BIF712 - Concepts of Programming with Perl

Outline information
Semester
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Last revision date 2017-05-29 00:25:19.993
Last review date 2017-08-07 00:17:31.595

Subject Title
Concepts of Programming with Perl

Subject Description
The aim of this course is to introduce students to the basic concepts of computer science, and to provide students with a practical ability in scientific programming. The course will teach programming in C covering the standard elements of the language. Various biological examples will be treated throughout the course.

The ability to write computer programs enables a bioinformatics researcher to
apply the power and speed of a computer to the solution of research programs such as
management and use of large data sets, and extraction of biological meaning and
relationships from experimental data.
This course will introduce the student to the basic aspects of computer
programming, with an emphasis on developing good programming habits.
The course will be taught using the Perl programming language. The Perl
programming language plays a key role in the field of bioinformatics, due to its powerful
pattern processing features and easy-to-learn structure. This course will provide the
student with a thorough understanding of the basics of the Perl language, with a focus on using Perl to solve bioinformatics problems. Students will learn to create both standalone
and Internet-based Perl programs, and will learn to accelerate the development process by making use of existing code libraries.

Credit Status
One credit towards the Bioinformatics (BIF) post-diploma program

Learning Outcomes
Upon successful completion of this subject the student will be able to:

Upon successful completion of this course, the student will be able to:

1.      Analyze existing computer programs by walk-through technique
2.      Analyze general and bioinformatics problems, and apply appropriate syntax to create computer programs to solve the problem
a.       Given a problem, design an appropriate algorithm to describe the steps necessary to solve the problem
b.      Given an algorithm, create pseudocode to analyze the steps necessary to solve the problem in terms of programming statements
c.       Give pseudocode, create, debug, and test a Perl program that solves the problem
3.      Use programming tools such as Komodo to create and edit Perl programs and HTML code
4.      Use Unix utilities to compile and run Perl program
5.      Analyze the requirements for a command line bioinformatics application, and use Perl to program a solution to the problem
6.      Analyze the requirements for a web-enabled bioinformatics application, and use Perl/CGI in combination with HTML5 to program a solution to the problem
7.      Create web-enabled graphical user interfaces for bioinformatics-oriented Perl programs
8.      Apply existing general-purpose Perl modules to the solution of bioinformatics programming problems
9.      Deploy completed code in a production environment, and test the application as a whole
10.  Methodically test and debug Perl and Perl/CGI programs
11.  Compose technical program documentation for Perl programs using internal comments
12.  Use relevant technical documentation to obtain the details necessary to apply Perl to the solution of general and bioinformatics programming problems

Cheating and Plagiarism
Each student should be aware of the College's policy regarding Cheating and Plagiarism. Seneca's Academic Policy will be strictly enforced.

To support academic honesty at Seneca College, all work submitted by students may be reviewed for authenticity and originality, utilizing software tools and third party services. Please visit the Academic Honesty site on http://library.senecacollege.ca for further information regarding cheating and plagiarism policies and procedures.

Discrimination/Harassment
All students and employees have the right to study and work in an environment that is free from discrimination and/or harassment. Language or activities that defeat this objective violate the College Policy on Discrimination/Harassment and shall not be tolerated. Information and assistance are available from the Student Conduct Office at student.conduct@senecacollege.ca.

Accommodation for Students with Disabilities
The College will provide reasonable accommodation to students with disabilities in order to promote academic success. If you require accommodation, contact the Counselling and Disabilities Services Office at ext. 22900 to initiate the process for documenting, assessing and implementing your individual accommodation needs.