BBSI Classes

During the first six weeks of the ten-week BBSI program, students will take 5 x 1.5 hours per week lectures from the faculty, and 11 computer lab sessions of 3 hours each. At the end of each lecture class, problems will be assigned to students that will strengthen fundamental concepts. Students will work on these assignments and familiarize themselves with computational and mathematical tools used in computational biology during the laboratory sessions under the supervision of TAs.  These sessions will ensure individualized attention, if and when needed. Afternoons are reserved for students to complete assignments, visit mentors’ laboratories to discuss potential research projects, peruse the literature to acquaint themselves with current research, and attend the weekly BBSI seminars and Journal Clubs, and other seminars of interest.
 



Students of the 2003 program in the computer lab session.
Each student had a specially configured desktop for use during these sessions

The table below gives a summary of the lectures, their duration and instructors. Click on the topic title for details about the topics and related laboratory sessions. Hold mouse over lecture links for description of class notes files. To print this schedule, click here.

Review of Mathematical and Biochemistry Concepts
> Differential Equations
> Linear Algebra
> Biochemistry Review I
 > Biochemistry Review II
 > Biochemistry Review III
 > Probability and Statistics

Bioinformatics
 > Sequence Analysis
> High-Throughput Data Analysis

Computer Visualization
 > Data Visualization
> Molecular Visualization

Fundamentals of Computational Biology
> Thermodynamics and Statistical Mechanics
> Protein Folding
> Kinetics: Theory and Methods

Multi-scale Simulations
> Molecular Simulations
> Subcellular Simulations
> Cellular Simulations

 

Coursework Schedule (pdf) (3073 BST-3) (Note Exceptions1, 2, 3, 4 )

 

Week

Day, Date

 Session I
9-10.30 am		 Session II
10.45 am-12.15 pm		 Lab
1.30-4.30 pm

1

 Mon, 5/25 No class No class  
Tue, 5/26 No class No class  
Wed, 5/27 Protein Structure and Dynamics I (IB) Computing Matlab (CHC)  
Thu, 5/28 Overview of Comp Struct Biol in the Post-Genomic Era (TL) Protein Structure and Dynamics II (GM)  
Fri, 5/29 Computing Primer (JB) Sequence-Structure-Function Relations (CC)  
2 Mon, 6/1 Molecular Visualization (JM) Molecular Visualization (JM) (JM)
Tue, 6/2 Linear Algebra (RC)1 Linear Algebra (RC)1 (RC)1
Wed, 6/3 Seminar (9:30-10:30 SN) Differential Equations (GBE) Differential Equations (GBE)
Thu, 6/4 Subcellular Simulations (GBE) Cellular Simulations (GBE) (GBE)4
Fri, 6/5 Molecular Simulations (JM) Molecular Simulations (JM)  (JM)
3 Mon, 6/8 Data Visulaization (JS)2 Data Visualization (JS)2 (JS)3
Tue, 6/9 Rule-Based Modeling (JF) Molecular Simulations (JM) (JF)
Wed, 6/10 Rule-Based Modeling (JF) Cellular Simulations (JS)2 (JS)3
Thu, 6/11 Cellular Simulations (JS)2 Kinetics (JS)2  
Fri, 6/12 Kinetics (JS)2 Probability & Statistics (HM) (JS)3

4

 Mon, 6/15 Probability & Statistics (HM) Cellular Simulations(RC)1 (HM)
Tue, 6/16 Thermodynamics & Statistical Mechanics (HM) Thermodynamics & Statistical Mechanics (HM)  
Wed, 6/17 Subcellular Simulations(RC)1 Sequence Analysis (TB) (RC)1
Thu, 6/18 High-Throughput Data Analysis (TB) Sequence Analysis (TB)  
Fri, 6/19 Sequence Analysis (TB) No class  

1206 Eberly Hall/JCC (computer lab), Eberly Hall
2Room 103, Pittsburgh Supercomputing Center, 300 South Craig
     3Computer Training Center, Pittsburgh Supercomputing Center, 300 South Craig
   4End by 3:45 to accomodate Seminar and Journal Club Schedules

IB, Ivet Bahar; TB, Takis Benos; JB, Jason Boles; CC, Carlos Camacho; CHC, Chakra Chennubhotla; RC, Rob Coalson; GBE, G. Bard
GM, Gabriela Mustata; Ermentrout; JF, Jim Faeder; TL, Tim Lezon; JM, Jeffrey Madura; HM, Hagai Meirovitch; JS, Joel Stiles