BIOINFORMATICS COMPUTATIONAL BIOLOGY An Introductory Course DEPARTMENT OF
BIOINFORMATICS & COMPUTATIONAL BIOLOGY (An Introductory Course) DEPARTMENT OF COMPUTER SCIENCE , UNIVERSITY OF COLORADO, COLORADO SPRINGS. CS 4850/5850 FALL 2020 © DR. OLUWATOSIN OLUWADARE, 2020 Lecture 1: Course Overview and Introduction 1 December 15, 2021
Introduction • Oluwatosin Oluwadare Ph. D. • Office hours: Mon/Wed 12: 00 -1: 30 PM and by appointment. • Office: Engineering Building - ENG 244 • Phone: 719 -255 -3004 • E-mail: ooluwada@uccs. edu • Website: https: //academics. uccs. edu/~ooluwada/index. html December 15, 2021 2
Research • Bioinformatics & Computational Biology • Machine learning & Data Mining • Deep Learning & Reinforcement Learning • Read more about my Research here: Google. Scholar, Research. Gate, Linked. In, Pub. Med December 15, 2021 3
Now it’s your turn • Name, program • Prior courses/experiences related to this subject • Why did you register for this course? • What will make you like/hate this course? • Anything else December 15, 2021 4
About Course • Time: Tue/Thurs 12: 15 pm -1: 30 pm • Classroom: Meet Remotely • Course Management: Canvas • For Grades posting and Announcements • Course Schedule/Website: https: //academics. uccs. edu/~ooluwada/courses/bioinformatics/ • All Resources, Projects, Homework, and Assignments will be posted on Course website. December 15, 2021 5
Textbook • Get an electronic copy from the UCCS Library. • References • • • 6 December 15, 2021 • Bioinformatics: The Machine Learning Approach, Pierre Baldi and Soren Brunak, 2001, MIT press. Exploring Bioinformatics: A Projectbased Approach, Second Edition, Caroline St. Clair and Jonathan E. Visick Jones & Bartlett Learning, 2015. Jiawei Han, Micheline Kamber, and Jian Pei. Data Mining: Concepts and Techniques, 3 rd ed. (2 nd edition is also fine), Morgan Kaufmann Publishers, June 2012. ISBN 9780123814791. Get an electronic copy from the UCCS Library. Panno, J. (2014). The cell: evolution of the first organism. Infobase Publishing.
Goals • Introduce fundamental problems, concepts, methods, and applications in Bioinformatics. • Emphasize both the methods and the practical use of bioinformatics tools and databases. • With focus in Genomics, walk students through a hands-on bioinformatics tools development • Audience: computer scientists, engineers, biologists, statisticians, … • Prerequisite: Some background in programming December 15, 2021 7
The Slides • The slides highlight the gist of most important concepts and techniques. • It may be simplified for ease of explanation. • Make notes of key points mentioned in class. • The class slides will be made from combination of textbooks and literatures. December 15, 2021 8
Class Expectations • To be successful in this course, you (the student) need to attend every lecture. Students are required to attend lectures. • Participate in class discussions. • Ask questions for clarity. • Submit assignments and projects on time. • Attend all lectures December 15, 2021 9
Grading Scheme • Midterm Exam: 20% (Date: October 22, 2020) • Course Project: 45% • Presentation(10%) (Must be done independently) • Report(35%) • Homework(HW): 15% (Must be done independently) • Reading Assignment: 15% (10 minutes presentation of a Research topic) • Attendance : 5% December 15, 2021 10
Homework (HW) : 15% of Class Grade • There will be four Homework (HW 1, HW 2, HW 3) • 5% each. • It will focus on : • Problem Solving, • Calculations, and • Relevant statistical analysis relevant to class topics. December 15, 2021 11
Course Project (CP): 45% of Class Grade • There will be one course project • It will focus on: • hands-on experience with big data, real application • Must design, implement (programming), and evaluate, • open to novel solutions, and • Will be based on implementation of relevant algorithms studied in class Write a paper publishable in a journal. Fear Not, I will walk you through the process December 15, 2021 12
Course Project (CP) : 45% of Class Grade (cont’d) • The project code and report should be submitted to Canvas on due date. • The report should include a title, student name, an abstract, an introduction to the problem, methods, results, conclusion, and references(if any). December 15, 2021 13
Reading Assignment(RA) : 15% of Class Grade • There will be two reading assignments (RA 1, RA 2) • 5% each • A 10 mins presentation/discussion of the scientific paper in class. • It will focus on: • Getting extra knowledge on recent techniques and algorithms. • Providing student with introduction on chosen project • Improve student’s understanding of relevant algorithms studied in class. • A series of literature review for related topics and researchoriented project. December 15, 2021 14
Programming Tools • Any general programming languages: C/C++, Java, Perl, Python • Specialized language packages: R, Matlab (or Octave) • Machine learning and data mining packages: Weka, NNClass, SVMlight December 15, 2021 15
Canvas • Assignment solution file(. pdf, . docx) • Submission (we don’t accept email submission or hard-copy) • Grades. December 15, 2021 16
Deadlines • Everything will be submitted through Canvas. • Due time: 11: 59 pm on Due Date provided on course website. • Late submission: 5 -point deduction per hour, till you get 0. (The raw score of each assignment is 100. So there is no point to submit it after 20 hours). December 15, 2021 17
Regrading • Regrading request must be made within 7 days after we post scores on Canvas. Instructor or TA will handle regrade requests. • If student is not satisfied with the regarding results, you get 7 days to request again. The instructor will regrade, and the decision is final. December 15, 2021 18
Announcements Check Canvas regularly for announcements and updates. December 15, 2021 19
Course Review • We will have a course review twice before the semester ends to ensure a smooth running of the class. • Check the course schedule for the dates we have scheduled for this. December 15, 2021 20
Academic Integrity • Cheating • Copying another's test or assignment • Communication with another during an exam or assignment (i. e. written, oral or otherwise) • Giving or seeking aid from another when not permitted by the instructor • Possessing or using unauthorized materials during the test • Buying, using, stealing, transporting, or soliciting a test, draft of a test, or answer key December 15, 2021 21
Academic Integrity • Plagiarism • Using someone else's work in your assignment without appropriate acknowledgement • Making slight variations in the language and then failing to give credit to the source • Collusion • Without authorization, collaborating with another when preparing an assignment December 15, 2021 22
23 Reasons why you chose the Right class? Clair, C. S. , & Visick, J. E. (2013). Exploring bioinformatics. Jones & Bartlett Publishers December 15, 2021 • Big Data • Making sense of these hundreds of billions of base pairs of genetic information is a daunting task • Bioinformatics is the new science that seeks to develop better ways to explore, analyze, and understand this vast wealth of genomic data.
Reasons why you chose the Right class? Booch, 2013 December 15, 2021 24
What is Big Data? • It refers to large set of data that is almost impossible to manage and process using traditional or commonly used business intelligence software tools within a tolerable elapsed time. Magoulas, Roger; Lorica, Ben (February 2009). "Introduction to Big Data". Release 2. 0. Sebastopol CA: O'Reilly Media. [Extra Reading] • What qualifies as being "big data" varies depending on the capabilities of the users and their tools, and expanding capabilities make big data a moving target. ” • For some organizations, facing hundreds of gigabytes of data for the first time may trigger a need to reconsider data management options. For others, it may take tens or hundreds of terabytes before data size becomes a significant consideration. December 15, 2021 25
December 15, 2021 Stephens, Zachary D. , et al. "Big data: astronomical or genomical? . " PLo. S biology 13. 7 (2015): e 1002195. 26
Lot of Jobs December 15, 2021 2 7 Google. images
Extra Reading Notes that will be beneficial for the currently discussed topic in class. December 15, 2021 28
Extra Reading • Big Data: Astronomical or Genomical? (Big. DAG) • Stephens ZD, Lee SY, Faghri F, Campbell RH, Zhai C, Efron MJ, Iyer R, Schatz MC, Sinha S, Robinson GE. Big data: astronomical or genomical? . PLo. S biology. 2015 Jul 7; 13(7): e 1002195. December 15, 2021 29
Questions? Let’s have a great semester December 15, 2021 30
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