NIH-NSF Bioengineering & Bioinformatics Summer Institute (BBSI)


  Program Description

Computational Biology, Bioengineering, and Bioinformatics exist at the interface of many different fields. The Bioengineering and    Bioinformatics Summer Institute (BBSI) is a NIH-NSF funded initiative designed to train a new generation of multidisciplinary investigators in these fields. The BBSI will identify and encourage promising young students through intensive cross-disciplinary mentoring, and thus transform the new generation's approach to biomedical computing problems of far greater complexity than those accessible to earlier generations. A major goal of this program is to identify talented students, increase their awareness on the quantitative and computer science methods in life sciences, and encourage them to consider career opportunities in the field of biomedical computing by providing them with an intergrative team-based hands-on research experience at an early stage of their studies.

The BBSI is a joint program of 10 weeks offered by the University of Pittsburgh (lead institution), the Pittsburgh Supercomputing Center, Duquesne University, and Carnegie Mellon University. This program will cover coursework required to conduct research, as well as prepare the participant for an academic or non-academic career in the fields of bioengineering, bioinformatics, and computational biology by participation in discussions, career guidance sessions, and interaction with different research groups.

  Program Title

The title of this Summer Institute is “Simulation and Computer Visualization of Biological Systems at Multiple Scales”. The BBSI will focus on computational and mathematical approaches to understanding the function and dynamics of molecular and cellular systems, using known structure, biochemical pathways and other data. Theory and methods covered in BBSI coursework will provide insights into essential concepts and tools selectively tailored to the complex machinery of molecular-to-cellular systems, and performing simulations at three levels: molecular, subcellular (microphysiological), and cellular.


The program of ten weeks is organized into coursework, laboratory research, and presentations. Students will spend four weeks completing comprehensive course work that will cover the theoretical and computational aspects of computational biology as applied to investigating molecular-to-cellular systems dynamics. At the same time, students will select a research lab to conduct research for the duration of the program. The last week will be dedicated to student presentations. In addition to lectures, weekly seminars, journal clubs, and two workshops are planned (see table below).

(1) Coursework and Computer Laboratory Sessions (weeks 1 - 4): See Class Schedule for details

(2) Laboratory Research (weeks 1 - 9): See Mentor List for faculty participants

(3) Research Presentations (week 10): Oral and Written presentation of research







Welcome Meeting

First day


1 h



Weeks 1 – 4


3 h/day

3 h/day x 5 days/week x 4 weeks

Computer Lab Sessions

Weeks 1 – 4


3 h/session

Total 13 sessions (39 h)


Weeks 1 – 8


1 h/week

1 h/day x 1 day/week

Student-organized Journal Club

Weeks 2 – 8


2 h/week

1 h/day x 2 day/week

Research Project

Weeks 1 – 9

Part time in weeks 1-4, full-time in weeks 5-9

Career Workshop Week 9 Afternoon 2 h/week 2 h/day x 1 day

Student Presentations

Week 10


7 h

(20 + 10) min/student x
4-5 students/day x
3 days/week

Closing Meeting

Week 10


1 h


  Program Dates

The program for the year 2008 will be held from May 19 – July 25.


All program participants will be awarded a stipend that will cover modest living expenses. Undergraduates students will receive $320/week for 10 weeks (total $3200); graduate students will receive $500/week (total $5000).


          Free housing is provided at Duquesne University to all participants for the duration of the program.

  Application Deadline

All material, including a completed application form and an official transcript, should have been received by March 9, 2008.


All applicants must meet the following criteria:

(1)        Must be US citizens or permanent residents.

(2)       Have a GPA of 3.0 or higher.

(3)      Undergraduate applicants should either be entering their junior or senior year, and should have completed at least eight basic science/technical courses, preferably five in basic life sciences and physical sciences (biology, chemistry and physics) and three in mathematics/computer science or engineering).

(4)     Graduate applicants should (i) have applied or be accepted to a Graduate Program in biological sciences, physical science, computer science, mathematics or engineering, either newly admitted, or (ii) be entering their second year of graduate school.

  Number of Students Admitted

11 undergraduate and 2 graduate students will be admitted to the program in 2008. The BBSI welcomes and encourages applications from women, under-represented minorities (African-Americans, Hispanic-Americans, Native-Americans, Alaskan natives, Pacific-Islanders) and persons with disabilities.

  For more information, contact

Maureen Hernandez
Assistant Programs Coordinator
Department of Computational and Systems Biology
University of Pittsburgh School of Medicine
3052 Biomedical Science Tower 3
3501 Fifth Avenue
Pittsburgh, PA 15260

Tel: 412-648-
Fax: 412-648-3163