Difference between revisions of "2016 AMS-536 Spring"

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| 2016.02.01 Mon ||| Group Study || Mathlab/LI-RED accounts setup <br> unix / vim / csh introduction <br> Visualization demo's  
 
| 2016.02.01 Mon ||| Group Study || Mathlab/LI-RED accounts setup <br> unix / vim / csh introduction <br> Visualization demo's  
 
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| 2016.02.03 Wed || Group Study || Confirm accounts <br> Set up ssh connection on '''personal laptops'''
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| 2016.02.03 Wed || Group Study || Confirm accounts <br> Set up ssh connection on personal laptops  
 
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| 2016.02.08 Mon || Group Study || Unix / Vim Challenges  
 
| 2016.02.08 Mon || Group Study || Unix / Vim Challenges  
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| 2016.03.30 Mon || Last, First and Last, First || Oral Presentations: Project Proposal
 
| 2016.03.30 Mon || Last, First and Last, First || Oral Presentations: Project Proposal
 
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| 2016.04.04 Wed || Shanbhoque, Prajna and Singleton, Courtney  || Oral Presentations: Project Proposal
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| 2016.04.04 Wed || Last, First and Last, First || Oral Presentations: Project Proposal
 
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| 2016.04.06 Mon || Yin, Xingyu and Zhang, Beibei  || Oral Presentations: Project Proposal
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| 2016.04.06 Mon || Last, First and Last, First || Oral Presentations: Project Proposal
 
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| 2016.04.11 Wed || Belfon, Kellon and Chiappone, Sam  || Oral Presentations: Project Proposal
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| 2016.04.11 Wed || Last, First and Last, First || Oral Presentations: Project Proposal
 
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| 2016.04.13 Mon || Jones, George and Liu, Cong  || Oral Presentations: Project Proposal
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| 2016.04.13 Mon || Last, First and Last, First || Oral Presentations: Project Proposal
 
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| 2016.04.15 Wed || '''Preliminary Written Report Due''' <br> Tian, Chuan and Cortes, Michael || Oral Presentations: Project Proposal
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| 2016.04.15 Wed || '''Preliminary Written Report Due''' <br> Last, First and Last, First || Oral Presentations: Project Proposal
 
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| 2016.04.20 Mon || Elmes, Matthew and Shanbhoque, Prajna  || Oral Presentations: Progress Report
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| 2016.04.20 Mon || Last, First and Last, First || Oral Presentations: Project Proposal
 
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| 2016.04.22 Wed || Belfon, Kellon and Yin, Xingyu || Oral Presentations: Progress Report
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| 2016.04.22 Wed || Last, First and Last, First || Oral Presentations: Project Proposal
 
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| 2016.04.27 Mon || Jiaye Guo || '''Virtual Screening Post-processing'''
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| 2016.04.27 Mon || Last, First and Last, First || Oral Presentations: Project Proposal
 
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| 2016.04.29 Wed || Zhang, Beibei and Singleton, Courtney  || Oral Presentations: Progress Report
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| 2016.04.29 Wed || Last, First and Last, First || Oral Presentations: Project Proposal
 
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| 2016.05.04 Mon || Chiappone, Sam and Jones, George  || Oral Presentations: Progress Report
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| 2016.05.04 Mon || Last, First and Last, First || Oral Presentations: Project Proposal
 
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| 2016.05.06 Wed || Liu, Cong and Tian, Chuan || Oral Presentations: Progress Report
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| 2016.05.06 Wed || '''Final Written Report due at start of class. Late papers will not be accepted.' <br> ''Hand hard copy to Brian Fochtman or Jiaye Guo (Math Tower room 3-129) and email electronic copy to rizzorc@gmail.com'' <br> Last, First and Last, First || Oral Presentations: Project Proposal
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| 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'''
 
 
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Revision as of 10:40, 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
(2) Firat Cosku and the LI-RED team for cluster support
(3) Pat Tonra for Mathlab support


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

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 Last, First and Last, First Oral Presentations: Project Proposal
2016.04.06 Mon Last, First and Last, First Oral Presentations: Project Proposal
2016.04.11 Wed Last, First and Last, First Oral Presentations: Project Proposal
2016.04.13 Mon Last, First and Last, First Oral Presentations: Project Proposal
2016.04.15 Wed Preliminary Written Report Due
Last, First and Last, First 		Oral Presentations: Project Proposal
2016.04.20 Mon Last, First and Last, First Oral Presentations: Project Proposal
2016.04.22 Wed Last, First and Last, First Oral Presentations: Project Proposal
2016.04.27 Mon Last, First and Last, First Oral Presentations: Project Proposal
2016.04.29 Wed Last, First and Last, First Oral Presentations: Project Proposal
2016.05.04 Mon Last, First and Last, First Oral Presentations: Project Proposal
2016.05.06 Wed Final Written Report due at start of class. Late papers will not be accepted.'
Hand hard copy to Brian Fochtman or Jiaye Guo (Math Tower room 3-129) and email electronic copy to rizzorc@gmail.com
Last, First and Last, First 		Oral Presentations: Project Proposal
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