Difference between revisions of "2019 AMS-536 Spring"

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| || '''SECTION 1: COMPUTING INFRASTRUCTURE AND TOOLS''' ||
 
| || '''SECTION 1: COMPUTING INFRASTRUCTURE AND TOOLS''' ||
 
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|-
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| 2018.01.28 Mon || '''First Day of Class''' <br> Group Study || Seawulf accounts setup <br> unix / vim / csh introduction <br> Discuss presentations and final projects (OHARE sheets)
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| 2019.01.28 Mon || '''First Day of Class''' <br> Group Study || Seawulf accounts setup <br> unix / vim / csh introduction <br> Discuss presentations and final projects (OHARE sheets)
 
|-
 
|-
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| 2018.01.30 Wed || Group Study || Seawulf accounts setup <br> unix / vim / csh introduction <br> Visualization demo's Chimera and VMD
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| 2019.01.30 Wed || Group Study || Seawulf accounts setup <br> unix / vim / csh introduction <br> Visualization demo's Chimera and VMD
 
|-
 
|-
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| 2018.02.04 Mon ||| Group Study || Seawulf accounts setup <br> unix / vim / csh introduction <br> Visualization demo's Chimera and VMD
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| 2019.02.04 Mon ||| Group Study || Seawulf accounts setup <br> unix / vim / csh introduction <br> Visualization demo's Chimera and VMD
 
|-
 
|-
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| 2018.02.06 Wed ||| Group Study || Seawulf accounts setup <br> unix / vim / csh introduction <br> Visualization demo's Chimera and VMD
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| 2019.02.06 Wed ||| Group Study || Seawulf accounts setup <br> unix / vim / csh introduction <br> Visualization demo's Chimera and VMD
 
|-
 
|-
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| 2018.02.11 Mon || Group Study || Seawulf queuing system <br>  
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| 2019.02.11 Mon || Group Study || Seawulf queuing system <br>  
 
|-
 
|-
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| 2018.02.13 Wed || Group Study ||  Seawulf queuing system <br>  Ethics in Writing (Rob)
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| 2019.02.13 Wed || Group Study ||  Seawulf queuing system <br>  Ethics in Writing (Rob)
 
|-
 
|-
 
| || '''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] ) ||
 
| || '''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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|-
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| 2018.02.18 Mon || '''Draft Student Project Proposal OHARE Sheet Due''' <br> Group Study || Tutorials: DOCK virtual screening <br> individual project discussion  
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| 2019.02.18 Mon || '''Draft Student Project Proposal OHARE Sheet Due''' <br> Group Study || Tutorials: DOCK virtual screening <br> individual project discussion  
 
|-
 
|-
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| 2018.02.20 Wed || Group Study || Tutorials: DOCK virtual screening <br> individual project discussion
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| 2019.02.20 Wed || Group Study || Tutorials: DOCK virtual screening <br> individual project discussion
 
|-
 
|-
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| 2018.02.25 Mon || '''Final Student Project Proposal OHARE Sheet Due''' <br> Group Study || Tutorials: DOCK virtual screening <br> individual project discussion
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| 2019.02.25 Mon || '''Final Student Project Proposal OHARE Sheet Due''' <br> Group Study || Tutorials: DOCK virtual screening <br> individual project discussion
 
|-
 
|-
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| 2018.02.27 Wed || Group Study || Tutorials: DOCK de novo design <br> individual project discussion
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| 2019.02.27 Wed || Group Study || Tutorials: DOCK de novo design <br> individual project discussion
 
|-
 
|-
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| 2018.03.04 Mon || Group Study || Tutorials: DOCK de novo design <br> individual project discussion
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| 2019.03.04 Mon || Group Study || Tutorials: DOCK de novo design <br> individual project discussion
 
|-
 
|-
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| 2018.03.06 Wed || Group Study || Tutorials: DOCK de novo design <br> individual project discussion
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| 2019.03.06 Wed || Group Study || Tutorials: DOCK de novo design <br> individual project discussion
 
|-
 
|-
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| 2018.03.11 Mon || Group Study || Tutorials: DOCK genetic algorithm <br> individual project discussion
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| 2019.03.11 Mon || Group Study || Tutorials: DOCK genetic algorithm <br> individual project discussion
 
|-
 
|-
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| 2018.03.13 Wed || Group Study || Tutorials: DOCK genetic algorithm  <br> individual project discussion
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| 2019.03.13 Wed || Group Study || Tutorials: DOCK genetic algorithm  <br> individual project discussion
 
|-
 
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| 2018.03.18 Mon || '''Spring Recess || Spring Recess'''
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| 2019.03.18 Mon || '''Spring Recess || Spring Recess'''
 
|-
 
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| 2018.03.20 Wed || '''Spring Recess || Spring Recess'''
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| 2019.03.20 Wed || '''Spring Recess || Spring Recess'''
 
|-
 
|-
 
| || '''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] ) ||
 
| || '''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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| 2018.03.25 Mon || Group Study || Tutorials: AMBER <br> individual project discussion
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| 2019.03.25 Mon || Group Study || Tutorials: AMBER <br> individual project discussion
 
|-
 
|-
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| 2018.03.27 Wed || Group Study || Tutorials: AMBER <br> individual project discussion
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| 2019.03.27 Wed || Group Study || Tutorials: AMBER <br> individual project discussion
 
|-
 
|-
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| 2018.04.01 Mon || Group Study || Tutorials: AMBER <br> individual project discussion
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| 2019.04.01 Mon || Group Study || Tutorials: AMBER <br> individual project discussion
 
|-
 
|-
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| 2018.04.03 Wed || Group Study || Tutorials: AMBER <br> individual project discussion
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| 2019.04.03 Wed || Group Study || Tutorials: AMBER <br> individual project discussion
 
|-
 
|-
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| 2018.04.08 Mon || Group Study || Tutorials: AMBER <br> individual project discussion
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| 2019.04.08 Mon || Group Study || Tutorials: AMBER <br> individual project discussion
 
|-
 
|-
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| 2018.04.10 Wed || Group Study || Tutorials: AMBER <br> finalize class wiki
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| 2019.04.10 Wed || Group Study || Tutorials: AMBER <br> finalize class wiki
 
|-
 
|-
 
| || '''SECTION 4: PROJECT PRESENTATIONS''' ||
 
| || '''SECTION 4: PROJECT PRESENTATIONS''' ||
 
|-
 
|-
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| 2018.04.15 Mon || '''Draft Paper Due''' <br> Oral Presentations  ||Oral Presentations (John, Yuzhang)
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| 2019.04.15 Mon || '''Draft Paper Due''' <br> Oral Presentations  ||Oral Presentations (John, Yuzhang)
 
|-  
 
|-  
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| 2018.04.17 Wed || Oral Presentations  || Oral Presentations (Ryota, Amie)
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| 2019.04.17 Wed || Oral Presentations  || Oral Presentations (Ryota, Amie)
 
|-
 
|-
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| 2018.04.22 Mon || Oral Presentations || Oral Presentations (Yong Mi, Niven)
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| 2019.04.22 Mon || Oral Presentations || Oral Presentations (Yong Mi, Niven)
 
|-
 
|-
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| 2018.04.24 Wed || Group Study  || Project Analysis/Troubleshooting
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| 2019.04.24 Wed || Group Study  || Project Analysis/Troubleshooting
 
|-
 
|-
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| 2018.04.29 Mon || '''Draft Paper Due''' <br> Group Study  || Project Analysis/Troubleshooting
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| 2019.04.29 Mon || '''Draft Paper Due''' <br> Group Study  || Project Analysis/Troubleshooting
 
|-
 
|-
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| 2018.05.01 Wed || Oral Presentations  || Oral Presentations (John, Yuzhang)
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| 2019.05.01 Wed || Oral Presentations  || Oral Presentations (John, Yuzhang)
 
|-
 
|-
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| 2018.05.06 Mon || Oral Presentations || Oral Presentations (Ryota, Yong Mi)
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| 2019.05.06 Mon || Oral Presentations || Oral Presentations (Ryota, Yong Mi)
 
|-
 
|-
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| 2018.05.08 Wed || '''Last Day Class'''<br> Oral Presentations || Oral Presentations (Amie, Niven)
+
| 2019.05.08 Wed || '''Last Day Class'''<br> Oral Presentations || Oral Presentations (Amie, Niven)
 
|-
 
|-
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| 2018.05.10 Fri || '''Final Written Report due by 5PM today.'''<br> || Give hard copy printout to Robert Rizzo (Math Tower room 1-111) or Lauren Prentis/Steve Telehany (Math Tower room 3-129) and email electronic copy to rizzorc -at- gmail dot com
+
| 2019.05.10 Fri || '''Final Written Report due by 5PM today.'''<br> || Give hard copy printout to Robert Rizzo (Math Tower room 1-111) or Lauren Prentis/Steve Telehany (Math Tower room 3-129) and email electronic copy to rizzorc -at- gmail dot com
 
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|}
 
|}

Latest revision as of 11:08, 22 January 2020


Instructor Dr. Robert C. Rizzo [631-632-9340, robert.rizzo@stonybrook.edu]
Teaching Assistant Lauren Prentis [631-632-8519, lep213 -at- gmail dot com] and Steve Telehany [631-632-8519, stephen dot telehany - at - stonybrook dot 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) Firat Cosku and the LI-RED and SEAWULF 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
2019.01.28 Mon First Day of Class
Group Study 		Seawulf accounts setup
unix / vim / csh introduction
Discuss presentations and final projects (OHARE sheets)
2019.01.30 Wed Group Study Seawulf accounts setup
unix / vim / csh introduction
Visualization demo's Chimera and VMD
2019.02.04 Mon Group Study Seawulf accounts setup
unix / vim / csh introduction
Visualization demo's Chimera and VMD
2019.02.06 Wed Group Study Seawulf accounts setup
unix / vim / csh introduction
Visualization demo's Chimera and VMD
2019.02.11 Mon Group Study Seawulf queuing system
2019.02.13 Wed Group Study Seawulf queuing system
Ethics in Writing (Rob)
SECTION 2: DOCK TUTORIAL ( see Joe Allen slides )
2019.02.18 Mon Draft Student Project Proposal OHARE Sheet Due
Group Study 		Tutorials: DOCK virtual screening
individual project discussion
2019.02.20 Wed Group Study Tutorials: DOCK virtual screening
individual project discussion
2019.02.25 Mon Final Student Project Proposal OHARE Sheet Due
Group Study 		Tutorials: DOCK virtual screening
individual project discussion
2019.02.27 Wed Group Study Tutorials: DOCK de novo design
individual project discussion
2019.03.04 Mon Group Study Tutorials: DOCK de novo design
individual project discussion
2019.03.06 Wed Group Study Tutorials: DOCK de novo design
individual project discussion
2019.03.11 Mon Group Study Tutorials: DOCK genetic algorithm
individual project discussion
2019.03.13 Wed Group Study Tutorials: DOCK genetic algorithm
individual project discussion
2019.03.18 Mon Spring Recess Spring Recess
2019.03.20 Wed Spring Recess Spring Recess
SECTION 3: AMBER TUTORIAL ( see Lingling Jiang slides )
2019.03.25 Mon Group Study Tutorials: AMBER
individual project discussion
2019.03.27 Wed Group Study Tutorials: AMBER
individual project discussion
2019.04.01 Mon Group Study Tutorials: AMBER
individual project discussion
2019.04.03 Wed Group Study Tutorials: AMBER
individual project discussion
2019.04.08 Mon Group Study Tutorials: AMBER
individual project discussion
2019.04.10 Wed Group Study Tutorials: AMBER
finalize class wiki
SECTION 4: PROJECT PRESENTATIONS
2019.04.15 Mon Draft Paper Due
Oral Presentations 		Oral Presentations (John, Yuzhang)
2019.04.17 Wed Oral Presentations Oral Presentations (Ryota, Amie)
2019.04.22 Mon Oral Presentations Oral Presentations (Yong Mi, Niven)
2019.04.24 Wed Group Study Project Analysis/Troubleshooting
2019.04.29 Mon Draft Paper Due
Group Study 		Project Analysis/Troubleshooting
2019.05.01 Wed Oral Presentations Oral Presentations (John, Yuzhang)
2019.05.06 Mon Oral Presentations Oral Presentations (Ryota, Yong Mi)
2019.05.08 Wed Last Day Class
Oral Presentations 		Oral Presentations (Amie, Niven)
2019.05.10 Fri Final Written Report due by 5PM today.
 Give hard copy printout to Robert Rizzo (Math Tower room 1-111) or Lauren Prentis/Steve Telehany (Math Tower room 3-129) and email electronic copy to rizzorc -at- gmail dot com
Retrieved from "https://ringo.ams.stonybrook.edu/index.php?title=2019_AMS-536_Spring&oldid=12144"