PLNT4610/PLNT7690 Bioinformatics

2017 COURSE INFORMATION

INSTRUCTOR

Dr. Brian Fristensky Office: 330 Agriculture Tel: 474-6085
Email: frist@cc.umanitoba.ca
OFFICE HOURS: 2:30 - 4:30 Tuesday, Thursday

COURSE DESCRIPTION

An introduction to the theory, strategies, and practice of data management and analysis in molecular biology. Topics include DNA and protein sequence analysis, biological databases, genomic mapping, and analysis of gene expression data. Prerequisites: PLNT 2530 (039.253) or the former 039.450 or PLNT 3140 (039.314) or MBIO 3410 (060.341) or PLNT 4310 or the former PLNT 4540 or consent of instructor.

By the end of the course, students should

LECTURES AND LABS

Place: Machray Hall 113 
Lectures and Lab:  8:30 - 9:45 Tuesday, Thursday

WWW SITE

Most course materials are available online at either of two URLs:
http://home.cc.umanitoba.ca/~frist/PLNT4610
http://home.cc.umanitoba.ca/~frist/PLNT7690

EVALUATION CRITERIA

This course is dual-numbered as both a graduate and undergraduate course. Assignments, exams, and presentations are apportioned somewhat differently, between the two.

Assignments:  3 @ 20% each

Assignments will be designed to test both understanding of theory and the ability to apply theory to a specific problem. Up to four assignments may be handed in, but only the top three grades will count. Students will post completed assignments to their web sites for viewing by the instructor.

Examples of possible topics include:

  • comparative genomics
  • genome organization
  • phylogeny of a multigene family
  • creation a database relating to an area of your own interest
  • data pipelines 

60%

Mid-term examination

20%

Final examination

20%

TOTAL
100%

Grading is according to the Letter Grade System (Undergraduate Calendar section 2 ) ranging from 0 to 4.5 or F to  A+.
Roughly speaking, a C corresponds to understanding of a large portion of the material, the B range encompasses mastery of most of the material, and the A range indicates original thinking and creativity. Put another way:

Grade Point

Letter Grade

Meaning

comments

4.5 (90 - 100%)

A+

Exceptional

synthesis, ability to put things together from different parts of the course, original and creative thinking

4.0 (80 - 89%)

A

Excellent

3.5 (70 - 79%)

B+

Very good

learning concepts or inferring them from the context; working with data eg. Given the results of an experiment, what does it tell you? Given an equation, can you use it correctly?

3.0 (60 - 69%)

B

Good

2.5 (50 - 59%)

C+

Satisfactory

memorization of facts

2.0 (40 - 49%)

C

Adequate

1.5 (30 - 39%)

D+

Marginal

1.0 (20 - 29%)

D

Marginal
This grading rubric should only be taken as a rough guide for how I construct assignment and exam questions. Not all questions and assignments can be precisely broken down in this fashion. How you answer the question is also important. Answers that use complete sentences with precise terminology and organized into coherent paragraphs, will be awarded more points than answers that do not have an obvious organization or do not express ideas in a clear, precise way. Communication is an important part of the scientific method.

LATE SUBMISSION POLICY

Due dates for assignments will given for each assignment. Grades on assignments handed in late will be decremented by 4 points per day late, for a maximum of  20 points (ie. the total value of the assignment).

THERE WILL BE NO DEFERRED MIDTERMS

A medical certificate must be presented within one week of a missed exam. Upon receipt of the medical certificate the final exam will be pro-rated to 40%

ACADEMIC INTEGRITY

All work is to be completed independently unless otherwise specified. Students are reminded that academic dishonesty including plagiarism, cheating and examination impersonation is subject to severe academic penalties as described  the University Policy on Academic Integrity, in the General Calendar.

Voluntary Withdrawal

Students will have their grades for at least two assignments and the midterm exam before the University VW date. When considering a VW, students should be aware that if you withdraw from a course, you may be given a lower priority in registering for that course in subsequent academic terms.

Student Accessibility Services

If you are a student with a disability, please contact SAS for academic accommodation supports and services such as note-taking, interpreting, assistive technology and exam accommodations.  Students who have, or think they may have, a disability (e.g. mental illness, learning, medical, hearing, injury-related, visual) are invited to contact SAS to arrange a confidential consultation.

Student Accessibility Services
http://umanitoba.ca/student/saa/accessibility/  

520 University Centre
204 474 7423
Student_accessibility@umanitoba.ca

Policy and Resource Document (Schedule A)

Students should  familiarize themselves with University policies regarding academic integrity, student discipline, and respectful learning environment, for example, and on academic and student supports that are available, including a statement regarding mental health with referral information to the Student Counselling Centre and University Health Services. A summary of this information can be found at http://intranet.umanitoba.ca/academic_support/catl/media/Text-for-Schedule-A-ROASS.docx.

Recording Class Lectures

No audio or video recording of lectures or presentations is allowed in any format, openly or surreptitiously, in whole or in part without permission of the Instructor.  Course materials (both paper and digital) are for the participant’s private study and research.

Copyright

Unless otherwise cited or referenced, all course content is licensed under the Creative Commons License Attribution Share-Alike 2.5 Canada.

Course Technology

It is the general University of Manitoba policy that all technology resources are to be used in a responsible, efficient, ethical and legal manner. The student can use all technology in classroom setting only for educational purposes approved by instructor and/or the University of Manitoba Student Accessibility Services. Student should not participate in personal direct electronic messaging / posting activities (e-mail, texting, video or voice chat, wikis, blogs, social networking (e.g. Facebook) online and offline “gaming” during scheduled class time. If student is on call (emergency) the student should switch his/her cell phone on vibrate mode and leave the classroom before using it. (©S Kondrashov. Used with permission)