San José State University
SMPD 287
Bioinformatics in Medical Product Development
Course Code: 29711

Spring 2013
Mondays 6:00-10:00 pm at Techmart Center (off campus)

Interesting links

What is bioinformatics? NCBI Tutorial.
An Introduction to the Double Helix.
Transcription and Translation at myDNA.
A Primer on Molecular Genetics from the U.S. Department of Energy.
The Human Genome - What's Next? from Current Science and Technology Center.

Cracking the Code of Life NOVA program. Requires Quick Time or Real Video Plug-in. Recommended segments: 1, 2, 6, 9, 10, 12, 13, 14, and 16.

Link to biotechnology companies in the Bay Area.

Information about the Instructor

Name: Sami Khuri
Office: 418 MacQuarrie Hall
Phone: 924-5081
Office Hours: Tuesdays and Thursdays: 1:15 to 2:15pm.

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

Admission to the MPDM program and completion of SMPD 286 and BUS 224C.

Textbooks

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)

You will find a wealth of information including links, explanations, definitions, etc... of each chapter of Discovering Genomics, Proteomics, and Bioinformatics at: wps.aw.com/bc_campbell_genomics_2/
A copy of my powerpoint slides (6 per page) will be available to the students enrolled in the class.
We shall have several topics covered by guest lecturers from the pharmaceutical industry. Please see the tentative schedule.

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

Class	Date	Lecturer(s)	Topics
One	March 18, 2013	Egle Cekanaviciute and Sami Khuri (4 hours)	Green sheet discussion Homework One discussion Data Management Plan (SP) Hands-On One: Human Traits Chapter One: Molecular Biology Review Hands-On Two: Huntington
Two	March 25, 2013	Sami Khuri (4 hours)	Chapter Two: What is Bioinformatics? (I) Why Bioinformatics in SMPD? Hands-On Three: Interesting Problems Hands-On Four: Transcription, Translation, and Databses Four Conventions for DNA, RNA, and proteins NCBI Sample Record Hands-On Five: Investigating Inherited Diseases (A,B) UCSC Genome Browser
Three	April 1, 2013	Sami Khuri (4 hours)	Chapter Two: What is Bioinformatics? (II) Genomic Variations: SNPs, Haplotypes, CNVs and Indels Hands-On Five: Investigating Inherited Diseases (C,D) UCSC Human Genome Browser Hands-On Six: Comparing Beta Globin Proteins Biology Workbench (I) Multiple Sequence Alignment (I)
Four	April 8, 2013	Sami Khuri (4 hours)	What is Bioinformatics? (III) Multiple Sequence Alignment (II) Why Bioinformatics in SMPD? Biology Workbench (II) Hands-On Seven: Multiple Sequence Alignment Transitions and Transversions Beta Globin Gene
Five	April 15, 2013	Sami Khuri (4 hours)	What is Bioinformatics? (IV) Why Bioinformatics in SMPD? Submit Homework One In-Class presentation by students as part of the assignment. Beta Globin Gene Hemoglobinopathies Chapter Three: Beta Thalassemia Hands-On Eight: Beta Thalassemia (I)
Six	April 22, 2013	Sami Khuri (4 hours)	What is Bioinformatics? (V) Homework One Returned Hands-On Eight: Beta Thalassemia (II) Human Genome Variation The BRCA1 gene and protein Hands-On Nine: BRCA1 (Part One)
Seven	April 29, 2013	Sami Khuri (4 hours)	What is Bioinformatics? (VI) Hands-On Nine: BRCA1 (Part Two) Math Minute 2.2 (DGPB) Chapter Four: Motifs and Logos Hands-On Ten: Motifs Position Weight Matrices (PWM) Hands-On Eleven: PWM
Eight	May 6, 2013	Sami Khuri (4 hours)	What is Bioinformatics? (VII) Submit Homework Two Math Minute 2.2 Handout (DGPB) Hands-On Eleven: PWM (End) Chapter Five: The MYH16 Gene and Protein Hands-On Twelve: The BIG Jaw
Nine	May 13, 2013	Jim Rogers and Dan McGann (4 hours)	Regulatory Standards 21 CFR Part 11: Electronic records and signatures FDA Guidance: Computerized systems used in clinical trials FDA Guidance: General Principles for software validation EU Reflection Paper on Electronic Source Data FDA Draft Guidance on Electronic Source Documentation Electronic Data Capture (EDC) Evolution of EDC Current Technology and Adoption EDC Architectures/Hosting Points to Consider Electronic Health Record Integration Safety Reporting Clinical Trial Data Collection Other Applications Demonstration of EDC System and Study Design Tool
Ten	May 20, 2013	Sami Khuri (4 hours)	General Review and In-Class Final Examination

Course Requirements

Problem Sets Two 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 15, 2013.
- Homework Two due on Monday, May 6, 2013.
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.
Final Examination:
Monday, May 20, 2013.

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 project, etc...).

Grading Policy

The final grade will be computed as shown below:

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

[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 11, 2013. The last day to drop with a full refund is February 4, 2013. According to University and Department guidelines, dropping after February 4, 2013, 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.)

San José State University SMPD 287 Bioinformatics in Medical Product Development Course Code: 29711

Spring 2013 Mondays 6:00-10:00 pm at Techmart Center (off campus)