, before using it), or write their own, or, as it happens in real life, mix the two things to accomplish the goal with a minimum effort but with enough effort to get out exactly what you need/want from your software or web application+{{ :​chapter_3_-_your_first_webpage_-_learning_html_and_css:​web_development_word_cloud_cp.png?nolink |}}
  
 ==== About ==== ==== About ====
start.txt · Last modified: 2013/03/02 11:15 by cellbiol