Difference between revisions of "2016 AMS-536 Spring"
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| 2016.02.10 Wed || Group Study || LI-RED queuing system <br> Chimera demo (Jiaye) <br> VMD demo (Brian) <br> Class Project Expectation: Ethics in Writing (Rob) | | 2016.02.10 Wed || Group Study || LI-RED queuing system <br> Chimera demo (Jiaye) <br> VMD demo (Brian) <br> Class Project Expectation: Ethics in Writing (Rob) | ||
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| − | | || '''SECTION 2: DOCK TUTORIAL''' ( [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2013.02.18.ams536.pdf see Joe Allen | + | | || '''SECTION 2: DOCK TUTORIAL''' ( [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2013.02.18.ams536.pdf see Joe Allen slides] ) || |
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| 2016.02.15 Mon || Group Study || Tutorials: DOCK <br> individual project discussion | | 2016.02.15 Mon || Group Study || Tutorials: DOCK <br> individual project discussion | ||
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| 2016.03.02 Wed || Group Study || Tutorials: DOCK <br> finalize class wiki tutorial | | 2016.03.02 Wed || Group Study || Tutorials: DOCK <br> finalize class wiki tutorial | ||
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| − | | || '''SECTION 3: AMBER TUTORIAL''' ( [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2012.02.29.ams536.lingling.amber_intro.pdf Lingling Jiang | + | | || '''SECTION 3: AMBER TUTORIAL''' ( [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2012.02.29.ams536.lingling.amber_intro.pdf see Lingling Jiang slides] ) || |
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| − | | 2016.03.07 Mon || Group Study | + | | 2016.03.07 Mon || Group Study || Tutorials: AMBER <br> individual project discussion |
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| 2016.03.09 Wed || '''Final Student Project Proposal OHARE Sheet Due''' <br> Group Study || Tutorials: AMBER <br> individual project discussion | | 2016.03.09 Wed || '''Final Student Project Proposal OHARE Sheet Due''' <br> Group Study || Tutorials: AMBER <br> individual project discussion | ||
Revision as of 10:36, 14 January 2016
| Instructor | Dr. Robert C. Rizzo [631-632-9340, robert.rizzo@stonybrook.edu] |
|---|---|
| Teaching Assistant | Brian Fochtman [631-632-8519, brianfochtman@gmail.com] and Jiaye Guo [631-632-8519, jguokelly@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 (Jiaye) VMD demo (Brian) Class Project Expectation: Ethics in Writing (Rob) |
| SECTION 2: DOCK TUTORIAL ( see Joe Allen slides ) | ||
| 2016.02.15 Mon | 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 | Draft Student Project Proposal OHARE Sheet Due Group Study |
Tutorials: DOCK individual project discussion |
| 2016.02.29 Mon | Group Study | Tutorials: DOCK individual project discussion |
| 2016.03.02 Wed | Group Study | Tutorials: DOCK finalize class wiki tutorial |
| SECTION 3: AMBER TUTORIAL ( see Lingling Jiang slides ) | ||
| 2016.03.07 Mon | Group Study | Tutorials: AMBER individual project discussion |
| 2016.03.09 Wed | Final Student Project Proposal OHARE Sheet Due Group Study |
Tutorials: AMBER individual project discussion |
| 2016.03.14 Mon | Spring Recess | Spring Recess |
| 2016.03.16 Wed | Spring Recess | Spring Recess |
| 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 finalize class wiki tutorial |
| SECTION 4: PROJECT PRESENTATIONS | ||
| 2016.03.30 Mon | Last, First and Last, First | Oral Presentations: Project Proposal |
| 2016.04.04 Wed | Shanbhoque, Prajna and Singleton, Courtney | Oral Presentations: Project Proposal |
| 2016.04.06 Mon | Yin, Xingyu and Zhang, Beibei | Oral Presentations: Project Proposal |
| 2016.04.11 Wed | Belfon, Kellon and Chiappone, Sam | Oral Presentations: Project Proposal |
| 2016.04.13 Mon | Jones, George and Liu, Cong | Oral Presentations: Project Proposal |
| 2016.04.15 Wed | Preliminary Written Report Due Tian, Chuan and Cortes, Michael |
Oral Presentations: Project Proposal |
| 2016.04.20 Mon | Elmes, Matthew and Shanbhoque, Prajna | Oral Presentations: Progress Report |
| 2016.04.22 Wed | Belfon, Kellon and Yin, Xingyu | Oral Presentations: Progress Report |
| 2016.04.27 Mon | Jiaye Guo | Virtual Screening Post-processing |
| 2016.04.29 Wed | Zhang, Beibei and Singleton, Courtney | Oral Presentations: Progress Report |
| 2016.05.04 Mon | Chiappone, Sam and Jones, George | Oral Presentations: Progress Report |
| 2016.05.06 Wed | Liu, Cong and Tian, Chuan | Oral Presentations: Progress Report |
| 2016.05.13 Wed | Final Written Report due by 5PM today. Late papers will not be accepted. See above for sample reports and detailed guidelines. | Hand hard copy to Brian Fochtman or Jiaye Guo (Math Tower room 3-129) and email electronic copy to rizzorc@gmail.com |
