BIF812 - Concepts of Programming with Java

Subject Title
Concepts of Programming with Java

Subject Description
This course will continue to develop the student's programming skills. A key focus of the course will be object-oriented concepts, introduced via the Java programming language. Originally designed as a language for controlling embedded devices, Java quickly established itself as an ideal language for developing platform-neutral solutions accessible via the Internet. Java is popular in the bioinformatics community as well, and some time will be spent examining selected classes of the Biojava project.

Students will be introduced to stand-alone and web-based software development using Java, with an emphasis on solving basic bioinformatics-oriented problems. An introduction to XML and its use in bioinformatics will also be included.

Credit Status
1 Credit towards the Bioinformatics Ontario Graduate Certificate program.

Prerequisites: All first semester BIF subjects.

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

• explain object-oriented concepts and apply them to the design and creation of software programs, using Java
• explain basic concepts of XML and explain how XML can be applied to bioinformatics data management
• apply the Java programming language to create web-enabled and stand-alone programs that solve basic bioinformatics and general programming problems
• apply appropriate parts of bioinformatics APIs such as Biojava to the solution of basic bioinformatics and general programming problems
• apply existing general-purpose Java libraries to the solution of basic bioinformatics and general programming problems
• deploy completed code in a production environment, and test the application as a whole
• methodically test and debug Java programs
• use software utilities to edit, compile and run Java programs
• compose technical program documentation for Java programs using internal comments and the Javadoc utility
• use relevant technical documentation to obtain the details necessary to apply Java to the solution of bioinformatics-related programming problems

Essential Employability Skills

    •  Communicate clearly, concisely and correctly in the written, spoken and visual form that fulfils the purpose and meets the needs of the audience.

    •  Respond to written, spoken, or visual messages in a manner that ensures effective communication.

    •  Apply a systematic approach to solve problems.

    •  Use a variety of thinking skills to anticipate and solve problems.

    •  Locate, select, organize, and document information using appropriate technology and information systems.

    •  Analyze, evaluate, and apply relevant information from a variety of sources.

    •  Interact with others in groups or teams in ways that contribute to effective working relationships and the achievement of goals.

    •  Manage the use of time and other resources to complete projects.

    •  Take responsibility for one's own actions, decisions, and consequences.

Academic Integrity
Seneca upholds a learning community that values academic integrity, honesty, fairness, trust, respect, responsibility and courage. These values enhance Seneca's commitment to deliver high-quality education and teaching excellence, while supporting a positive learning environment. Ensure that you are aware of Seneca's Academic Integrity Policy which can be found at: http://www.senecapolytechnic.ca/about/policies/academic-integrity-policy.html Review section 2 of the policy for details regarding approaches to supporting integrity. Section 2.3 and Appendix B of the policy describe various sanctions that can be applied, if there is suspected academic misconduct (e.g., contract cheating, cheating, falsification, impersonation or plagiarism).

Please visit the Academic Integrity website http://open2.senecac.on.ca/sites/academic-integrity/for-students to understand and learn more about how to prepare and submit work so that it supports academic integrity, and to avoid academic misconduct.

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@senecapolytechnic.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 Accessibility Services Office at ext. 22900 to initiate the process for documenting, assessing and implementing your individual accommodation needs.

Camera Use and Recordings - Synchronous (Live) Classes
Synchronous (live) classes may be delivered in person, in a Flexible Learning space, or online through a Seneca web conferencing platform such as MS Teams or Zoom. Flexible Learning spaces are equipped with cameras, microphones, monitors and speakers that capture and stream instructor and student interactions, providing an in-person experience for students choosing to study online.

Students joining a live class online may be required to have a working camera in order to participate, or for certain activities (e.g. group work, assessments), and high-speed broadband access (e.g. Cable, DSL) is highly recommended. In the event students encounter circumstances that impact their ability to join the platform with their camera on, they should reach out to the professor to discuss. Live classes may be recorded and made available to students to support access to course content and promote student learning and success.

By attending live classes, students are consenting to the collection and use of their personal information for the purposes of administering the class and associated coursework. To learn more about Seneca's privacy practices, visit Privacy Notice.