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Graduate Course Proposal Form Submission Detail - BCH6886
Tracking Number - 4891

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Current Status: Approved by SCNS - 2014-11-01
Campus: Tampa
Submission Type: New
Course Change Information (for course changes only):
Comments: for bioinformatics & Comp Biology Program Change (5/5/14) required. To Chair. Approved 5/19/14. To USF Sys 5/20/14. to SCNS 5/28/14. Approved effective 11/1/14

Detail Information

  1. Date & Time Submitted: 2014-01-24
  2. Department: Medical Sciences
  3. College: MD
  4. Budget Account Number: USF01HSC61440010000 0000000000000
  5. Contact Person: Vladimir Uversky
  6. Phone: 9745816
  7. Email:
  8. Prefix: BCH
  9. Number: 6886
  10. Full Title: Fundamentals of Structural Bioinformatics
  11. Credit Hours: 4
  12. Section Type: C - Class Lecture (Primarily)
  13. Is the course title variable?: N
  14. Is a permit required for registration?: N
  15. Are the credit hours variable?: N
  16. Is this course repeatable?: N
  17. If repeatable, how many times?: 0
  18. Abbreviated Title (30 characters maximum): Bioinfo
  19. Course Online?: C - Face-to-face (0% online)
  20. Percentage Online: 0
  21. Grading Option: R - Regular
  22. Prerequisites:
  23. Corequisites:
  24. Course Description: This lecture-based, nonrestrictive course covers basics of molecular bioscience data management/analysis. This course comprises a mixed delivery mode consisting of traditional didactic lectures coupled with student assignments and presentations.

  25. Please briefly explain why it is necessary and/or desirable to add this course: Replacing Selected Topics with Permanent number; already listed in program
  26. What is the need or demand for this course? (Indicate if this course is part of a required sequence in the major.) What other programs would this course service? It is expected that 25-30 students will take this course each time it is offered.
  27. Has this course been offered as Selected Topics/Experimental Topics course? If yes, how many times? Yes, 3 or more times
  28. What qualifications for training and/or experience are necessary to teach this course? (List minimum qualifications for the instructor.) Ph.D.

    Knowledge of bioinformatics, computational biology, structural biology, molecular biology, biochemistry, molecular medicine

  29. Objectives: The overall goal of this course is to provide a survey of commonly used computational and bioinformatics tools and databases. Focus is on general computational methods, tools and databases related to molecular biology, genomics, and proteomics, their bio-basis, on how to evaluate results of the analysis. Some qualitative algorithm descriptions are included.
  30. Learning Outcomes: Information resources, introduction to biological databases

    Students will understand information resources and will be familiar with major biological databases.

    Homology & sequence alignment

    Students will learn how to perform homology analysis and how to apply sequence alignment tools.

    Database search

    Students will gain knowledge on major techniques for biological database searches.

    Gene modeling, prediction and regulation;

    Students will understand how to predict genes and how to model genes and their regulation

    Gene expression & microarray analysis

    Basic knowledge for understanding gene expression and Microarray analysis will be provided.

    RNA structure

    Students will learn about structure and function of various RNAs

    Multiple alignments & Trees

    Students will understand how to perform multiple sequence alignment and how to build a phylogenetic trees.

    Protein family & pattern recognition

    Students will understand how to recognize patterns in sequences and how to assemble protein families.

    Protein secondary structure

    Students will learn about various types of protein secondary structure

    Protein tertiary structure, protein folding problem, protein databank

    Students will learn about protein tertiary structure, protein folding problem, and protein databank

    Intrinsically disordered proteins

    Students will learn the concept of protein intrinsic disorder

    Homology modeling and protein modeling

    Students will understand how perform homology modeling and protein modeling

    Human diseases

    Students will learn about involvement of proteins in various diseases


    Students will gain knowledge on major principles and methodologies in proteomics and genomics

  31. Major Topics: Information resources, introduction to biological databases

    Homology & sequence alignment

    Database search

    Gene modeling, prediction and regulation;

    Gene expression & microarray analysis

    RNA structure

    Multiple alignments & Trees

    Protein family & pattern recognition

    Protein secondary structure

    Protein tertiary structure, protein folding problem, protein databank

    Intrinsically disordered proteins

    Homology modeling and protein modeling

    Human diseases


  32. Textbooks: Understanding Bioinformatics. Marketa Zvelebil and Jeremy O. Baum.

    Garland Science, Taylor & Francis Group, New York (2008). ISBN 0-8153-

    4024-9. Although the course will generally follow this textbook, some topics will be covered using other sources, including research articles and reviews.

  33. Course Readings, Online Resources, and Other Purchases: Students are encouraged to read bioinformatics textbooks, scientific books on structural biology and use online access to various biological databases and bioinformatics/computational biology tools.
  34. Student Expectations/Requirements and Grading Policy: Midterm 50% of grade (1st half of the course)

    Final 50% of grade (entire course)

    Extra Credit:

    There are two types of projects for gaining extra credits: paper evaluation assignments and group projects. Up to 7pts of extra credit can be earned through a paper evaluation assignment (see below for the details of this assignment). Up to 50pts of extra credit can be earned through successful participation in the group project (see below for the details of group project).

    The final course grade will be based on a percentage performance basis for the course using the following grading scale:

    A 92-100%

    A- 89-91

    B+ 87-88

    B 82-86%

    B- 79-81

    C+ 77-78

    C 72-76%

    C- 69-71

    D+ 67-68

    D 62-66%

    D- 59-61

    F 0-59%

  35. Assignments, Exams and Tests: MIDTERM:

    Midterm will comprise of 20 essay type questions.


    Final exam will comprise of 20 essay type questions covering the entire course.


    A paper for the evaluation will be given by instructor. Student will need to read, understand, and analyze this paper. Based on this analysis, a short written report summarizing major findings of the paper should be written. In the report, the following points should be considered:

    a) Explanation of the reason for endorsing the work. (Note: This part should be short and concise - please formulate your opinion in 3-5 sentences)

    b) Details regarding the significance of the work with special attention to the following points:

    (i) How the study fits with accepted viewpoints

    (ii) A brief analysis of the study, stating any strengths and weaknesses compared with other studies

    (iii) Directions for future research

    Section (b) should reference other work where appropriate and should be within 300-500 words range.


    Group assignments will be given to the research teams at the beginning of the course. These assignments represent a set of real scientific problem and will require hand-on computer work and basic knowledge of biology. Each student team may be asked to give a brief presentation for one of their assignments. The purposes of these assignments are to further develop students expertise in topic-specific applications related to bioinformatics. Each student team will be required to produce and submit an original report for each assignment. Reports can be of any appropriate length and can be submitted in any suitable format or organization. It is anticipated that the successfully completed assignments and written reports will be used as basis for the potential publications in the scientific journals. Grades received for the reports and student presentations will contribute to the final course grade calculations as extra credit points.

  36. Attendance Policy: Students are encouraged to attend the lectures and participate in class discussions. Students are expected to be active members of the class. Each student should log into the class at least twice a week to check for announcements and to monitor any course changes. Lecture notes will be posted in advance on canvas. However, sample questions similar to exam/quiz questions will not be included in lecture note, but will be regularly reviewed in class.

    Course Attendance at First Class Meeting Policy for Graduate Students: For structured courses, 6000 and above, the College/Campus Dean will set the first-day class attendance requirement. Check with the College for specific information. This policy is not applicable to courses in the following categories: Educational Outreach, Open University (TV), FEEDS Program, Community Experiential Learning (CEL), Cooperative Education Training, and courses that do not have regularly scheduled meeting days/times (such as, directed reading/research or study, individual research, thesis, dissertation, internship, practica, etc.). Students are responsible for dropping undesired courses in these categories by the 5th day of classes to avoid fee liability and academic penalty. (See USF Regulation Registration - 4.0101,

    Attendance Policy for the Observance of Religious Days by Students: In accordance with Sections 1006.53 and 1001.74(10)(g) Florida Statutes and Board of Governors Regulation 6C-6.0115, the University of South Florida (University/USF) has established the following policy regarding religious observances: (

    In the event of an emergency, it may be necessary for USF to suspend normal operations. During this time, USF may opt to continue delivery of instruction through methods that include but are not limited to: Blackboard, Elluminate, Skype, and email messaging and/or an alternate schedule. Its the responsibility of the student to monitor Blackboard site for each class for course specific communication, and the main USF, College, and department websites, emails, and MoBull messages for important general information.

  37. Policy on Make-up Work: Extensions are only given due to extreme circumstances, or emergencies. Acceptable reasons for requesting a make-up exam are medical (individual or immediate family only), legal (accident or court case, individual only), or funeral (immediate family only). Reasons for requesting a make-up must relate specifically to the time period of the missed exam. Students are required to provide appropriate documentation, which will be determined acceptable by the instructor before being granted an extension of time to submit missed assignments. The instructor retains the right to make additional inquires concerning the documentation.
  38. Program This Course Supports: Bioinformatics & Computational Biology Master's
  39. Course Concurrence Information: Molecular Medicine Master's

    Molecular Medicine Ph.D.

    Biotechnology Master's

- if you have questions about any of these fields, please contact or