Perl Programming for Biologists

Perl programming

Perl is a powerful programming tool widely used in the analysis of biological data. It not only combines the modern robustness of Java with the expedient pragmatism of scripting languages but also offers both the low-level system access of C and the high-level elegance of Lisp. Perl is widely used in bioinformatics due to its powerful text-processing capacity. It allows the easy implementation of NLP and bio-informatics algorithms and the extraction and generation of textual data. Perl programming

Perl is also easy to learn, is portable and multiplatform, has a large library of extensions, is component-oriented, is good in prototyping, and is efficient in the slicing, dicing, twisting, wringing, smoothing, summarizing and otherwise mangling of text. The objective of this course is to equip biologists who have little or no programming experience with the requisite skills.

This training will teach you how to:

  • Install the Perl interpreter
  • Manipulate files and directories
  • Use arrays and array functions to solve a variety of problems
  • Use the powerful regular expression capabilities of Perl.
  • Generate reports, use hashes to solve biological problems, and write programs that solve common biological problems...       Continue Reading »

Dates: The second week of every month.
Duration: 5 days.
Venue: Nairobi, Kenya.
PREREQUISITES

This training is aimed at researchers who have little or no programming skills and who are applying or planning to use bioinformatics techniques in their work.

FEES
  • Kshs. 10,000/- (Inclusive of VAT 16%) for East African residents. Non-East African students pay 25% more on all charges.Fee covers tuition, training material, certificate, drinks and meals only.

  • Groups with a minimum of 5 people will enjoy a 10% discount and early bird registration (at least 2 weeks before the start) will be offered a 5% discount
  • There will be a 10% administrative charge for cancellations received in writing up to 20 working days before the start of the course. No refunds will be made for cancellations received within 20 working days of the course start date or for the inability to attend the course for whatever reasons. KIBs is not liable for non-attendance due to travel disruptions, health problems or any other reason that might lead to a delegate not being able to attend the course. Substitutions may, of course, be made at any time, providing you inform us in writing.
  • Fee is payable by bankers cheque or cash deposit to: Fee is payable by bankers cheque or MPESA to: Bioinformatics Institute of Kenya. A/C No. 01192845321700, Cooperative Bank, Co-op House Branch, Nairobi, Kenya. SWIFT Code KCOOKENAXXX. Branch Code: XXX. MPESA PAY BILL: Business number: 400222. Account number: 1679821#PERL. PAYPAL: accounts@kibs.co.ke..

REGISTRATION

To register, please download the booking form fill it and send it to us through: Email: training@kibs.co.ke.

TOOLS AND SOFTWARE
Active State Perl Interpreter
Notepad ++
CGI.pm Module
Course material including a comprehensive training manual and a CD with software
TRAINING PROGRAM

DAY 1. GETTING STARTED WITH PERL

Getting Started with Perl

  • What is Perl?
  • Where Can I Get Perl?
  • Installing the Perl interpreter and checking that it has correctly installed
  • Checking if the path to the Perl interpreter has been added to the path list in C:/Autoexec.bat
  • A Simple Perl Program
  • Simple I/O
  • Perl Variables
  • Control Flow - Decisions
  • Control Flow - Loops
  • Altering Loop Control Flow
  • Statement Modifiers
  • What Is True And What Is False?
  • The Special Variable $_

Perl Operators

  • Introduction
  • Table Of Perl Operators
  • Arithmetic Operators
  • String Operators
  • Relational Operators
  • Logical Operators
  • Bitwise Operators
  • Assignment Operators
  • The Conditional Operator
  • Range Operator
  • String Functions
  • The eval Function

Input/Output

  • Introduction
  • String Literals
  • The print Function
  • Here Documents
  • The printf Function
  • The sprintf Function
  • Filehandles
  • Opening Disk Files
  • File Open Errors
  • The die and warn Functions
  • File Operators

DAY 2. ARRAYS AND SUB-ROUTINES

Arrays

  • Basic Concepts
  • Assigning Values To An Array
  • Accessing Array Elements
  • Array Functions
  • push and pop
  • shift
  • sort, reverse, and chop
  • split and join
  • grep
  • splice
  • Command Line Arguments
  • Associative Arrays

Subroutines

  • CALLING SUBROUTINES
  • Passing Arguments to Subroutines
  • Returning Values from Subroutines
  • The require Function
  • Packages and Modules
  • The @INC Array
  • Predefined Subroutines
  • Comparison Subroutines for Sorting

DAY 3. PATTERN MATCHING, REGULAR EXPRESSIONS AND ACCESSING SYSTEM RESOURCES

Pattern Matching

  • Introduction
  • Regular Expression Syntax
  • The Match Operator
  • Regular Expression Meta-Characters
  • Anchors
  • Single Character Matches
  • Some Special Issues
  • Character Classes
  • Multiple Character Matches
  • Alternation
  • The Substitution Operator
  • The Translation Operator
  • Remembered Matches
  • Greedy Regular Expressions
  • Nested Remembered Patterns
  • Matching for Multiple Occurrences in a Loop

Accessing System Resources

  • Introduction
  • File and Directory System Calls
  • The stat Function
  • The utime Function
  • The fork Function
  • The exec and wait Functions
  • Handling Signals
  • The system Function
  • Command Substitution
  • Opening Pipe Files

DAY 4. GENERATING REPORTS WITH PERL, PERL AND CGI, AND COMMAND LINE OPTIONS AND DEBUGGING

Generating Reports with Perl

  • Formats
  • Formatting Examples
  • Multi-Line Values
  • Multi-Line Text Blocks
  • Sending a Report to a File
  • The select Function
  • The Special Variable $~
  • Top-of-Page Formats
  • Bottom-of-Page Formats
  • A Sample Report

Perl and CGI

  • What is CGI?
  • Web Servers and Browsers
  • HTML
  • HTML Forms
  • Form Elements
  • A Typical CGI Application
  • CGI Input
  • CGI Output
  • Using the CGI.pm Module
  • CGI Environment Variables

Command Line Options and Debugging

  • Running Perl on the Command Line
  • Summary of Command Line Options
  • The Perl Debugger
  • Perl Debugger Commands
  • Other Debugging Aids
  • The strict Module

DAY 5. SOLVING BIOLOGICAL PROBLEMS USING PERL

DAY 5. EXERCISES

DAY 5. AWARD OF CERTIFICATES

Video/Audio Resources

We have simplified learning through our informative video and audio tutorials on different topics of bioinformatics.

View our video collections »

The resources are available in DVD, mp3, and VCD formats.

View our audio collections »

Books and Publications

We have an archive of books and tutorials on different bioinformatics topics. You can browse our collections below and make your order.

Books and tutorials are available in both printed format and as e-books.

Continue Reading »