Bioinformatics II
This is BTC549 course website. During this course students will learn programming skills necessary to solve common bioinformatics problems. During the labs students will be introduced to programming tools and will have hands-on experience. Students also will learn Linux operating system, command line and task automation. Also students will use relational database, such as MySQL to store and retrieve data.
Syllabus
2010-2011 academic year/Spring-11
BTC 549 section 1
BIOINFORMATICS II
Name:Alexandra Martynova-Van Kley
Department: Biotechnology Email: avankley@sfasu.edu
Phone: 6930 Office: SRC, bld C, room 102
Office Hours: 10.00-12.00 Class meeting time and place: Tuesdays 9:00-11:50, SRC bld B classroom
Department: Biotechnology Email: avankley@sfasu.edu
Phone: 6930 Office: SRC, bld C, room 102
Office Hours: 10.00-12.00 Class meeting time and place: Tuesdays 9:00-11:50, SRC bld B classroom
Text and Materials: There are no
required books. All the material will be covered during
the lectures. There are several recommended books, the
list is available on the course website.
Course Requirements: Grade A in Bioinformatics I (BTC548). You
must turn in 10 homework exercises to be allowed to take
the final exam.
Grading Policy:
| Two exams | 100 pts x 2 |
| 10 Lab reports | 10 pts x 10 |
| Total Points | 300 pts |
- 89 – 100% = A
- 79 – 88% = B
- 69 – 78% = C
- 59 – 68% = D
Academic Integrity (A-9,1)
Academic integrity is a responsibility of all university faculty and students. Faculty members promote academic integrity in multiple ways including instruction on the components of academic honesty, as well as abiding by university policy on penalties for cheating and plagiarism.Definition of Academic Dishonesty
Academic dishonesty includes both cheating and plagiarism. Cheating includes but is not limited to (1) using or attempting to use unauthorized materials to aid in achieving a better grade on a component of a class; (2) the falsification or invention of any information, including citations, on an assigned exercise; and/or (3) helping or attempting to help another in an act of cheating or plagiarism. Plagiarism is presenting the words or ideas of another person as if they were your own. Examples of plagiarism are (1) submitting an assignment as if it were one's own work when, in fact, it is at least partly the work of another; (2) submitting a work that has been purchased or otherwise obtained from an Internet source or another source; and (3) incorporating the words or ideas of an author into one's paper without giving the author due credit. Please read the complete policy at http://www.sfasu.edu/policies/academic_integrity.aspWithheld Grades Semester Grades Policy (A-54)
Ordinarily, at the discretion of the instructor of record and with the approval of the academic chair/director, a grade of WH will be assigned only if the student cannot complete the course work because of unavoidable circumstances. Students must complete the work within one calendar year from the end of the semester in which they receive a WH, or the grade automatically becomes an F. If students register for the same course in future terms the WH will automatically become an F and will be counted as a repeated course for the purpose of computing the grade point average. The circumstances precipitating the request must have occurred after the last day in which a student could withdraw from a course. Students requesting a WH must be passing the course with a minimum projected grade of C.Students with Disabilities
To obtain disability related accommodations, alternate formats and/or auxiliary aids, students with disabilities must contact the Office of Disability Services (ODS), Human Services Building, and Room 325, 468-3004 / 468-1004 (TDD) as early as possible in the semester. Once verified, ODS will notify the course instructor and outline the accommodation and/or auxiliary aids to be provided. Failure to request services in a timely manner may delay your accommodations. For additional information, go to http://www.sfasu.edu/disabilityservices/.Books
Recommended Books:- Practical Computing for Biologists, Steven Haddock
- Beginning Python: From Novice to Professional, Magnus Lie Hetland
- Matplotlib for Python Developers, Sandro Tosi
- A Primer on Scientific Programming with Python, Hans Petter Langtangen
- MySQL Cookbook, Paul Dubois
- Learning MySQL, Seyed M.M.
- A Beginner's Guide to R (Use R), Alain F. Zuur
- Data Manipulation with R (Use R), Phil Spector
- R for Medicine and Biology, P. D. Lewis
Lectures, Labs, Homework
Course Calendar
| Date | Lecture topics | Homework |
|---|---|---|
| January 25 | Computer Setup and Introduction to Shell (pdf) | hw1 |
| February 1 | Advanced Shell (pdf) | hw2 |
| February 8 | Introduction to Python (pdf) | hw3 |
| February 15 | Python (pdf) | hw4 |
| February 22 | Python (pdf) | hw5 |
| March 1 | Python | hw6 |
| March 8 | Midterm Exam | |
| March 15 | Spring Break | |
| March 22 | MySQL (pdf) | hw7 |
| March 29 | MySQL | hw8 |
| April 5 | R-statistical language | hw9 |
| April 12 | R-statistical language | hw10 |
| April 19 | R-statistical language | hw11 |
| April 26 | Take topic for Final exam | |
| May 3 | Final Exam due | |
| May 10 | Discussion |