BIOE505  - Computational Bioengineering

​Schedule

Instructor

Sergei Maslov: maslov@illinois.edu
Office: IGB 3103
Office hours: by appointment

Hours

Tuesdays:   2PM - 3:50PM
Thursdays: 2PM - 3:50PM

0018 Campus Instructional Facility

Laptop computers, software and iClickers

You will need a laptop in this class. Laptops need to have Matlab installed with Bioinformatics and Statistics & Machine Learning toolboxes.
Matlab is available free of charge to all students and faculty
To install MATLAB and Simulink, please view the offering on the WebStore site and follow the detailed instructions. For any issues or questions, you can email webstore@illinois.edu for support. An alternative to buying Matlab is to use CITRIX for UIUC students and connect to EWS Windows Lab Software.

I would like you all to have an iClicker and bring it to every class.  On amazon.com a new iClicker costs around $40. It is also sold at UIUC Bookstore. Used ones are cheaper.An alternative solution is using a mobile or desktop app: https://www.iclicker.com/students/apps-and-remotes/apps Your iClicker answers WILL NOT be used for grading. I need them to see if I lost some of you and what could I rephrase to better explain the material

Description

The course will provide students with fundamental knowledge and techniques in
computational bioengineering, focusing on statistical methods including:

Statistics methods will be illustrated using examples from
genomics & systems biology:

Suggested Textbooks

Grading

Midterm exam 40%

Final exam 60%

Homework (ungraded) will build on topics covered
in lectures and will consist of problem sets related to
topics covered in lecture

Sexual Misconduct Reporting Obligation

The University of Illinois is committed to combating sexual misconduct. Faculty and staff members are required to report any instances of sexual misconduct to the University’s Title IX Office. In turn, an individual with the Title IX Office will provide information about rights and options, including accommodations, support services, the campus disciplinary process, and law enforcement options.

A list of the designated University employees who, as counselors, confidential advisors, and medical professionals, do not have this reporting responsibility and can maintain confidentiality, can be found here: wecare.illinois.edu/resources/students/#confidential.

Other information about resources and reporting is available here: wecare.illinois.edu.

Academic Integrity

The University of Illinois at Urbana-Champaign Student Code should also be considered as a part of this syllabus. Students should pay particular attention to Article 1, Part 4: Academic Integrity. Read the Code at the following URL: http://studentcode.illinois.edu/.

Academic dishonesty may result in a failing grade. Every student is expected to review and abide by the Academic Integrity Policy: https://studentcode.illinois.edu/article1/part4/1-401/. Ignorance is not an excuse for any academic dishonesty. It is your responsibility to read this policy to avoid any misunderstanding. Do not hesitate to ask the instructor(s) if you are ever in doubt about what constitutes plagiarism, cheating, or any other breach of academic integrity.

Religious Observances
Illinois law requires the University to reasonably accommodate its students' religious beliefs, observances, and practices in regard to admissions, class attendance, and the scheduling of examinations and work requirements. You should examine this syllabus at the beginning of the semester for potential conflicts between course deadlines and any of your religious observances. If a conflict exists, you should notify your instructor of the conflict and follow the procedure at https://odos.illinois.edu/community-of-care/resources/students/religious-observances/ to request appropriate accommodations. This should be done in the first two weeks of classes.

Disability-Related Accommodations
To obtain disability-related academic adjustments and/or auxiliary aids, students with disabilities must contact the course instructor and the Disability Resources and Educational Services (DRES) as soon as possible. To contact DRES, you may visit 1207 S. Oak St., Champaign, call 217-333-4603, e-mail disability@illinois.edu or go to https://www.disability.illinois.edu.  If you are concerned you have a disability-related condition that is impacting your academic progress, there are academic screening appointments available that can help diagnosis a previously undiagnosed disability. You may access these by visiting the DRES website and selecting “Request an Academic Screening” at the bottom of the page.

Family Educational Rights and Privacy Act (FERPA)
Any student who has suppressed their directory information pursuant to Family Educational Rights and Privacy Act (FERPA) should self-identify to the instructor to ensure protection of the privacy of their attendance in this course. See https://registrar.illinois.edu/academic-records/ferpa/ for more information on FERPA.

Anti-racist, inclusive community

The Grainger College of Engineering is committed to the creation of an anti-racist, inclusive community that welcomes diversity along a number of dimensions, including, but not limited to, race, ethnicity and national origins, gender and gender identity, sexuality, disability status, class, age, or religious beliefs. The College recognizes that we are learning together in the midst of the Black Lives Matter movement, that Black, Hispanic, and Indigenous voices and contributions have largely either been excluded from, or not recognized in, science and engineering, and that both overt racism and micro-aggressions threaten the well-being of our students and our university community.

Safe and encouraging learning environment

The effectiveness of this course is dependent upon each of us to create a safe and encouraging learning environment that allows for the open exchange of ideas while also ensuring equitable opportunities and respect for all of us. Everyone is expected to help establish and maintain an environment where students, staff, and faculty can contribute without fear of personal ridicule, or intolerant or offensive language. If you witness or experience racism, discrimination, micro-aggressions, or other offensive behavior, you are encouraged to bring this to the attention of the course director if you feel comfortable. You can also report these behaviors to the Bias Assessment and Response Team (BART). Based on your report, BART members will follow up and reach out to students to make sure they have the support they need to be healthy and safe. If the reported behavior also violates university policy, staff in the Office for Student Conflict Resolution may respond as well and will take appropriate action. 

Syllabus written and maintained by Prof. Sergei Maslov
Department of Bioengineering
University of Illinois at Urbana-Champaign