BBSI @ Pitt 2007 Schedule
(click
here for the 2007
Participants)
This page contains the coursework schedule, class and computer laboratory notes,
ethics groups, schedule, and presentations, and the
schedules of the seminar speakers for the 2007 program.
Hold mouse over lecture links for description of class notes files.
Coursework Schedule (pdf) (3073 BST-3) (Note Exceptions1, 2, 3, 4, 5, 6) 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, 5/21 | No class | No class | |
| Tue, 5/22 | Linear Algebra (RC)1 | Linear Algebra (RC)1 | Mathcad Primer & Lab Exercise (RC)1,2 | |
| Wed, 5/23 | Differential Equations (GBE) | Differential Equations (GBE) | ||
| Thu, 5/24 | Syllabus & Biochemistry Review I (JW) | Biochemistry Review II (JW) | Computing Primer (JB) | |
| Fri, 5/25 | Biochemistry Review III & Intro to Microarray Technology (JW) | Sequence Analysis (TB) | ||
| 2 | Mon, 5/28 | No class | No class | |
| Tue, 5/29 | Sequence Analysis (TB)3 | Sequence Analysis (TB)3 | ||
| Wed, 5/30 | High-Throughput Data Analysis (TB) | Probability & Statistics (HM) | (HM) | |
| Thu, 5/31 | Data Visualization (JS)4 | Data Visualization (JS)4 | (JS)5 | |
| Fri, 6/1 | Probability & Statistics (HM) | Molecular Visualization (JM) | ||
| 3 | Mon, 6/4 | Thermodynamics & Statistical Mechanics (HM) |
Molecular
Visualization (JM) AMBER-2005 CHARMM-1998 Chimera MMTSB VMD |
Lab Exercise(JM) |
| Tue, 6/5 | Thermodynamics & Statistical Mechanics (HM) |
Subcellular
Simulations (RC)1 PDE Notes Real-world Examples |
||
| Wed, 6/6 | Molecular Simulations (JM) | Cellular Simulations (RC)1 | Lab Exercise and Mathcad File (RC)1 | |
| Thu, 6/7 | Molecular Simulations (JM) | Molecular Simulations (JM) | (JM) | |
| Fri, 6/8 | Overview of Comp Struct Biol in the Post-Genomic Era (HM) and Sequence-Structure-Function Relations (HM) | Theory and Lab Exercise (EE) | ||
|
4 |
Mon, 6/11 | No class | No class | |
| Tue, 6/12 | Kinetics (JS)4 | Kinetics (JS)4 | ||
| Wed, 6/13 | Cellular Simulations (JS)4 | Cellular Simulations (JS)4 | (JS)5 | |
| Thu, 6/14 | Subcellular Simulations (GBE) | Cellular Simulations (GBE) | (GBE) | |
| Fri, 6/15 |
Dynamics of Living Systems Protein Structure and Dynamics (IB) |
Folding Kinetics & Molecular Dynamics Simulations (IB) | (IB) | |
| 5 | Thu, 6/21 |
Bioinformatics
Workshop (AC)6 presentation | links |
Bioinformatics Workshop (AC)6 |
1307 Eberly
Hall/JCC (computer lab), Eberly Hall
2End by 3:40PM to allow short break before seminar at 4:00PM
3Lesson this day will be taught in three 1-hour sessions:
9:45-10:45 am, 11:00 am-12:00 noon, and 1:30-2:30 pm
4Room 103, Pittsburgh Supercomputing Center, 300 South Craig
5Computer Training Center, Pittsburgh Supercomputing Center, 300
South Craig
6Lesson this day will be taught in two 1.5-hour sessions:
10:00-11:30am and 1:30-3:00pm
IB,
Ivet Bahar; TB, Takis Benos; AC, Ansuman Chattopadhyay; JB, Jason Boles; RC, Rob Coalson;
GBE, G. Bard Ermentrout; EE, Eran Eyal; JM, Jeffry Madura; HM, Hagai
Meirovitch; JS, Joel Stiles; JW, Judy Wieber
Seminar Schedule
| Number |
Date |
Speaker |
Affiliation |
Type |
| 1 | May 22 | Michael Grabe, PhD |
Assistant Professor, Biological
Sciences School of Arts & Sciences, University of Pittsburgh |
Research |
| 2 | May 29† | Rich Roberts, PhD |
Joint Research Director New England Biolabs, Beverly, Massachusetts |
Research + Career Discussion |
| 3 | June 5 | Ivan Maly, PhD |
Assistant Professor,
Computational Biology School of Medicine, University of Pittsburgh |
Research |
| 4 | June 19 | Megan Spence, PhD |
Assistant Professor, Chemistry School of Arts & Sciences, University of Pittsburgh |
Research |
| 5 | June 22** | Student Participation |
Ethics Forum for all REU
students at the University of Pittsburgh and Duquesne University |
Ethics |
| 6 | June 26 | Keith Boyce |
Associate Director,
Bioinformatics Immune Tolerance Network Pittsburgh, PA |
Career |
| 7 | June 29* | Doug Fox, PhD |
Director, Gaussian, Inc. Director of Technical Support Pittsburgh, PA |
Career |
| 8 | July 10 | John Vries, MD |
Associate Professor,
Computational Biology School of Medicine, University of Pittsburgh |
Research |
| 9 | July 17 | Xiang-Qun (Sean) Xie, PhD, MBA |
Professor,
Pharmaceutical Sciences |
Research |
| 10 | July 19†† | Student Participation |
Career Workshop for BBSI @ Pitt
students (panel discussion and Q&A with individuals representing a variety of career paths) |
Career |
†Senior Vice Chancellor’s
Laureate Lecture Series, 3:30 pm, Scaife Hall, Auditorium 6
*2 pm-3 pm (rescheduled from June 12)
**Friday, June 22, 9 am-1:30 pm,
William Pitt Union,
Benedum Hall, and
Sennott Square
††3 pm-5 pm, 6014 BST3
Journal Club Schedule
(pdf) (Thursday, 4-5 pm, 3073 BST-3) top| Number | Date |
Student
Presenter (Faculty Mentor) |
Paper Title |
| 1 | May 31 |
Casey Overby (Sanjeev Shroff) |
Pressure-calcium
relationships in perfused mouse hearts, MacGowan et al., Am J Physiol
Heart Circ Physiol 290: H2614–H2624, 2006 (paper | presentation) |
| 2 | May 31 |
Manjula Kasoji (Bino John) |
Regulatory
circuit of human microRNA biogenesis. Lee et al., PLoS
Computational Biology, doi:10.1371/journal.pcbi.0030067.eor (paper | presentation) |
| 3 | May 31 |
Ankur Agarwal (Takis Benos) |
DNA Familial
Binding Profiles Made Easy: Comparison of Various Motif Alignment
and Clustering Strategies, Mahony et al., PLoS Comput Biol.
2007 Mar 30;3(3):e61. Epub 2007 Feb 15. (paper | presentation) |
| 4 | Jun 8 |
Alex Heitman (Jeffry Madura) |
Electrostatics of
nanosystems: Application to microtubules and the ribosome Nathan A.
Baker et al., PNAS, 98, 10037-10041 (2001).
doi:10.1073/pnas.181342398 (paper | presentation) |
| 5 | Jun 8 |
Fred Doamekpor (G. Bard Ermentrout) |
Initiation,
Propagation, and Termination of Epileptiform Activity in Rodent
Neocortex In Vitro Involve Distinct Mechanisms, David Pinto et al.,
The Journal of Neuroscience, 25(36):8131– 8140 (2005). (paper | presentation) |
| 6 | Jun 8 |
Kia Montgomery (Billy Day) |
Total Synthesis and Biological Evaluation of C16 Analogs of (–)-Dictyostatin,
Won-Hyuk Jung et al., Journal of Medicinal Chemistry, 50
(2007), in press. (paper | presentation) |
| 7 | Jun 14 |
Neil Parikh (G. Bard Ermentrout) |
A reduced mathematical
model of the acute inflammatory response: I. Derivation of model and
analysis of anti-inflammation (2006) Angela Reynolds et al.,
Journal of Theoretical Biology, 242, 220–236. (paper | presentation) |
| 8 | Jun 14 |
Andrej Savol (Carlos Camacho) |
Anchor residues in
protein–protein interactions, Deepa Rajamani et al., PNAS,
101, 11287–11292 (2004). doi:10.1073/pnas.0401942101 (paper | presentation) |
| 9 | Jun 14 |
Rusty Stough (Jeffry Madura) |
Solvent and mutation
effects on the nucleation of amyloid {beta}-protein folding (2005)
Luis Cruz et al., PNAS, 102, 18258-18263.
doi:10.1073/pnas.0509276102. (paper | presentation) |
| 10 | Jun 28 |
Akrita Bhatnagar (Joel Stiles) |
The exocytotic
event in chromaffin cells revealed by patch amperometry (1997) A.
Albillos et al., Nature, 389, 509-12. (paper | presentation) |
| 11 | Jun 28 |
Alissa Verone (Joel Stiles) |
High calcium concentrations shift
the mode of exocytosis to the kiss-and-run mechanism (1999) Eva Ales et al.,
Nat Cell Biol. 1, 40-44. (paper | presentation) |
| 12 | Jun 28 |
Rahul Kumar (Michael Sacks) |
Cyclic flexure and laminar flow
synergistically accelerate mesenchymal stem cell-mediated engineered tissue
formation: Implications for engineered heart valve tissues (2006) George C.
Engelmayr, Jr., et al., Biomaterials 27, 6083–6095. (paper | presentation) |
| 13 | Jul 5 |
Pavol Genzor (Martin Schmidt) |
Mark Johnston (1999)
Feasting, fasting and fermenting: glucose sensing in yeast and other cells,
Trends in Genetics 15, 29-33. (paper | presentation) |
| 14 | Jul 5 |
Lisa Gabor (Judith Klein-Seetharaman) |
Yanjun Qi, Ziv Bar-Joseph, and
Judith Klein-Seetharaman (2006) Evaluation of Different Biological Data and
Computational Classification Methods for Use in Protein Interaction Prediction,
PROTEINS: Structure, Function, and Bioinformatics 63:490–500 (paper | presentation) |
| 15 | Jul 5 |
Kamaldeep Singh (Judith Klein-Seetharaman) |
Harold J Drabkin,
Christopher Hollenbeck, David P Hill and Judith A Blake (2005) Ontological
visualization of protein-protein interactions, BMC Bioinformatics, 6:29
doi:10.1186/1471-2105-6-29. (paper | presentation) |
| 16 | Jul 12 |
Brook Chernet (Immune Tolerance Network) |
William R Pearson and Michael
L Sierk (2005) The limits of protein sequence comparison?, Current Opinion in
Structural Biology 20, 15:1–7. (paper | presentation) |