CoSBBI: Computer Science, Biology and Biomedical Informatics


Room: BAUM 407A

Time: 10 am - 12 noon

Textbook: Translational Bioinformatics, PLOS Computational Biology Collection


CoSBBI Team:
Mike Becich
  CoSBBI Co-Director, DBMI Chair
  becich@pitt.edu

Joyeeta Dutta-Moscato
  CoSBBI Co-Director
  jod30@pitt.edu

Andrew J. King
  Instructor, Webmaster
  ajk77@pitt.edu

Arielle Fisher
  Instructor, Events Coordinator
  arf56@pitt.edu

Amie Draper
  Instructor, Boot Camp Co-Coordinator
  ajd109@pitt.edu

Adam Handen
  Instructor, Boot Camp Co-Coordinator
  handena@pitt.edu

Kevin Lu
  Programming TA
  kevin.n.lu123@gmail.com

Ritwik Gupta
  Programming TA
  ritwikg2004@live.com



Syllabus:

Date
Time
Topic
Presenter
Reading Assignments & Handouts
Week 1
16 June
Monday

UPCI Orientation
17 June
Tuesday

Visit Hillman Cancer Center
18 June
Wednesday

Visit NLM Informatics Training Conference
19 June
Thursday
10:00 AM
10:30 AM
Welcome & Introduction to Biomedical Informatics
Intro to Molecular Biology & Bioinformatics
Mike Becich
Erik Polinko
Chapter 1: Biomedical Knowledge Integration
Becich Lecture Notes
Polinko Lecture Notes
20 June
Friday
10:00 AM
11:00 AM
Tools and resources in research
Bioinformatics
Tanja Bekhuis
Arielle Fisher
Fisher Lecture Notes
The Inner Life of the Cell (Video)
Week 2
23 June
Monday
10:00 AM
Programming Boot Camp 1
Installation, Variables, & Conditionals
Adam Handen
TA: Ritwik Gupta
Bootcamp Description
Bootcamp Schedule

1. DNA Mass to Length Converter
2. Gene Finder
24 June
Tuesday
10:00 AM
Programming Boot Camp 2
Loops & Data Structures
Amie Draper
TA: Kevin Lu
Reading One
Reading Two
Reading Three
3. Transcription and Translation
25 June
Wednesday
10:00 AM
Programming Boot Camp 3
Files & File Parsing
Adam Handen
TA: Ritwik Gupta
4. PDB and FASTA Files
26 June
Thursday
10:00 AM
Programming Boot Camp 4
Functions
Jonathan Young
TA: Kevin Lu
Young Lecture Notes
Functions Lecture
Circle
Answers
5. Clinical Decision Support
27 June
Friday
10:00 AM
Programming Boot Camp 5
Packages & Other Languages
Jeya Balasubramanian
TA: Ritwik Gupta
Balasubramanian Lecture Notes
This Python simulator has some useful pre-installed modules
that can be explored.
Week 3
30 June
Monday
10:00 AM
11:00 AM
Probability & Statistics
Information Visualization
Joyeeta Dutta-Moscato
Chapter 2: Data-Driven View of Disease Biology
Dutta-Moscato Lecture Notes (Prob & Stat)
Dutta-Moscato Lecture Notes (Info Graphics)
Handouts
Homework
01 July
Tuesday
10:00 AM
11:00 AM
Data Mining & Machine Learning
Joyeeta Dutta-Moscato
& Jeya Balasubramanian
Data Mining in Cancer Research
Dutta-Moscato Lecture Notes (Data Mining)
Linear Demo
Kmeans Demo
Overfitting Demo
02 July
Wednesday
10:00 AM
11:00 AM
Protein Interactions
Research Hour
Adam Handen &
Sri Chaparala
Madhavi Ganapathiraju
Chapter 4: Protein Interactions and Disease
Handen Lecture Notes
Chaparala Lecture Notes
03 July
Thursday
10:00 AM
11:00 AM
Decision Analysis & Clinical Decision Support Systems
Research Hour
Amie Draper
Rich Tsui
Draper Lecture Notes
04 July
Friday
No Class - Happy 4th of July
Week 4
07 July
Monday
10:00 AM
11:00 AM
Network Approach in Systems Biology
Research Hour
Andrew King
Songjian Lu
Chapter 5: Network Biology Approach to Complex Diseases
Nature Education: Complex Diseases
King Lecture Notes (Network Bio)
Lu Reading: Data to Knowledge
Lu Lecture Notes

08 July
Tuesday
10:00 AM
11:00 AM
Structural Variation and Medical Genomics
Research Hour
Andrew King
Uma Chandran
Chapter 6: Structural Variation and Medical Genomics
King Lecture Notes (Structural Variation)
Chandran Lecture Notes
09 July
Wednesday
10:00 AM
11:00 AM
Biomarker Discovery
Research Hour
Jeya Balasubramanian
Roger Day
Chapter 10: Mining Genome-Wide Genetic Markers
Day Lecture Notes
10 July
Thursday
10:00 AM
11:00 AM
Introduction to GWAS
Research Hour
Viji Avali
Shyam Visweswaran
Chapter 11: Genome-Wide Association Studies
Avali Lecture Notes
Visweswaran Lecture Notes
11 July
Friday
10:00 AM
11:00 AM
Student Research Update
Journal Club
Week 5
14 July
Monday
10:00 AM
LEAN Manufacturing Process Management Framework
to Improve Healthcare
Tania Lyon
Lyon Lecture Notes
15 July
Tuesday
10:00 AM
11:00 AM
Pathology Informatics
Industry Spotlight: Omnyx
Anil Parwani
Raghavan Venugopal
Medical Laboratory Informatics
Venugopal Lecture Notes
16 July
Wednesday

NIH Trip
17 July
Thursday
Room 407B
10:00 AM
11:00 AM
Cancer Genome Analysis
Industry Spotlight: GenomOncology
Jon Young
Manuel Glynias
Chapter 14: Cancer Genome Analysis
18 July
Friday
10:00 AM
11:00 AM
Student Research Update
Journal Club
Week 6
21 July
Monday

Career Development & Leadership Seminar
22 July
Tuesday
10:00 AM
01:15 PM
Clinical Informatics/EHR data mining
Tour of Parwani Lab
Adam Roth
Anil Parwani
Chapter 13: Mining Electronic Health Records in the Genomics Era
Roth Lecture Notes (Data Mining)
23 July
Wednesday
10:00 AM
11:00 AM
Clinical Informatics/Text mining
Research Hour: Global Health Informatics
Adam Roth
Arielle Fisher
Chapter 16: Text Mining for Translational Bioinformatics
Roth Lecture Notes (Text Mining)
Fisher Lecture Notes (Global Health)
Fisher Lecture Notes (Lab Turnaround Time)
New Patient Registration at Kamuzu Central Hospital (Video)
24 July
Thursday
Room 407B
10:00 AM
11:00 AM
Pharmacogenomics
Research Hour
Katrina Romagnoli
Rich Boyce
Chapter 7: Pharmacogenomics
Lecture Notes
25 July
Friday
10:00 AM
11:00 AM
Usability and user-centered design
Research Hour
Katrina Romagnoli
Harry Hochheiser
Pickering "Novel Representation of Clinical Information in the ICU"
Week 7
28 July
Monday
9:30 AM
10:00 AM
Post Test
Student Research Update & Writing abstracts
29 July -
01 August

Extra time for Research Project
Week 8
04 August
Monday
9 AM - 12 PM
Trip to Pittsburgh Supercomputing Center
05 August
Tuesday
9 AM - 11 AM
Tour of zebrafish facility
06 August
Wednesday
11 AM - 1 PM
Barbecue on the deck!
07 August
Thursday

Extra time for Research Project
08 August
Friday

Final Day Presentations