Difference between revisions of "2015 AMS-536 Spring"

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(Created page with "<br> {| align="center" border="2" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:80%" |- style="background:white" ! style="width:10%" | '''Ins...")
 
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| 2014.01.28 Wed || Group Study || Confirm Mathlab accounts work <br> Go over unix / vim / csh tutorials <br> Seawulf account setup  
 
| 2014.01.28 Wed || Group Study || Confirm Mathlab accounts work <br> Go over unix / vim / csh tutorials <br> Seawulf account setup  
 
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| 2014.02.02 Mon || Group Study || SNOW STORM, CLASS CANCELLED
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| 2014.02.02 Mon || Group Study || Confirm Mathlab accounts work <br> Go over unix / vim / csh tutorials <br> Seawulf account setup
 
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| 2014.02.04 Wed || Group Study || SNOW STORM, CLASS CANCELLED
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| 2014.02.04 Wed || Group Study || Visualization/analysis software <br> VMD, Chimera, and MOE
 
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| 2014.02.09 Mon || Group Study || Visualization/analysis software <br> VMD, Chimera, and MOE
 
| 2014.02.09 Mon || Group Study || Visualization/analysis software <br> VMD, Chimera, and MOE
 
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| 2014.02.11 Wed || Group Study || Visualization/analysis software <br> VMD, Chimera, and MOE
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| 2014.02.11 Wed || Group Study || Ethics in Writing (Rob)
 
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| || '''SECTION 2: DOCK TUTORIAL''' ||
 
| || '''SECTION 2: DOCK TUTORIAL''' ||
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| || '''SECTION 4: PROJECT PRESENTATIONS''' ||
 
| || '''SECTION 4: PROJECT PRESENTATIONS''' ||
 
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| 2014.03.30 Mon || Lu Bai and Mike || Oral Presentations: Project Proposal
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| 2014.03.30 Mon || X and X || Oral Presentations: Project Proposal
 
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| 2014.04.01 Wed || Ivan and Arkin || Oral Presentations: Project Proposal
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| 2014.04.01 Wed || X and X || Oral Presentations: Project Proposal
 
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| 2014.04.06 Mon || Tianao and Junjie || Oral Presentations: Project Proposal
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| 2014.04.06 Mon || X and X || Oral Presentations: Project Proposal
 
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| 2014.04.08 Wed || Mosavverul and Jessica || Oral Presentations: Project Proposal
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| 2014.04.08 Wed || X and X || Oral Presentations: Project Proposal
 
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| 2014.04.13 Mon || Kai and Fangfei || Oral Presentations: Project Proposal
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| 2014.04.13 Mon || X and X || Oral Presentations: Project Proposal
 
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| 2014.04.15 Wed || '''Preliminary Written Report Due''' <br> Yan and Yao || Oral Presentations: Project Proposal
 
| 2014.04.15 Wed || '''Preliminary Written Report Due''' <br> Yan and Yao || Oral Presentations: Project Proposal
 
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| 2014.04.20 Mon || Lu Bai and Ivan || Oral Presentations: Progress Report
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| 2014.04.20 Mon || X and X || Oral Presentations: Progress Report
 
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| 2014.04.22 Wed || Mike and Arkin || Oral Presentations: Progress Report
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| 2014.04.22 Wed || X and X || Oral Presentations: Progress Report
 
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| 2014.04.27 Mon || Tianao and Junjie || Oral Presentations: Progress Report
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| 2014.04.27 Mon || X and X || Oral Presentations: Progress Report
 
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| 2014.04.29 Wed || Mosavverul and Jessica || Oral Presentations: Progress Report
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| 2014.04.29 Wed || X and X || Oral Presentations: Progress Report
 
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| 2014.05.04 Mon || Kai and Fangfei || Oral Presentations: Progress Report
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| 2014.05.04 Mon || X and X || Oral Presentations: Progress Report
 
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| 2014.05.06 Wed || Yan and Yao || || '''Last Day of Class''' ||
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| 2014.05.06 Wed || X and X || || '''Last Day of Class''' ||
 
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| 2014.05.13 Wed || '''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 Dr. William J. Allen (Math Tower room 3-129) and email electronic copy to rizzorc@gmail.com'''
 
| 2014.05.13 Wed || '''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 Dr. William J. Allen (Math Tower room 3-129) and email electronic copy to rizzorc@gmail.com'''
 
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Revision as of 15:01, 26 August 2014


Instructor Dr. Robert C. Rizzo [631-632-9340, robert.rizzo@stonybrook.edu]
Teaching Assistant 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 2:30PM - 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
(2) Yan Yu and the Seawulf team for cluster support
(3) Pat Tonra for Mathlab support


Project Information

Project Proposal 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

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
2014.01.26 Mon First Day of Class
Group Study 		Mathlab account setup
Discuss oral presentations and written report
handouts for unix / vim / csh tutorials
2014.01.28 Wed Group Study Confirm Mathlab accounts work
Go over unix / vim / csh tutorials
Seawulf account setup
2014.02.02 Mon Group Study Confirm Mathlab accounts work
Go over unix / vim / csh tutorials
Seawulf account setup
2014.02.04 Wed Group Study Visualization/analysis software
VMD, Chimera, and MOE
2014.02.09 Mon Group Study Visualization/analysis software
VMD, Chimera, and MOE
2014.02.11 Wed Group Study Ethics in Writing (Rob)
SECTION 2: DOCK TUTORIAL
2014.02.16 Mon Group Study Tutorials: DOCK
individual project discussion Allen, W.
2014.02.18 Wed Group Study Tutorials: DOCK
individual project discussion
2014.02.23 Mon Group Study Tutorials: DOCK
individual project discussion
2014.02.25 Wed Group Study Tutorials: DOCK
individual project discussion
2014.03.02 Mon Group Study Tutorials: DOCK
finalize class wiki tutorial
SECTION 3: AMBER TUTORIAL
2014.03.04 Wed Group Study Tutorials: AMBER
individual project discussion Jiang L.
2014.03.09 Mon Group Study Tutorials: AMBER
individual project discussion
2014.03.11 Wed Group Study Tutorials: AMBER
individual project discussion
2014.03.16 Mon Spring Recess Spring Recess
2014.03.18 Wed Spring Recess Spring Recess
2014.03.23 Mon Group Study Tutorials: AMBER
individual project discussion
2014.03.25 Wed Approved Project Proposal Sheet Due
Group Study 		Tutorials: AMBER
finalize class wiki tutorial
SECTION 4: PROJECT PRESENTATIONS
2014.03.30 Mon X and X Oral Presentations: Project Proposal
2014.04.01 Wed X and X Oral Presentations: Project Proposal
2014.04.06 Mon X and X Oral Presentations: Project Proposal
2014.04.08 Wed X and X Oral Presentations: Project Proposal
2014.04.13 Mon X and X Oral Presentations: Project Proposal
2014.04.15 Wed Preliminary Written Report Due
Yan and Yao 		Oral Presentations: Project Proposal
2014.04.20 Mon X and X Oral Presentations: Progress Report
2014.04.22 Wed X and X Oral Presentations: Progress Report
2014.04.27 Mon X and X Oral Presentations: Progress Report
2014.04.29 Wed X and X Oral Presentations: Progress Report
2014.05.04 Mon X and X Oral Presentations: Progress Report
2014.05.06 Wed X and X Last Day of Class
2014.05.13 Wed 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 Dr. William J. Allen (Math Tower room 3-129) and email electronic copy to rizzorc@gmail.com
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