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 |
- |
| Orientation to Lab and Project |
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 |
When not engaged in educational activities |
||
| Career Workshop | Week 9 | Afternoon | 2 h/week | 1 h/day x 2 day/week |
|
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 Exceptions) top
|
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 | No class | Class at 12:30-3:45 | (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) | Sequence Analysis (TB) | ||
| Wed, 6/17 | Subcellular Simulations(RC)1 | Thermodynamics & Statistical Mechanics (HM) | (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 accommodate 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
Seminar Schedule
| Number |
Date |
Speaker |
Affiliation |
Type |
| 1 | Jun 3† | Mahadev Satyanarayanan, PhD | Experimental Computer Scientist, Carnegie Mellon University |
Career |
| 2 | Jun 16 | Michael Grabe, PhD |
Assistant Professor, Department of Biological Sciences, University of Pittsburgh |
Research |
| 3 | Jun 18* | Hanna Salman, PhD |
Assistant Professor, Department of Physics and Astronomy, University of Pittsburgh |
Research |
| 4 | Jun 23 | Dan Zuckerman, PhD |
Associate Professor, Department of Computational and Systems Biology, University of Pittsburgh |
Research |
| 5 | Jun 30 | Tim Lezon, PhD |
Postdoctoral Associate, Department of Computational and Systems Biology, University of Pittsburgh |
Research |
| 6 | Jul 7 | Gabriela Mustata, PhD |
PharmacoInformatics Specialist, Department of Computational and Systems Biology, University of Pittsburgh |
Career |
| 7 | Jul 14 | Jason Berberich, PhD |
Senior Research Engineer, ICx Technologies |
Career |
| 8 | Jul 21 | Elodie Ghedin, PhD |
Assistant Professor, Center for Vaccine Research, University of Pittsburgh |
Research |
† Wed, June 3, 9:30 am-10:30 am
* 1:30pm-2:30pm
Journal Club Schedule
(pdf) (Thursday, 4-5 pm, 3073 BST-3) top| Number | Date |
Student
Presenter (Faculty Mentor) |
Paper Title |
| 1 | 6/4 | Eunice Yi (Michael Sacks) |
Residual strains in conduit arteries |
| 2 | 6/4 | Chad Miller (TBD) |
How Dopamine Transporter Interacts with Dopamine: Insights from Molecular Modeling and Simulation |
| 3 | 6/4 | Theresa Downey (Jeff Madura) |
A Neutral, Water-Soluble, α-Helical Peptide: The Effect of Ionic Strength on Helix-Coil Equilibrium |
| 4 | 6/11 | Victor Rusu (Shlomo Taasan) |
Models in Epidemiology |
| 5 | 6/11 | Lauren Anderson (Michael Sacks) |
Tissue-to-cellular level deformation coupling in cell micro-integrated elastomeric scaffolds |
| 6 | 6/11 | Kathryn Myer (Jeff Madura) |
|
| 7 | 6/25 | Minjal Pancholi (Joel Stiles) |
|
| 8 | 6/25 | Amy Scarbrough (Michael Grabe) |
The Crystal Structure of a Sodium Galactose Transporter Reveals Mechanistic Insights into Na+/Sugar Symport |
| 9 | 7/2 | Yao Sun (Jim Faeder) |
|
| 10 | 7/2 | Geet Garg | |
| 11 | 7/2 | Damilola Adepegba (Billy Day) |
Chemical Library Screens Targeting an HIV-1 Nef/Host Cell Kinase Complex Identify Novel Anti-retroviral Compounds |
| 12 | 7/9 | Hannah Watkins (Michael Sacks) |
|
| 13 | 7/9 | Yagmur Muftuoglu (Michael Sacks) |
|
| 14 | 7/16 | Logan Woodall (Pei Tang) |
Anesthetic Modulation of Protein Dynamics: Insight from an NMR Study |
| 15 | 7/16 | Naved Siddiqui | Protein complex identification by supervised graph local clustering |
| 16 | 7/16 | Laura Gump (Michael Sacks) |
|
| 17 | 7/23 | Devashish Ghosh | |
| 18 | 7/23 | Lorane Psalmond (G. Bard Ermentrout) |
Glomerulus-Specific, Long-Latency Activity in the Olfactory Bulb Granule Cell Network |