Course Director: Umit Catalyurek, PhD, Department of Biomedical Informatics
Office: 3167B Graves Hall

Class Hours: Tue & Thu 9:00–10:18am    Location: 3167 Graves Hall

#	Date	Lecturer	Topic
1	January 4	Umit Catalyurek	Intoduction
2	January 9	Ilya Ioshikes	Sequence Analysis
3	January 11	Ilya Ioshikes	Gene Regulation (or Mass Spectrometry or RLGS)
4	January 16	Daniel Janies	Sequence Databases
5	January 18	Daniel Janies	Phylogenetics: Basic theory, optimization (tree search) and parallelization
6	January 23	Scott Oster/Shannon Hastings/Stephen Langella	caBIG – overall architecture
7	January 25	Metin Gurcan	Computer-Aided Diagnosis - 1
8	January 30	Metin Gurcan	Computer-Aided Diagnosis - 2
9	February 1	Ashish Sharma/Tony Pan	IVI middleware
10	February 6	Kun Huang	Image Analysis, Visualization, Classification
11	February 8	Kun Huang	Image Analysis on Microscopy
12	February 13	Students	Paper presentation
13	February 15	Students	Paper presentation
14	February 20	Philip Payne	Clinical information systems
15	February 22	Philip Payne	Translational research
16	February 27	Umit Catalyurek	Microarray – Design and Analysis
17	March 1	Umit Catalyurek	Biomedical Informatics and High Performance Computing
18	March 6	Students	Term Project Presentation
19	March 8	Students	Term Project Presentation
	March 13,15	Exam Week	No class

 

Grading:

Class participation	10%
Homework(s)	15%
Paper presentation	20%
Progress Report	10%
Term Project Report	30%
Term Project Presentation	15%

 

Term Projects:

Project Proposals are due Jan 18th, 2007
Progress reports are due Feb 15th, 2007
Final reports are due March 13th, 2007
           
Sample topics:

1. Image Analysis: Implement a software system that will automatically retrieve images from a PACS system (BMI will run a software PACS system on its own machines) and will execute an image analysis code, such as segmenting nuclei
2. DICOM/PACS: Design, architect and implement a picture archival system that will run on distributed heterogeneous cluster of machines.
3. Classification of tumors and identification of differentially expressed genes using gene expression data.

Reports and homeworks are due at the beginning of class (9am) on the due date.