Bif 400 – Bioinformatics Senior Seminar Generic Syllabus



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BIF 400 – Bioinformatics Senior Seminar

Generic Syllabus



Instructor: Debra T. Burhans, Ph.D.

Office Hours – held in SH 1029 C

Office: SH 1029 C

Mon 1-2:30, Tue 8:30-10:30, Weds 1-2, Fri – 8-9

Phone: 716-888-2433

and by appointment

E-mail: burhansd@canisius.edu



Course Web Page:

Materials will be stored on D2L



Contact me if you need to set up an appointment at another time. I’m in my office much of the time when I’m not teaching.

Course: BIF400 Writing Component: MF 10-10:50 SH 1007

Algorithm/Computational Component W 10-10:50 SH 005




DESCRIPTION – BIOINFORMATICS CONTENT

This course involves the exploration and application of algorithms, particularly to problems in bioinformatics. Algorithm types we will cover include: dynamic programming, divide and conquer (recurrence relations, recursion), exhaustive search, greedy algorithms, graph algorithms, pattern matching, clustering, Hidden Markov Models, and randomized algorithms. We will use the Perl programming language for coding as well as MatLab, and possibly R. We will be using a unix/linux OS. In the lab we will use the unix side of Macs via the terminal. We will explore the unix shell and its use for shell scripting and pipeline creation. Our exercises will combine our own implementations with existing tools.


DESCRIPTION – WRITING CONTENT

This course also fulfills the Advanced Writing Intensive core curriculum requirement. This requirement involves completing 20 pages of polished prose by the end of the semester. We will engage in a variety of writing experiences, in and outside of class, including the creation of a tutorial, review, and other short papers in addition to a final paper that is a minimum of 7 pages in length.


COURSE MATERIAL – NOTES and BOOKS

Materials from this course can be found on the course’s D2L pages. We are also using Dr. Jane Fisher’s Writing Guide, which will be handed out in class on the first day and will be posted on D2L. In addition, those of you who kept your reference from FYS 101, Hacker’s Rules for Writers, will find it extremely helpful.


PREREQUISITES/COREQUISITES

This class assumes familiarity programming equivalent to CSC 212/L. No familiarity with Biology or Perl is required. In addition, students are expected to have completed introductory writing courses at Canisius (FYS 101 and ENG 101).


COURSE GOALS/OBJECTIVES
GENERAL:

  • Students will understand basic biology concepts sufficient to work on molecular biology problems

  • Students will become proficient in Perl programming and familiar with the unix/linux OS

  • Students will master a number of advanced algorithmic techniques and will demonstrate this by hands on problem solving.



ADVANCED WRITING INTENSIVE ATTRIBUTE:

Designated courses at the 200-level or above with significant emphasis on using writing as a way to learn and that are designed to develop basic and advanced skills in analyzing and representing ideas through strong written prose.



Content: Students will demonstrate the ability to write an effectively developed logical argument.

Objectives:

  • Integrate appropriate ideas and evidence, in accordance with course content

  • Organize those ideas and that evidence strategically for a given audience and purpose

Skills: Students will demonstrate an understanding of appropriate or discipline-specific writing styles, standards, and conventions through a process that includes revision.

Objectives:

  • Sentence Structure: Write grammatically correct sentences that are fluid and include smooth transitions.

  • Word Choice: Use vocabulary that is appropriate for the purpose and audience/field

  • Mechanics: Employ correct punctuation, spelling, capitalization, and documentation conventions

  • Ethical Use of Sources: Appropriate citation and attribution of ideas, information, and evidence

COMPUTER SCIENCE AND BIOINFORMATICS:

  • Translate a problem description to a formal representation

  • Implement, justify and test acceptable computational solutions

  • Trace and analyze algorithms

  • Solve a problem by quantitative methods

  • Describe which algorithms would be appropriate to use and explain why, given a problem

  • Design effective data representations for the storage and manipulation of large datasets where needed

  • Utilize and understand statistical methods for the analysis of large datasets where appropriate


ATTENDANCE

You are expected to attend class. This is key for the writing component, as we will engage in in-class writing exercises and editing sessions. Let the instructor know as soon as possible in case of extenuating circumstances. If you know in advance that you must miss a class please discuss it ahead of time with the instructor.


SPECIAL ACCOMODATIONS

Students with any special instructional needs due to documented learning disabilities or health problems should advise the instructor of these needs by the close of the first week of classes.


GRADES

You BIF400 grade will be computed as follows:

Programming/Problem solving 25%

Writing 75%

Grades for the writing component are broken into three parts: 15% in-class work; 55% shorter writing assignments; 30% final paper
COURSE GRADE

Your course grade will be based on your overall class performance. A typical percentage to grade mapping is the following, though it may be necessary to revise cutoffs downward, depending on the class. Note that this would be advantageous for the students.

93+ = A, 90-2 = A- , 87-89 = B+, 83-86 = B, 80-82 = B-, 77-79 = C+, 73-76 = C, 70-72 = C-, 60-69 = D

below 60 results in an F in the course

COURSE SCHEDULE for WRITING COMPONENT
Week 1 (1-18) - Introduction

In class writing: (WA1) Introduce Yourself - background, why computing/biology, your writing experiences, likes, dislikes

Discuss issues/interests/strengths/weaknesses with regard to writing

Grammar worksheets – common problems/examples affect/effect, its/it’s, their/there/they’re, etc.

Read Don’t Fear the Robots

Due: WA1 (final)

[Assess Content Goal 1, Objectives a, b; Assess Skills Goal 1, Objectives a, b, c]

Week 2 (1-26) – Writing a Summary

Discuss: Don’t Fear the Robots

In class vocabulary definitions, audience, analysis by students of Don’t Fear the Robots

In class: WA2 beginnings, Don’t Fear the Robots

[Content Goal 1, Objectives a, b]
Week 3 (2-1) – Good Arguments

Read Genetically Modified Babies (Darnovsky)

Due: (WA2) Don’t Fear the Robots draft 1

Grammar concept reviews (topics based on student paper reviews)

[Content Goal 1 Objectives a, b]

Week 4 (2-8) – Writing a Position Paper

Discuss Darnovsky

In-Class writing: (WA3) Darnovsky, arguments for and against

Due: WA3 your initial arguments (submit both for and against separately)

[Content Goal 1, Objectives a, b; Skills Goal 1, Objectives b, d]

Week 5 (2-15) – Writing about Science (Genomes)

Discuss genome paper (WA4) and genomes in general, review of appropriate resources and tools

Due: WA2 final

Due: WA3 decision as to how to argue, further development of arguments that support your position

[Assess Content Goal 1, Objectives a, b; Content Goal 1, Objectives a, b; Skills Goal 1, Objectives b, c, d]
Week 6 (2-22) – Using appropriate reference materials

Due: WA3 draft 1

Due: topic for WA4 and brief overview/introduction – initial

[Assess Content Goal 1, Objectives a, b; Skills Goal 1, Objective d]



Week 7 (2-29) – Personal Reflection

Writing Assignment/Topic

In class: (WA5) What is Computer Science? Class discussion and reflection, paper represents a personal reflection/synthesis

Due: WA5 draft 1

Due: WA4 3 pages plus references – draft 1

[Content Goal 1, Objective b; Assess Skills Goal 1, Objectives a, b, c, d]

Week 8 (3-7) – Student evaluation and assessment of class work

In class: students evaluate genome papers, anonymous reviews, use writing assessment rubric

Due: WA4 draft 2

Due: WA3 final

[Assess Content Goal 1, Objectives a, b; Assess Skills Goal 1, Objectives b, d]

Week 9 (3-14) – Writing for a specific audience

Read and discuss Sex Redefined – will be writing position piece on this for WA6

Due: WA6 Audience Description, approach

Due: WA5 final

[Assess Skills Goal 1, Objectives a, b; Content Goal 1, Objectives a, b; Skills Goal 1, Objective b]

Week 10 (3-21) – Writing Issues – Overview and Questions

Due: WA6 draft 1

Writing issues – based on student work thus far

[Content Goal 1, Objectives a, b; Skills Goal 1, Objectives a, b, c, d]



Week of 3-28 SPRING BREAK – NO CLASSES
Week 11 (4-4) – The art of persuasion – did students succeed?

Discussion WA6 and the associated article, Sex Redefined, students read their papers out loud to class, group assessment of impact/effectiveness

Due: WA6 final draft

Due: WA4 final draft

[Assess Content Goal 1, Objectives a, b; Assess Skills Goal 1, Objectives a, b, c, d]
Week 12 (4-11) – Genres and Styles

(WA7) Final paper assigned, discussed – students develop topic ideas and genre

Due: (WA7) Final paper proposal and several initial paragraphs
Week 13 (4-18) (Progress meetings)

Individual Progress meetings – review work completed, outstanding, etc.

Due: Draft 1 WA7

[Content Goal 1, Objectives a, b; Skills Goal 1, Objectives a, b, c, d]


Week 14 (4-25) (work)

In-class: time to work on final paper, assist students with writing issues and references as needed

Due: Draft 2 WA7
Week 15 (5-2) (Final paper individual meetings)

Individual meetings scheduled to discuss final paper (WA7)


Final Exam Week 5-9

Due: 5-13 final draft WA7



[Assess Content Goal 1, Objectives a, b; Assess Skills Goal 1, Objectives a, b, c, d]





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