San José State University
SMPD 287
Bioinformatics in Medical Product Development
Course Code: 29651

Link to biotechnology companies in the Bay Area.

Information about the Instructor

Name: Sami Khuri
Office: 207 MacQuarrie Hall
Phone: 924-5081
Office Hours: By appointment

Course Description

Provides business and regulatory perspectives on electronic information technologies, processes and standards in the conduct of clinical trials. Special emphasis: data collection, clinical trial & data management randomization and drug supply, statistical processes, safety databases and electronic regulatory submission, electronic records and signatures, sys validation processes, and data standards. The course also covers the main topics in bioinformatics, such as the analysis of DNA and protein sequences, building phylogenetic trees, microarray analysis and pharmacogenomics.

Prerequisites

Textbooks [No required textbooks]

Recommended: Understanding Bioinformatics by Marketa Zvelebil and Jeremy Baum, Garland Science, 2008, ISBN 0-815-34024-9.
Recommended: Bioinformatics and Functional Genomics by : Jonathan Pevsner Wiley-Blackwell, 2015, Third Edition, ISBN 978-1-118-58178-0. (BFG)
Recommended: Discovering Genomics, Proteomics, and Bioinformatics by : A. Malcolm Campbell and Laurie J. Heyer, Pearson Benjamin Cummings, 2007, Second Edition, ISBN 0-8053-8219-4. (DGPB)
Recommended: Practical Guide to Clinical Data Management by : Susanne Prokscha, Taylor and Francis, 2007, Second Edition, ISBN 0-8493-7615-7. (SP)

1. You will find a wealth of information including links, explanations, lectures, etc... of each chapter of Bioinformatics and Functional Genomics, at: http://www.bioinfbook.org/php/?q=book3
2. A copy of my powerpoint slides (6 per page) will be available at Canvas, to the students enrolled in the class.
3. We shall have topics in Regulatory Standards, Electronic Data Capture, and more, covered by guest lecturers, from the pharmaceutical industry. Please see the tentative schedule.

Tentative schedule that will be updated very frequently. Please, check regularly.

Course Requirements

1. Problem Sets
   Three homework assignments. The purpose of the assignments is to develop your understanding of the material and your skills in problem-solving. Assignments are due in the beginning of the lecture on the following dates:
   • Homework One due on Monday, April 4, 2016.
   • Homework Two due on Monday, April 25, 2016.
   • Homework Three due on Monday, May 9, 2016.
   
   
2. Hands-On Exercises
   We will have a number of hands-on exercises. The purpose of the hands-on exercises is to develop your understanding of the material.
   
   

3. Take-Home Final Examination:
   Due by midnight (PST) on Monday, May 23, 2016.
   

Class Attendance

Class attendance is strongly encouraged. In class, we shall cover many topics and examples that are neither in the class notes nor in the textbook. If you miss a lecture, it is your responsibility to find out what was covered in class (this includes: handouts given out during your absence, corrected typos and errors, examples discussed in class - that are neither in the book nor in the notes - clarifications and changes made to assignments or the take-home exam, etc...).

Grading Policy

The final grade will be computed as shown below:

Homework: 30%
Hands-On Exercises: 40%
Take-Home Final Exam: 30%

[97, 100] A+
[93, 97) A
[90, 93) A-
[87, 90) B+
[82, 87) B
[80, 82) B-
[77, 80) C+
[72, 77) C
[70, 72) C-
[67, 70) D+
[62, 67) D
[60, 62) D-
[0, 60) F

Add/Drop Policy

For those wishing to add this course, the deadline is February 16, 2016. The last day to drop with a full refund is February 9, 2016. According to University and Department guidelines, dropping after February 9, 2016, requires a serious and compelling reason to drop a course. Grades alone do not constitute reason to drop a course. Students who stop attending without officially dropping will be issued a U at the end of the semester which is counted as an F in calculations of GPA. See University Catalog.

Academic Integrity

Your own commitment to learning, as evidenced by your enrollment at San José State University, and the University's Academic Integrity Policy requires you to be honest in all your academic course work. Faculty members are required to report all infractions to the Office of Student Conduct and Ethical Development. The "Policy on Academic Integrity" can be found here.

Disability Resource Center

If you need course adaptations or accommodations because of a disability, or if you need special arrangements in case the building must be evacuated, please make an appointment with us as soon as possible, or see us during office hours. Presidential Directive 97-03 requires that students with disabilities requesting accommodations must register with DRC to establish a record of their disability. (Please let us know as soon as possible in order to more effectively accommodate your needs.)