CS 4710 Lab

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CS 4710 Lab

• August 27, 2002

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Introductions

• Heather Mahaney
• PhD student in the CoC
• Office CRB 367
• Office Hours MWF 1-2 CoC commons?
• mahaneyh_at_cc.gatech.edu

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What to expect

• Tuesdays - Lecture in CoC 102
• Thursdays - Lab in French Building
• Text - Beginning Perl for Bioinformatics
• Topics
• Basic programming in Perl
• Software Engineering Principles
• Web Design in HTML
• Unix

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Computer Science Biology

• Computation
• Analysis
• Simulation
• Storage
• Searching
• Robotics
• Programming

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Programming Languages

• Set of rules used to program a computer
• Syntax - how commands are formed
• Semantics - what the commands mean
• Types of commands
• Statements - evaluated for effect
• Expressions - evaluated for value

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Programming Languages

• How does it work?
• Source Code
• Interpreters
• Machine Language

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Programming

• Programming is a process!
• Identify the problem
• Design the program
• Write the code
• Run and Test the program
• Evaluate and Edit the result

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Goals

• Programmers want their programs to be
• Clearly coded
• Efficient
• Fast
• Robust
• Easy to test
• Easy to use
• What the user asked for

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The Problem

• What tasks should the program perform?
• Who is the program being designed for?
• How is it going to be used?

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The Design

• A plan for your program
• Inputs
• What values does the program need ?
• How does the program get the values?
• Algorithm - set of instructions used to solve a
  specific problem
• Pseudocode - informal program in English
• Outputs
• What do you want to display?
• How should it be displayed?

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Programming Conventions

• Break the problem into procedures or tasks
• small
• independently testable
• interconnecting

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Programming Conventions

• Comments
• Text in a program meant to give information about
  the code
• Ignored by the interpreter
• In Perl comments follow the

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Programming Conventions

• Variables
• Store a value
• number
• string
• object
• Constant or changing
• Naming
• Describe what the variable is doing
• Start with a character but may include digits

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Why use Perl?

• Easy to learn
• Analyzing and manipulating sequences
• Quick to program
• Platform independent

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Thursday

• Assignment
• Read Chapter 3 and Chapter 4 to page 40.
• Visit the Perl website, www.perl.com, and
  download Perl onto your computer