BIOE310  - Computational Tools for Biological Data

Schedule

Instructor

Sergei Maslov: maslov@illinois.edu
Office: IGB 3406

Teaching Assistants

Dalton Jayne  (djayne2@illinois.edu)

Novia Gonsalvez (ngong2@illinois.edu)

Lecture Hours

Wednesdays:1PM - 2:30PM
Fridays: 1PM - 2:20PM

Lecture Location

3031 Campus Instructional Facility

Laptop computers with Matlab Installed

You will need a laptop in this class. Laptops need to have Matlab installed with Bioinformatics and Statistics & Machine Learning toolboxes.
An alternative to buying Matlab is to use CITRIX for UIUC students and connect to EWS Windows Lab Software.

iClickers

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 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:

Grading:

Attendance  10%
Homework   20%
Midterm 1    20%
Midterm 2    20%
Final Exam    30%

Exams:

Midterm 1 

Miidterm 2 

Final Exam 

Suggested Textbooks

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

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Campus Academic Policies & Statements

Academic Integrity

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

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). 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.

Students with Disabilities

The University of Illinois Champaign-Urbana, is committed to ensuring that all students, including students with disabilities, do not experience barriers to learning and participating fully in class. Students who have a letter of accommodation from Disability Resources and Educational Services (DRES) are advised to share that with instructors as soon as possible to ensure accommodation needs can be discussed and met.

To obtain disability-related academic accommodations, disabled students are encouraged to contact DRES as soon as possible. To contact DRES, please visit 1207 S. Oak Street, Champaign, call (217) 333-1970, email disability@illinois.edu, or visit the DRES website (https://dres.illinois.edu/).

Family Educational Rights and Privacy Act (FERPA)

See FERPA – Office of the Registrar (https://registrar.illinois.edu/academic-records/ferpa/) for more information on the Family Educational Rights and Privacy Act (FERPA).

Mental Health

Significant stress, mood changes, excessive worry, substance/alcohol misuse or interferences in eating or sleep can have an impact on academic performance, social development, and emotional wellbeing. The University of Illinois offers a variety of confidential services including individual and group counseling, crisis intervention, psychiatric services, and specialized screenings which are covered through the Health Service Fee. If you or someone you know experiences any of the above mental health concerns, it is strongly encouraged to contact or visit any of the University’s resources provided below. Getting help is a smart and courageous thing to do for yourself and for those who care about you.

If you are in immediate danger, call 911. 

This statement is approved by the University of Illinois Counseling Center.

Community of Care

As members of the Illinois community, we each have a responsibility to express care and concern for one another. If you come across a classmate whose behavior concerns you, whether regarding their well-being or yours, we encourage you to refer this behavior to the Connie Frank CARE Center (formerly the Student Assistance Center) in the Office of the Dean of Students.  You may do so by calling (217) 333-0050 or by submitting an CARE online referral (https://odos.illinois.edu/community-of-care/referral). Based on your report, staff in the Connie Frank CARE Center will reach out to offer support and assistance. 

Further, as a Community of Care, we want to support you in your overall wellness. We know that students sometimes face challenges that can impact academic performance (examples include mental health concerns, food insecurity, homelessness, personal emergencies). Should you find that you are managing such a challenge and that it is interfering with your coursework, you are encouraged to contact the Connie Frank CARE Center (https://odos.illinois.edu/community-of-care/CAREcenter) (formerly the Student Assistance Center) in the Office of the Dean of Students for support and referrals to campus and/or community resources.

Ombuds Assistance & Resources for Students (OARS)

OARS is housed in the Office of the Dean of Students and serves as a confidential, impartial, informal, and independent resource for students seeking guidance, clarity, and resolution when facing challenges or conflicts with university faculty, staff, policies, procedures, or practices. The office exists to provide a space where students can feel heard, discuss their concerns, explore potential options and pathways for resolving disputes and, when appropriate, be referred to other campus resources. The Student Ombudsperson listens without judgment, helps clarify issues, identifies possible pathways forward, and supports students in making their own decisions. For more information, please visit the Ombuds Assistance & Resources for Students (OARS) (https://oars.illinois.edu/).

Disruptive Behavior

Behavior that persistently or grossly interferes with classroom activities is considered disruptive behavior and may be subject to disciplinary action. Such behavior inhibits other students’ ability to learn and an instructor’s ability to teach. A student responsible for disruptive behavior may be required to leave class pending discussion and resolution of the problem and may be reported using the Public Incident Report Form (https://go.illinois.edu/ReportMisconduct), email (conflictresolution@illinois.edu), or phone (217) 333-3680 to the Office for Student Conflict Resolution (https://conflictresolution.illinois.edu/) for disciplinary action.  

Emergency Response Recommendations

For emergency response recommendations and building floor plans, review Public Safety's Run, Hide, Fight information (https://police.illinois.edu/em/run-hide-fight/), Emergency Action Plans (https://eoc.illinois.edu/plans/eap/), and Facility Access Maps (https://facilityaccessmaps.fs.illinois.edu/archibus/schema/ab-products/essential/workplace/index.html). I encourage you to review these resources within the first 10 days of class.  

Religious Observances

It is the policy of the University of Illinois Urbana-Champaign to reasonably accommodate its students’ religious beliefs, observances, and practices that conflict with a student’s class attendance or participation in a scheduled examination or work requirement, consistent with state and federal law. Students must make requests for accommodation in advance of the conflict to allow time for both consideration of the request and alternate procedures to be prepared. Requests should be directed to the instructor. An optional resource to assist students in making such requests can be found on the Religious Observances website (https://odos.illinois.edu/resources/students/religious-observances) of the Office of the Dean of Students.  

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 supportive measures, resources, 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 on We Care Student Resources  (https://wecare.illinois.edu/resources/students/#confidential) and on the Illinois app. Other information about resources and reporting is available on At Illinois We Care (https://wecare.illinois.edu/) and on the Illinois app.

Veterans and Military Students

As a military-friendly institution, and per federal regulations and Illinois statutes, the University of Illinois Urbana-Champaign has established policies and procedures to accommodate military-connected students. In addition to the support available at the Chez Veterans Center (https://chezveteranscenter.ahs.illinois.edu/), members of the National Guard or Reserves and active-duty military personnel with military obligations (e.g., deployments, training, drills) are encouraged to communicate these, in advance whenever possible, to the instructor. For policy details, see the Student Code on Excused Absences and Departure from the University for U.S. Military or other U.S. National Defense Services (https://studentcode.illinois.edu/article3/part3/3-313).