The following schedules are available from this page. Click the pdf link for a
printable schedule.
(i) Program Schedule (html, pdf)
(ii) Coursework Schedule (html, pdf)
(iii) Weekly Schedule (pdf)
(iv) Seminar Schedule (html, pdf)
(v) Ethics Forum Schedule (pdf)
(vi) Journal Club Schedule (html, pdf)
(vii) Student Presentations Schedule (pdf)
Program Schedule (pdf)
|
Activity |
Dates |
Time |
Duration |
Frequency |
|
Welcome Meeting |
First day |
Afternoon |
1 h |
- |
| Lab Meetings/Orientation |
Week 1 |
TBD |
TBD | TBD |
|
Lectures |
Weeks 2 5 |
Morning |
3 h/day |
3 h/day x 5 days/week x 4 weeks |
|
Computer Lab Sessions |
Weeks 2 5 |
Afternoon |
3 h/session |
Total 13 sessions (39 h) |
|
Seminars |
Weeks 2 9 |
Afternoon |
1 h/week |
1 h/day x 1 day/week |
|
Student-organized Journal Club |
Weeks 2 9 |
Afternoon |
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 |
Afternoon |
7 h |
(20 + 10) min/student x
|
|
Closing Meeting |
Week 10 |
Morning |
1 h |
- |
Coursework Schedule (pdf) (3073 BST-3) (Note Exceptions1, 2, 3, 4) top
|
Week |
Day, Date |
Session I 9-10.30 am |
Session II 10.45 am-12.15 pm |
Lab 1.30-4.30 pm |
|
2 |
Mon, 5/26 | No class | No class | |
| Tue, 5/27 | Biochemistry Review I (JW) | Overview of Comp Struct Biol in the Post-Genomic Era (TL) | ||
| Wed, 5/28 | Biochemistry Review II (JW) | Probability & Statistics (HM) | Computing Primer (JB) | |
| Thu, 5/29 |
Biochemistry Review III Intro to Microarrays (JW) |
Probability & Statistics (HM) | (HM)4 | |
| Fri, 5/30 | Linear Algebra (RC)1 | Linear Algebra (RC)1 |
Mathcad Primer (RC)1 |
|
| 3 | Mon, 6/2 | Molecular Visualization (JM) |
Molecular Visualization (JM) VMD paper Chimera paper |
(JM) |
| Tue, 6/3 | Differential Equations (GBE) | Differential Equations (GBE) | ||
| Wed, 6/4 | Subcellular Simulations (GBE) | Cellular Simulations (GBE) | (GBE) | |
| Thu, 6/5 | Molecular Simulations (JM) | Molecular Simulations (JM) | ||
| Fri, 6/6 | Data Visualization (JS)2 | Data Visualization (JS)2 | (JS)3 | |
| 4 | Mon, 6/9 | Sequence Analysis (TB) | Molecular Simulations (JM) | (JM) |
| Tue, 6/10 | Sequence Analysis (TB) | Sequence Analysis (TB) | ||
| Wed, 6/11 | Rule-Based Modeling (JF) | Thermodynamics & Statistical Mechanics (HM) | ||
| Thu, 6/12 | Rule-Based Modeling (JF) | Thermodynamics & Statistical Mechanics (HM) | (JF)4 | |
| Fri, 6/13 | Kinetics (JS)2 | Kinetics (JS)2 | (JS)3 | |
|
5 |
Mon, 6/16 | Cellular Simulations (JS)2 | Cellular Simulations (JS)2 | (JS)3 |
| Tue, 6/17 | High-Throughput Data Analysis (TB) | Sequence-Structure-Function Relations (CC) | ||
| Wed, 6/18 | Subcellular Simulations (RC)1 | Cellular Simulations (RC)1 | (RC)1 | |
| Thu, 6/19 |
Protein Structure and Dynamics Protein Modeling (AM) |
No class | ||
| Fri, 6/20 | No class (Ethics Forum) | No class (Ethics Forum) |
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 accommodate Seminar and Journal Club schedules
TB, Takis Benos; JB, Jason Boles;
CC, Carlos Camacho; RC, Rob Coalson; GBE, G. Bard Ermentrout; JF, Jim Faeder;
TL, Tim Lezon; JM, Jeffry Madura; AM, Artem Mamonov; HM, Hagai
Meirovitch; JS, Joel Stiles; JW, Judy Wieber
|
|
Seminar Schedule
| Number |
Date |
Speaker |
Affiliation |
Type |
| 1 | 5/20 | Greg Hood |
Neuroscience Specialist, Pittsburgh Supercomputing Center |
Research |
| 2 | 6/3 | Gilles Clermont |
Assistant Professor, Department of Critical Care Medicine, University of Pittsburgh |
Research |
| 3 | 6/5* | Maria Kurnikova |
Assistant Professor, Department of Chemistry, Carnegie Mellon University |
Research |
| 4 | 6/10 | Jared Knickelbein |
Graduate Student Researcher, School of Medicine, University of Pittsburgh |
Career |
| 5 | 6/17 | Marta Bueno |
Research Associate, School of Medicine, University of Pittsburgh |
Research |
| 6 | 6/20 | Student Participation | Ethics Forum for all REU students at the University of Pittsburgh and Duquesne University | Ethics |
| 7 | 6/24 | G. Elisabeta (Liz) Marai |
Assistant Professor, Department of Computer Science, University of Pittsburgh |
Research |
| 8 | 6/27 | Chakra Chennubhotla |
Assistant Professor,
Computational Biology, School of Medicine, University of Pittsburgh |
Research |
| 9 | 7/1 | Gabriela Mustata |
Pharmacoinformatics Specialist,
Computational Biology, School of Medicine, University of Pittsburgh |
Career |
| 10 | 7/8 | Ansuman Chattopadhyay |
Head of Molecular Biology
Information Service, University of Pittsburgh |
Career + Bioinformatics Workshop |
| 11 | 7/11 | Markus Dittrich |
Postdoctoral Researcher, Center for Quantitative Biological Stimulation, Pittsburgh Supercomputing Center |
Research |
| 12 | 7/15** | Student Participation | Career Workshop for BBSI @ Pitt students (panel discussion and Q&A with individuals representing a variety of career paths) | Career |
Friday, June 20, 9 am-1:30 pm,
William Pitt Union,
Benedum Hall, and
Sennott Square
*2 pm - 3 pm, 3073
BST3
**3 pm- 5 pm, 6014
BST3
Friday, 11 am-12 pm, 3073
BST3
1:30 pm - 4 pm, 3073
BST3
Journal Club Schedule
(pdf) (Thursday, 4-5 pm, 3073 BST-3) top| Number | Date |
Student
Presenter (Faculty Mentor) |
Paper Title |
| 1 | 5/29 |
Jessica Wehner (Vanathi Gopalakrishnan) |
Comparison of probabilistic combination methods for protein secondary structure prediction (2004) Y. Liu et al., Bioinformatics, 20, 30993107 |
| 2 | 5/29 |
Edwin
Kamau (Gabriela Mustata) |
Induced-fit or preexisting equilibrium dynamics? Lessons from protein crystallography and MD simulations on acetylcholinesterase and implications for structure-based drug design (2008) Y. Xu, et al. Protein Sci. 17, 601-605 |
| 3 | 6/5 |
Kathryn Kinzler (G. Bard Ermentrout) |
From nonlinearity to optimality: pheromone trail foraging by ants (2003) D.J.T. Sumpter and M. Beekman, Animal Behaviour, 66, 273280 |
| 4 | 6/5 |
Anita
Anburajan (John Rosenberg) |
Statistical methods for the objective design of screening procedures for macromolecular crystallization (2000) D. Hennessy et al., Acta Cryst. D56, 817827 |
| 5 | 6/5 |
Brian
Chen (Hugh Nicholas) |
Genome Landscapes and Bacteriophage Codon Usage (2008) J.B. Lucks et al., PLoS Comput Biol 4, e1000001 |
| 6 | 6/12 |
Davis
Buenger (Jim Faeder) |
Abstract interpretation of cellular signaling networks (2008) V. Danos et al. Lecture Notes in Computer Science, 4905, 83-97 |
| 7 | 6/12 |
Abdallah Bukari (Jeffry Madura) |
The Structure of the Potassium Channel: Molecular Basis of K+ Conduction and Selectivity, D.A. Doyle, et al. (1998) Science 280, 69-77 |
| 8 | 6/12 |
Arti
Khana (Takis Benos) |
Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution (2005) E. Ghedin et al., Nature, 437, 1162-1166 |
| 9 | 6/19 |
Jessica Wagner (Silvia Wognum and Michael Sacks) |
Contribution of the extracellular matrix to the viscoelastic behavior of the urinary bladder wall (2007) J. Nagatomi et al., Biomechan Model Mechanobiol, (Online) 1617-7940 |
| 10 | 6/19 |
William Glassford (Chakra Chennubhotla) |
Markov propagation of allosteric effects in biomolecular systems: application to GroELGroES (2006) C. Chennubhotla and I. Bahar, Molecular Systems Biology, 2, 36 |
| 11 | 6/26 |
Anna
Kirk (Carlos Camacho) |
Rajamani D, Thiel S, Vajda S, Camacho C. (2004) Anchor residues in protein-protein interactions. PNAS 101, 11287- 11292 |
| 12 | 6/26 |
John
Schmidt (Judith Klein-Seetharaman) |
|
| 13 | 6/26 |
Anthony Sosso (Jeffry Madura) |
|
| 14 | 7/10 |
Jacqueline Barnes (Joel Stiles) |
|
| 15 | 7/10 |
Nilgun
Yilmaz (Jim Faeder) |
|
| 16 | 7/10 |
Shiksha Mantri (Bino John) |
|
| 17 | 7/17 |
Yan Gu (Ivet Bahar) |
|
| 18 | 7/17 |
Arif
Harmanci (Judith Klein-Seetharaman, Chakra Chennubhotla) |
|
| 19 | 7/17 |
Matthew Rockar (Jeffry Madura) |