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2019 Summer - Bioinformatics and Programming Syllabus
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2019 Summer - Bioinformatics and Programming Syllabus
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Biology 589: Bioinformatics and Programming Summer 2019 - Session 2
Blended Course: Online and In-Person
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Instructor: Dr. Christopher Stieha Office Hours (by appointment)
Office: Roddy 273
Phone: (717) 871 – 4081
Email: FirstName.LastName ||at|| millersville
Email policy: Barring unusual circumstances, I will respond within two business days. If you do not receive a response within two business days, please resend the email because it did not reach me. Although I will attempt to respond quickly, please do not expect a response after 5 pm.
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TEXTBOOKS
Required
Shaw, Z. 2017. Learn Python 3 the Hard Way: A Very Simple Introduction to the Terrifyingly Beautiful World of Computers and Code. Pearson, New York, NY, USA. ISBN-13: 978-0321884916
Chang, J., B. Chapman, I. Friedbreg, T. Hamerlryck, M. de Hoon, P. Cock, T. Antao, E. Talevich, and B. Wilczyński. 2018. Biopython Tutorial and Cookbook (Biopython 1.73). Accessed 10 June 2019.
http://biopython.org/DIST/docs/tutorial/Tutorial.html
Supplemental Online Material
Sweigart, A. 2015. Automate the Boring Stuff with Python. No Starch Press, San Francisco, CA, USA. ISBN-13: 978-1593275990
Available online at https://automatetheboringstuff.com/
Updates at https://nostarch.com/automatestuff
Chacon, S. and B. Straub. 2014. Pro Git, 2nd Edition. Apress Media LLC, NeW York, NY, USA. ISBN-13: 978-1484200773
Available online at https://git-scm.com/book/en/v2
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COURSE OBJECTIVES
By the end of this course, you should be able to
1) Define, understand, and apply programming terminology and techniques
2) Solve problems and create tools using correct programming techniques
3) Develop basic structure of programming and organizing programming projects using files, folders, and git
3) Implement programming techniques and bioinformatic tools in the python programming language
4) Design, implement, analyze, interpret, and report results of analyses in bioinformatics
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SUCCESS
Please inform me of any disabilities or special needs that may impact your performance in this course. I will do my best to accommodate you and support your success in this class.
ATTENDANCE
Attendance is required as daily updates to the course website (https://github.com/sdmiller93/Summer-I-Bioinformatics---Programming-Foundations) and partipation in meetings, whether in-person, online, or over the phone. If you miss a day, you must contact me BEFORE the next class to determine if you are eligible to make up the points. Valid excuses are documented illness or injury, death in the family, jury duty, participation in University-sponsored activities, etc. on a case-by-case basis. If participating in a University-sponsored activity, you must inform me of the absence at the beginning of the course. Even if you do not have a valid excuse, you are responsible for the material that we covered.
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GRADING
Activity Course Points Percentage of Grade
Programming Exercises 100 50%
Final Project 100 50%
Total 200
Programming Exercises: Daily exercises to teach programming concepts and bioinformatic tools and test on the understanding of the techniques and tools. Completed excercises to be uploaded daily to course website.
Final Project: Project designed in collaboration with the instructor and research advisors to analyze a data set using tools and techniques developed in the class. Final results to reported as a written report as well as presentation.
Grading Scale: The lower limits for each letter grade is: A = 93%; A- = 90%; B+ = 87%; B = 83%; B- = 80%; C+ = 77%; C = 73%; C- = 70%; D+ = 67%; D = 63%; D- = 60%. Anything below 60% is an F.
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Honesty
Cheating and plagiarism, defined in Millersville University’s Student Handbook and Academic Honesty and Dishonesty brochure, will result in a 0 for the exam or assignment. Further action may be taken, such as referral to Student Affairs and failure of the class. I understand you talk to your fellow students and may work together on in-class exercises, but you must turn in your own work.
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TITLE IX
Millersville University and its faculty are committed to assuring a safe and productive educational environment for all students. In order to meet this commitment, comply with Title IX of the Education Amendments of 1972, 20 U.S.C. §1681, et seq., and act in accordance with guidance from the Office for Civil Rights, the University requires faculty members to report to the University’s Title IX Coordinator incidents of sexual violence shared by students. The only exceptions to the faculty member’s reporting obligation are when incidents of sexual violence are communicated by a student during a classroom discussion, in a writing assignment for a class, or as part of a University-approved research project. Faculty members are obligated to report to the person designated in the University Protection of Minors policy incidents of sexual violence or any other abuse of a student who was, or is, a child (a person under 18 years of age) when the abuse allegedly occurred.
Information regarding the reporting of sexual violence, and the resources that are available to victims of sexual violence, is available at www.millersville.edu/titleix
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ACTIVITY SCHEDULE
Lecture topics may change depending on the rate at which we are covering material. If class is canceled due to University closing and delays, supplementary work may be required.
Date Topic Exercises
10 June Install, printing, Math and Operators Shaw 0, 1, 2, 3; set up git
11 June Variables, Strings, and Printing Shaw 4, 5, 6, 7
12 June Printing, Escape Sequences Shaw 8, 9, 10, 11
13 June Prompting in code and command line Shaw 11, 12, 13, 14
14 June Reading and Writing Files Shaw 15, 16, 17
17 June Functions Shaw 18, 19, 20, 21
18 June Strings, Bytes, and Econdings Shaw 23, 24, 25
19 June Booleans and If-statements Shaw 27, 28, 29, 30
20 June Control Flow and lists Shaw 31, 32, 33, 34
21 June Branches, Debugging, Lists and Review Shaw 35, 36, 37, 38
24 June Dictionaries Shaw 39, 40
25 June Object-Oriented (OO) Programming Shaw 41, 42
26 June How to Program Shaw 43
27 June OO: Inheritance and Composition Shaw 44, 45
28 June Review
01 July Biopython Quick Start Biopython Ch 2
02 July Sequence Objects and Annotation Biopython Ch 3, 4
03 July Sequence Input/Ouput Biopython Ch 5
04 July HOLIDAY
05 July Multiple Sequence Alignment Objects Biopython Ch 6
08 July BLAST Biopython Ch 7, 8
09 July Accessing NCBI's Entrez Database Biopython Ch 9
10 July Cluster Analysis Biopython Ch 15
11 July KEGG Biopython Ch 18
12 July Review Biopython Ch 20