Syllabus

Place and Time

Thomas Building 121 | Monday, Wednesday 2:30pm - 3:45pm

This course is now on-line only. It will be held using the folliowing link every Monday and Wednesday 2:30pm - 3:45pm

Instructor

Anton Nekrutenko
aun1@psu.edu
Wartik 505
Office hours by appointment only

When contacting instructor use the above e-mail and include “BMMB554” in the subject line (simply click on e-mail address).

Course logistics

This course does not use Canvas. Canvas is a convoluted system with too many features and undefined purpose. Instead, this course is served from GitHub. Each new lecture will be created as a new entry under “Lectures” section of the website.

Do not contact me through Canvas! I will not check my Inbox there. Instead, contact me via e-mail as described above.

Grading

Attendance (25%)

Homework (30%)

Final Project (45%)

A short homework will be given once a week. We will discuss project requirements before the spring break.

Topics

We will cover a breadth of topics. The course will be divided into several blocks:

#	What	Details
1	Essential Tools	Python, NumPy, Pandas, Matplotlib, SQL, Jupyter, Git, GitHub, Galaxy
2	Sequencing data	Modern sequencing technologies and analysis algorithms
3	Statistical refresher	From descriptive statistics to multivariate analysis
4	Analytical aspects of major applications	From SNPs to TADs hands-on

Final Project

We will get into specifics of the final project before spring break.

ECoS Teaching Statement

In an examination setting, unless the instructor gives explicit prior instructions to the contrary, violations of academic integrity shall consist of any attempt to receive assistance from written or printed aids, from any person or papers or electronic devices, or of any attempt to give assistance, whether the student doing so has completed his or her own work or not. Other violations include, but are not limited to, any attempt to gain an unfair advantage in regard to an examination, such as tampering with a graded exam or claiming another’s work to be one’s own. Other assessments (including ANGEL-administered quizzes and assessments as well as homework assignments) are expected to represent your own independent work unless specifically stated otherwise. Failure to comply will lead to sanctions against the student in accordance with the Policy on Academic Integrity in the Eberly College of Science. The Eberly College of Science Code of Mutual Respect and Cooperation (www.science.psu.edu/climate/Code-of-Mutual-Respect-final.pdf) embodies the values that we hope our faculty, staff, and students possess and will endorse to make The Eberly College of Science a place where every individual feels respected and valued, as well as challenged and rewarded. The Eberly College of Science is committed to the academic success of students enrolled in the College’s courses and undergraduate programs. When in need of help, students can utilize various College and University wide resources for learning assistance (http://www.science.psu.edu/advising/success). Penn State welcomes students with disabilities into the University’s educational programs. If you have a disability-related need for reasonable academic adjustments in this course, contact the Office for Disability Services (ODS) at 814-863-1807 (V/TTY). For further information regarding ODS, please visit the Office for Disability Services Web site at http://equity.psu.edu/ods/.   In order to receive consideration for course accommodations, you must contact ODS and provide documentation (see the documentation guidelines). If the documentation supports the need for academic adjustments, ODS will provide a letter identifying appropriate academic adjustments. Please share this letter and discuss the adjustments with your instructor as early in the course as possible. You must contact ODS and request academic adjustment letters at the beginning of each semester.