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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.
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.
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.
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
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
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.
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.
You BIF400 grade will be computed as follows:
Programming/Problem solving 25%
Grades for the writing component are broken into three parts: 15% in-class work; 55% shorter writing assignments; 30% final paper
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.