San José State University
SMPD 287
Bioinformatics in Medical Product Development
Course Code: 29664

Spring 2010
Wednesdays 6:00-10:00 pm at Rose Orchard (off campus)

Interesting links

What is bioinformatics? NCBI Tutorial.
An Introduction to the Double Helix.
Transcription and Translation (Flash).
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 3:20pm.

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

Discovering Genomics, Proteomics, and Bioinformatics by : A. Malcolm Campbell and Laurie J. Heyer, Pearson Benjamin Cummings, 2007, Second Edition, ISBN 0-8053-8053-4. (DGPB)

Practical Guide to Clinical Data Management by : Susanne Prokscha, Taylor and Francis, 2007, Second Edition, ISBN 0-8493-7615-7.

You will find a wealth of information including links, explanations, definitions, etc... of each chapter of Discovering Genomics, Proteomics, and Bioinformatics at: http://wps.aw.com/bc_campbell_genomics_2/
We shall cover most of the topics from chapters 1, 4, and 6, and some selected topics from chapters 3, 7, and 9 from Discovering Genomics, Proteomics, and Bioinformatics.
Before reaching the end of a chapter, I will announce which topics of the following chapter will be covered.
Please bring the textbooks every Wednesday to class.
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	January 27, 2010	Sami Khuri (4 hours)	Green sheet discussion Review of drug development phases in clinical trials Introduction to Clinical Data Management Data Management Plan Why Bioinformatics in SMPD? What is Bioinformatics?
Two	February 3, 2010	Jim Rogers and Alan Arroyo (2 hours) Sami Khuri (2 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 Implementation of computer systems in a regulated environment What is wrong with my child? (DGPB)
Three	February 10, 2010	Sami Khuri (4 hours)	Hands-On 2: Multiple Sequence Alignment Hands-On 3: Dystrophin The Big Jaw Problem Hands-On 4: The myh16 Protein Genome Sequence Acquisition and Analysis (DGPB) How do you find Motifs? (DGPB) Hands-On 5: Motifs
Four	February 17, 2010	Eugenia Budman (3 hours) Sami Khuri (1 hour)	Data Management: Quality, Integrity, Compliance What is Clinical Data Management (DM)? Where does DM fit? DM mission DM responsibilities Building databases Managing Safety data Overview of Data Quality: data cleaning/regulations Database Closure Migrating and Archiving Data Overview of regulations for DM Working with CROs DM professionals - jobs, levels, skills How to work with DM DM today and tomorrow
Five	February 24, 2010	Sami Khuri (4 hours)	What makes Humans different? (DGPB) NADPH Oxidase-Nox1 (DGPB) What have we learned from Metazaon Genomes? (DGPB) Hands-On 6: Nox1 Hands-On 7: What makes Humans different
Six	March 3, 2010	Mariam Mirgoli (2 hours) Sami Khuri (2 hours)	Clinical Data Project Management (CDPM) CDPM Process Overview: Protocol -> CRF -> Database CRF design - CDASH standards Data Management Plans Database design Standardization of Terminology: MedDRA, WHO, etc Database Audits EDC at Abbott AV Electronic patient reported outcomes at Abbott AV IVRS at Abbot AV Human Genomic Variation (DGPB)
Seven	March 10, 2010	Jim Rogers and Alan Arroyo (4 hours)	Electronic Data Capture (EDC) Electronic patient reported outcomes Interactive voice response systems What EDC does and doesn't do EDC Architectures/Hosting Role of the Sponsor Vendor responsibilities Minimizing risk, maximizing opportunity When to use EDC Next systems
Eight	March 17, 2010	Sami Khuri (4 hours)	Hands-On Eight: Human Genomic Variation (I) Hands-On Nine: Human Genomic Variation (II) Microarray Analysis (DGPB)
Nine	March 24, 2010	John Aitken (4 hours)	Electronic Document Management and Regulatory Submission Publishing for INDs and NDAs How electronic document management systems are used in the pharmaceutical industry to manage documents intended for submission to FDA in INDs and NDAs Steps involved in the preparation and submission of an IND or NDA
Ten	April 7, 2010	Sami Khuri	Exam

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 posted at Blackboard and are due in the beginning of the lecture on the following dates:
- Homework One due on Wednesday, March 17, 2010.
- Homework Two due on Wednesday, March 31, 2010.
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.
Take-Home Final Examination:
Given on: Wednesday, March 31, 2010.
Due on: Wednesday, April 7, 2010.

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%
Take-Home Final: 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 12, 2010. The last day to drop with a full refund is February 5, 2010. According to University and Department guidelines, dropping after February 5, 2010, 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: 29664

Spring 2010 Wednesdays 6:00-10:00 pm at Rose Orchard (off campus)