Difference between revisions of "2016 AMS-536 Spring"

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| Dr. Robert C. Rizzo  [631-632-9340, robert.rizzo@stonybrook.edu]
 
| Dr. Robert C. Rizzo  [631-632-9340, robert.rizzo@stonybrook.edu]
 
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|-
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| '''Teaching Assistant''' || Brian Fochtman [631-632-8519, brianfochtman@gmail.com] and Jiaye Guo [631-632-8519, jguokelly@gmail.com]
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| '''Teaching Assistant''' || Courtney Singleton [631-632-8519, Courtney.Singleton@stonybrookmedicine.edu] and Yuchen Zhou [631-632-8519, chris.yuchen.zhou@gmail.com]
 
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| '''Course No.''' || AMS-536 / CHE-536
 
| '''Course No.''' || AMS-536 / CHE-536
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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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| 2016.02.10 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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| 2016.02.10 Wed || Group Study ||  LI-RED queuing system <br> Chimera demo (Courtney) <br> VMD demo (Yuchen) <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 Joe Allen Presentation] ) ||
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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 slides] ) ||
 
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| 2016.02.15 Mon || Group Study || Tutorials: DOCK <br> individual project discussion  
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| 2016.02.15 Mon || '''Draft Student Project Proposal OHARE Sheet Due''' <br> Group Study || Tutorials: DOCK <br> individual project discussion  
 
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| 2016.02.17 Wed || Group Study || Tutorials: DOCK <br> individual project discussion
 
| 2016.02.17 Wed || Group Study || Tutorials: DOCK <br> individual project discussion
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| 2016.02.22 Mon || Group Study || Tutorials: DOCK <br> individual project discussion
 
| 2016.02.22 Mon || Group Study || Tutorials: DOCK <br> individual project discussion
 
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| 2016.02.24 Wed || '''Draft Student Project Proposal OHARE Sheet Due''' <br> Group Study || Tutorials: DOCK <br> individual project discussion
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| 2016.02.24 Wed || Group Study || Tutorials: DOCK <br> individual project discussion
 
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| 2016.02.29 Mon || Group Study || Tutorials: DOCK <br> individual project discussion
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| 2016.02.29 Mon || '''Final Student Project Proposal OHARE Sheet Due''' <br> 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
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| 2016.03.02 Wed || Group Study || Tutorials: DOCK <br> individual project discussion
 
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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 presentation] ) ||
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| 2016.03.07 Mon || Group Study || Tutorials: DOCK <br> individual project discussion
 
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| 2016.03.07 Mon || Group Study <br> '''NOTE: TODAY IS FRIDAY BUT FOLLOWS MON SCHEDULE''' || Tutorials: AMBER <br> individual project discussion
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| 2016.03.09 Wed || Group Study || Tutorials: DOCK <br> finalize class wiki
 
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| 2016.03.09 Wed || '''Final Student Project Proposal OHARE Sheet Due''' <br> Group Study || Tutorials: AMBER <br> individual project discussion
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| 2016.03.14 Mon || '''Spring Recess || Spring Recess'''
 
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| 2016.03.14 Mon || Spring Recess || Spring Recess
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| 2016.03.16 Wed || '''Spring Recess || Spring Recess'''
 
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| 2016.03.16 Wed || Spring Recess || Spring Recess
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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 see Lingling Jiang slides] ) ||
 
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| 2016.03.21 Mon || Group Study || Tutorials: AMBER <br> individual project discussion
 
| 2016.03.21 Mon || Group Study || Tutorials: AMBER <br> individual project discussion
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| 2016.03.23 Wed || Group Study || Tutorials: AMBER <br> individual project discussion
 
| 2016.03.23 Wed || Group Study || Tutorials: AMBER <br> individual project discussion
 
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| 2016.03.28 Mon || Group Study || Tutorials: AMBER <br> finalize class wiki tutorial
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| 2016.03.28 Mon || Group Study || Tutorials: AMBER <br> individual project discussion
 
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| || '''SECTION 4: PROJECT PRESENTATIONS''' ||
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| 2016.03.30 Wed || Group Study || Tutorials: AMBER <br> individual project discussion
 
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| 2016.03.30 Mon || Last, First and Last, First || Oral Presentations: Project Proposal
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| 2016.04.04 Mon || Group Study || Tutorials: AMBER <br> individual project discussion
 
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| 2016.04.04 Wed || Shanbhoque, Prajna and Singleton, Courtney  || Oral Presentations: Project Proposal
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| 2016.04.06 Wed || Group Study || Tutorials: AMBER <br> finalize class wiki
 
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| 2016.04.06 Mon || Yin, Xingyu and Zhang, Beibei  || Oral Presentations: Project Proposal
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| || '''SECTION 4: PROJECT PRESENTATIONS''' ||
 
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| 2016.04.11 Wed || Belfon, Kellon and Chiappone, Sam  || Oral Presentations: Project Proposal
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| 2016.04.11 Mon || Maffucci, Katie and Prentis, Lauren <br> '''Draft Paper Due''' <br> || Oral Presentations
 
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| 2016.04.13 Mon || Jones, George and Liu, Cong || Oral Presentations: Project Proposal
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| 2016.04.13 Wed || Lyczek, Agatha and Awwa, Monaf || Oral Presentations
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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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| 2016.04.20 Mon || Elmes, Matthew and Shanbhoque, Prajna  || Oral Presentations: Progress Report
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| 2016.04.18 Mon || Sanchez Reyes, Omar and Jiang, Belei || Oral Presentations
 
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| 2016.04.22 Wed || Belfon, Kellon and Yin, Xingyu || Oral Presentations: Progress Report
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| 2016.04.20 Wed || She, Yaping and Guo, Haoyue || Oral Presentations
 
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| 2016.04.27 Mon || Jiaye Guo || '''Virtual Screening Post-processing'''
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| 2016.04.25 Mon || Maffucci, Katie and Prentis, Lauren <br> '''Draft Paper Due''' <br> || Oral Presentations
 
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| 2016.04.29 Wed || Zhang, Beibei and Singleton, Courtney  || Oral Presentations: Progress Report
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| 2016.04.27 Wed || Lyczek, Agatha and Awwa, Monaf || Oral Presentations
 
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| 2016.05.04 Mon || Chiappone, Sam and Jones, George  || Oral Presentations: Progress Report
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| 2016.05.02 Mon || Sanchez Reyes, Omar and Jiang, Belei || Oral Presentations
 
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| 2016.05.06 Wed || Liu, Cong and Tian, Chuan || Oral Presentations: Progress Report
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| 2016.05.04 Wed || '''Last Day Class'''<br> She, Yaping and Guo, Haoyue || Oral Presentations
 
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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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| 2016.05.05 Thur || '''Final Written Report due by 1PM today.'''<br> || 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
 
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|}
 
|}

Latest revision as of 14:42, 19 February 2019


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
(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 (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
Retrieved from "https://ringo.ams.stonybrook.edu/index.php?title=2016_AMS-536_Spring&oldid=11547"