Difference between revisions of "2013 AMS-536 Spring"
From Rizzo_Lab
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! style="width:10%" | '''Instructor''' | ! style="width:10%" | '''Instructor''' | ||
| Dr. William J. Allen [631-632-8519, william.allen@stonybrook.edu] | | Dr. William J. Allen [631-632-8519, william.allen@stonybrook.edu] | ||
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|- | |- | ||
| '''Course No.''' || AMS-536 / CHE-536 | | '''Course No.''' || AMS-536 / CHE-536 | ||
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'''Project Approval Sheet''' | '''Project Approval Sheet''' | ||
| − | *[http:// | + | *[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/projectA.student.info.doc project.student.info.doc] |
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'''Final Report Guidelines and Example Final Papers''' | '''Final Report Guidelines and Example Final Papers''' | ||
| − | *[http:// | + | *[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/project.guidelines.pdf project.guidelines.pdf] |
| − | *[http:// | + | *[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/project.example.dGhyd.pdf project.example.dGhyd.pdf] |
| − | *[http:// | + | *[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/project.example.MMPS.pdf project.example.MMPS.pdf] |
<br> | <br> | ||
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| 2013.02.13 || Group Study || Visualization/analysis software <br> VMD, Chimera, and MOE | | 2013.02.13 || Group Study || Visualization/analysis software <br> VMD, Chimera, and MOE | ||
|- | |- | ||
| − | | 2013.02.18 || Group Study || Tutorials: DOCK <br> individual project discussion [http:// | + | | 2013.02.18 || Group Study || Tutorials: DOCK <br> individual project discussion [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2013.02.18.ams536.pdf Allen, W.] |
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| 2013.02.20 || Group Study || Tutorials: DOCK <br> individual project discussion | | 2013.02.20 || Group Study || Tutorials: DOCK <br> individual project discussion | ||
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| 2013.03.04 || Group Study || Tutorials: DOCK <br> wiki editing | | 2013.03.04 || Group Study || Tutorials: DOCK <br> wiki editing | ||
|- | |- | ||
| − | | 2013.03.06 || Group Study || Tutorials: AMBER <br> individual project discussion [http:// | + | | 2013.03.06 || Group Study || Tutorials: AMBER <br> individual project discussion [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2012.02.29.ams536.lingling.amber_intro.pdf Jiang L.] |
|- | |- | ||
| 2013.03.11 || Group Study || Tutorials: AMBER <br> individual project discussion | | 2013.03.11 || Group Study || Tutorials: AMBER <br> individual project discussion | ||
Latest revision as of 09:18, 7 August 2013
| Instructor | Dr. William J. Allen [631-632-8519, william.allen@stonybrook.edu] |
|---|---|
| Course No. | AMS-536 / CHE-536 |
| Location/Time | Math Tower, Room S235 (COMPUTER LAB next to SINC site), Mon/Wed 2:20PM - 3:40PM |
| Office Hours | Anytime or by appointment, Math Tower, Room 3-129, Dept. of Applied Math & Statistics |
| Teaching Assistant | Yuchen Zhou, Math Tower, Room 3-129, Dept. of Applied Math & Statistics |
Project Information
Project Approval 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 |
| 2013.01.28 | First Day of Class and Organizational Meeting Group Study |
Mathlab account setup Discuss research paper and presentations handouts for unix / vim / csh tutorials |
| 2013.01.30 | Group Study | Confirm Mathlab accounts work Go over unix / vim / csh tutorials Seawulf account setup |
| 2013.02.04 | Group Study | Continue unix / vim / csh tutorials Logging into Seawulf |
| 2013.02.06 | Group Study | Finish unix / vim / csh tutorials Csh scripting exercises Transfering files to Seawulf |
| 2013.02.11 | Group Study | Visualization/analysis software VMD, Chimera, and MOE |
| 2013.02.13 | Group Study | Visualization/analysis software VMD, Chimera, and MOE |
| 2013.02.18 | Group Study | Tutorials: DOCK individual project discussion Allen, W. |
| 2013.02.20 | Group Study | Tutorials: DOCK individual project discussion |
| 2013.02.25 | Group Study | Tutorials: DOCK individual project discussion |
| 2013.02.27 | Group Study | Tutorials: DOCK individual project discussion |
| 2013.03.04 | Group Study | Tutorials: DOCK wiki editing |
| 2013.03.06 | Group Study | Tutorials: AMBER individual project discussion Jiang L. |
| 2013.03.11 | Group Study | Tutorials: AMBER individual project discussion |
| 2013.03.13 | Group Study | Tutorials: AMBER individual project discussion |
| 2013.03.18 | Spring Recess | Spring Recess |
| 2013.03.20 | Spring Recess | Spring Recess |
| 2013.03.25 | Group Study | Tutorials: AMBER individual project discussion |
| 2013.03.27 | Group Study | Tutorials: AMBER wiki editing |
| 2013.04.01 | Deadline for project proposal discussion Foda, Zack and Kasavajhala, Koushik |
Project Proposal |
| 2013.04.03 | Ralph, Brian and Guo, Jiaye | Project Proposal |
| 2013.04.08 | Shan, Jiahui and Krantsevich, Nick | Project Proposal |
| 2013.04.10 | Xing, Weiliang and Stenzoski, Natalie | Project Proposal |
| 2013.04.15 | Krantsevich, Artem and Chen, Yuan | Project Proposal |
| 2013.04.17 | Preliminary Report Due Huang, He and Chen, Ye |
Project Proposal |
| 2013.04.22 | Ralph, Brian and Kasavajhala, Koushik | Progress Report |
| 2013.04.24 | Guo, Jiaye and Krantsevich, Nick | Progress Report |
| 2013.04.29 | Foda, Zach and Shan, Jiahui | Progress Report |
| 2013.05.01 | Xing, Weiliang and Stenzoski, Natalie | Progress Report |
| 2013.05.06 | Chen, Yuan and Krantsevich, Artem | Progress Report |
| 2013.05.08 | Last Day of Class Chen, Ye and Huang, He |
Progress Report |
| 2013.05.15 | Final written report due by 5PM today. Late papers will not be accepted. See above for sample reports and detailed guidelines. | Give hard copy to Yuchen Zhou (Math Tower room 3-129) and email electronic copy to Joe |
