2016 AMS-536 Spring
From Rizzo_Lab
| Instructor | Dr. Robert C. Rizzo [631-632-9340, robert.rizzo@stonybrook.edu] |
|---|---|
| Teaching Assistant | Courtney Singleton [631-632-8519, Courtney.Singleton@stonybrookmedicine.edu] and Yuchen Zhou [631-632-8519, chris.yuchen.zhou@gmail.com] |
| Course No. | AMS-536 / CHE-536 |
| Location/Time | Math Tower, Room S235 (COMPUTER LAB next to SINC site), Mon/Wed 2:30PM - 3:50PM |
| Office Hours | Anytime or by appointment, Math Tower, Room 3-129, Dept. of Applied Math & Statistics |
| Acknowledgments | The AMS-536 instructors would like to thank: (1) Chemical Computing Group at http://www.chemcomp.com for generously providing MOE software teaching licenses |
Project Information
Student Project Proposal OHARE Sheet
Oral Presentation Guidlines: These meetings should be formal and your chance to tell a complete story. Talks should be presented in PPT format and be 30 minutes long. The purpose of your talks is for you to clearly and concisely present your overall progress to date including appropriate background material and interpretation of your results. Talks should be arranged in the following order:
- Introduction/Background (include biological relevance)
- Specifics of Your System
- Computational Details (theory)
- Computational Details (system setup)
- Results and Discussion (include a critical interpretation of your results)
- Conclusions
- Future
- Acknowledgments
Final Report Guidelines and Example Final Papers
Tutorials, Software Links, and Other Relevant Class Information
- Rizzo_Lab_Information_and_Tutorials
- Cheat Sheet: Unix, Vi, C_Shell_Scripting
Schedule
- Each participant please update the Wiki as required with the title of your talk.
- Please note that a doctors excuse will be required if you miss your scheduled oral presentation date because of illness.
| Date | Participant | Talk |
| SECTION 1: COMPUTING INFRASTRUCTURE AND TOOLS | ||
| 2016.01.25 Mon | First Day of Class Group Study |
Mathlab/LI-RED accounts setup unix / vim / csh introduction Discuss presentations and final projects |
| 2016.01.27 Wed | Group Study | Mathlab/LI-RED accounts setup unix / vim / csh introduction Visualization demo's |
| 2016.02.01 Mon | Group Study | Mathlab/LI-RED accounts setup unix / vim / csh introduction Visualization demo's |
| 2016.02.03 Wed | Group Study | Confirm accounts Set up ssh connection on personal laptops |
| 2016.02.08 Mon | Group Study | Unix / Vim Challenges |
| 2016.02.10 Wed | Group Study | LI-RED queuing system Chimera demo (Courtney) VMD demo (Yuchen) Class Project Expectation: Ethics in Writing (Rob) |
| SECTION 2: DOCK TUTORIAL ( see Joe Allen slides ) | ||
| 2016.02.15 Mon | Draft Student Project Proposal OHARE Sheet Due Group Study |
Tutorials: DOCK individual project discussion |
| 2016.02.17 Wed | Group Study | Tutorials: DOCK individual project discussion |
| 2016.02.22 Mon | Group Study | Tutorials: DOCK individual project discussion |
| 2016.02.24 Wed | Group Study | Tutorials: DOCK individual project discussion |
| 2016.02.29 Mon | Final Student Project Proposal OHARE Sheet Due Group Study |
Tutorials: DOCK individual project discussion |
| 2016.03.02 Wed | Group Study | Tutorials: DOCK individual project discussion |
| 2016.03.07 Mon | Group Study | Tutorials: DOCK individual project discussion |
| 2016.03.09 Wed | Group Study | Tutorials: DOCK finalize class wiki |
| 2016.03.14 Mon | Spring Recess | Spring Recess |
| 2016.03.16 Wed | Spring Recess | Spring Recess |
| SECTION 3: AMBER TUTORIAL ( see Lingling Jiang slides ) | ||
| 2016.03.21 Mon | Group Study | Tutorials: AMBER individual project discussion |
| 2016.03.23 Wed | Group Study | Tutorials: AMBER individual project discussion |
| 2016.03.28 Mon | Group Study | Tutorials: AMBER individual project discussion |
| 2016.03.30 Wed | Group Study | Tutorials: AMBER individual project discussion |
| 2016.04.04 Mon | Group Study | Tutorials: AMBER individual project discussion |
| 2016.04.06 Wed | Group Study | Tutorials: AMBER finalize class wiki |
| SECTION 4: PROJECT PRESENTATIONS | ||
| 2016.04.11 Mon | Maffucci, Katie and Prentis, Lauren Draft Paper Due |
Oral Presentations |
| 2016.04.13 Wed | Lyczek, Agatha and Awwa, Monaf | Oral Presentations |
| 2016.04.18 Mon | Sanchez Reyes, Omar and Jiang, Belei | Oral Presentations |
| 2016.04.20 Wed | She, Yaping and Guo, Haoyue | Oral Presentations |
| 2016.04.25 Mon | Maffucci, Katie and Prentis, Lauren Draft Paper Due |
Oral Presentations |
| 2016.04.27 Wed | Lyczek, Agatha and Awwa, Monaf | Oral Presentations |
| 2016.05.02 Mon | Sanchez Reyes, Omar and Jiang, Belei | Oral Presentations |
| 2016.05.04 Wed | Last Day Class She, Yaping and Guo, Haoyue |
Oral Presentations |
| 2016.05.05 Thur | Final Written Report due by 1PM today. |
Give hard copy printout to Robert Rizzo (Math Tower room 1-111) or Yuchen Zhou/Courtney Singleton (Math Tower room 3-129) and email electronic copy to rizzorc@gmail.com |
