Practical Computing for Biologists-E2
| Numbering Code | U-LAS14 20050 LE68 | Year/Term | 2022 ・ Second semester | |
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| Number of Credits | 2 | Course Type | Lecture | |
| Target Year | Mainly 1st & 2nd year students | Target Student | For science students | |
| Language | English | Day/Period | Tue.2 | |
| Instructor name | CARLTON, Peter (Graduate School of Biostudies Associate Professor) | |||
| Outline and Purpose of the Course |
This class will introduce students to basic but powerful computational tools that are increasingly becoming an essential part of biological research. We will learn how to navigate a command line environment in a UNIX computer system, explore some useful open source software for DNA and protein analysis, and learn the basics of Python programming for analyzing biological sequence and images. Each class will start with a background lecture and proceed to hands-on guidance. The ultimate aim of the class is to provide an introduction that will facilitate your further exploration of computational biology. |
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| Course Goals |
-To discover current bioinformatics and biological image analysis software -To be able to design analyze DNA sequences using open online software -To learn general principles of programming using the Python language -To develop a foundation for further exploration of the exciting world of bioinformatics |
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| Schedule and Contents |
1. Overview of the course. How are computers used in biology? 2. Getting the computer to do stuff: introduction to the "Shell" (terminal) 3. Introduction to manipulating text files and how DNA sequences are stored as text files 4. The EMBOSS molecular biology suite: Searching protein and DNA sequences for features 5. Searching for sequences within the human genome and proteome 6. Detailed work with DNA sequences: introduction to Benchling and DNA cloning (making a new DNA sequence from existing ones) 7. Beginning programming with Python, a general computer language that can be adapted for biology 8. Expanding Python with modules 9. Searching DNA sequences with Python 11. Plotting data with Python 12. Imaging for biologists: Image fundamentals (pixels, intensity, scaling) using Fiji 13. Measuring 2D and 3D objects in images 14. Review of the entire class 15. Feedback (test review and Q&A session) |
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| Evaluation Methods and Policy |
Grading will be based on three areas: active participation, quizzes, and a final exam. "Active participation" will be measured by: class attendance, asking questions/giving comments on PandA (as a rule, each student should ask at least 1 question/give one comment on PandA for each class), and answering questions during in-person classes. Quizzes: short homework assignments. 3 will be given in total, at week 4, 8, and 12 of the class. The final exam will be a 3-page exam with short answers, multiple choice questions, and a short English writing assignment. Each area will contribute 1/3rd of the total grade. |
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| Course Requirements |
A laptop computer with a wireless internet connection is highly recommended for this class. Windows users should install the program "Cygwin" (from http://www.cygwin.com) to provide a shell environment; Mac and UNIX users can use the built-in terminal program. All students should also install "Anaconda" from http://www.anaconda.com to provide a Python environment. Provisions can be made for students who do not have their own laptop. |
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| Study outside of Class (preparation and review) | Students will have to understand technical vocabulary in English. This may require studying and research outside of class hours. | |||
| Textbooks | Textbooks/References | Practical Computing for Biologists, Haddock and Dunn, (Sinauer Associates), ISBN:978-0-87893-391-4, Textbook purchase is suggested but optional. See also the companion website at http://practicalcomputing.org | ||
