Difference between revisions of "2015 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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| '''Teaching Assistant''' || Dr. William J. Allen [631-632-8519, william.allen@stonybrook.edu]
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| '''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
 
| '''Course No.''' || AMS-536 / CHE-536
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== Project Information ==
 
== Project Information ==
  
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'''Project Proposal Sheet'''
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'''Student Project Proposal OHARE Sheet'''
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*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/projectA.student.info.doc project.student.info.doc]
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*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/studentproject.OHARE.template.docx studentproject.OHARE.template.docx]
  
  
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| || '''SECTION 1: COMPUTING INFRASTRUCTURE AND TOOLS''' ||
 
| || '''SECTION 1: COMPUTING INFRASTRUCTURE AND TOOLS''' ||
 
|-
 
|-
−
| 2014.01.26 Mon || '''First Day of Class''' <br> Group Study || Mathlab account setup <br> Discuss oral presentations and written report <br> handouts for unix / vim / csh tutorials
+
| 2015.01.26 Mon || ''Snow Day'' || Hot Cocoa <br> Sledding <br> Snowball fights
 
|-
 
|-
−
| 2014.01.28 Wed || Group Study || Confirm Mathlab accounts work <br> Go over unix / vim / csh tutorials <br> Seawulf account setup
+
| 2015.01.28 Wed || '''First Day of Class''' <br> Group Study || Mathlab/Seawulf accounts setup <br> unix / vim / csh introduction <br> Discuss presentations and final projects
 
|-
 
|-
−
| 2014.02.02 Mon || Group Study || Confirm Mathlab accounts work <br> Go over unix / vim / csh tutorials <br> Seawulf account setup
+
| 2015.02.02 Mon || ''Snow Day'' || Shoveling and such
 
|-
 
|-
−
| 2014.02.04 Wed || Group Study || Visualization/analysis software <br> VMD, Chimera, and MOE
+
| 2015.02.04 Wed || Group Study || Confirm Mathlab accounts <br> Set up Seawulf accounts <br> Set up ssh connection on '''personal laptops'''
 
|-
 
|-
−
| 2014.02.09 Mon || Group Study || Visualization/analysis software <br> VMD, Chimera, and MOE
+
| 2015.02.09 Mon || Group Study || Unix / Vim Challenges
 
|-
 
|-
−
| 2014.02.11 Wed || Group Study || Ethics in Writing, Rizzo Rob
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| 2015.02.11 Wed || Group Study || Seawulf queuing system <br> Chimera demo (Jiaye) <br> VMD demo (Brian) <br> Class Project Expectation: Ethics in Writing (Rob)
 
|-
 
|-
−
| || '''SECTION 2: DOCK TUTORIAL''' ||
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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] ) ||
 
|-
 
|-
−
| 2014.02.16 Mon || 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.]
+
| 2015.02.16 Mon || Group Study || Tutorials: DOCK <br> individual project discussion  
 
|-
 
|-
−
| 2014.02.18 Wed || Group Study || Tutorials: DOCK <br> individual project discussion
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| 2015.02.18 Wed || Group Study || Tutorials: DOCK <br> individual project discussion
 
|-
 
|-
−
| 2014.02.23 Mon || Group Study || Tutorials: DOCK <br> individual project discussion
+
| 2015.02.23 Mon || Group Study || Tutorials: DOCK <br> individual project discussion
 
|-
 
|-
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| 2014.02.25 Wed || Group Study || Tutorials: DOCK <br> individual project discussion
+
| 2015.02.25 Wed || '''Draft Student Project Proposal OHARE Sheet Due''' <br> Group Study || Tutorials: DOCK <br> individual project discussion
 
|-
 
|-
−
| 2014.03.02 Mon || Group Study || Tutorials: DOCK <br> finalize class wiki tutorial
+
| 2015.03.02 Mon || Group Study || Tutorials: DOCK <br> individual project discussion
 
|-
 
|-
−
| || '''SECTION 3: AMBER TUTORIAL''' ||
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| 2015.03.04 Wed || Group Study || Tutorials: DOCK <br> finalize class wiki tutorial
 
|-
 
|-
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| 2014.03.04 Wed || 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.]
+
| || '''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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| 2014.03.09 Mon || Group Study || Tutorials: AMBER <br> individual project discussion  
+
| 2015.03.06 Fri || Group Study <br> '''NOTE: TODAY IS FRIDAY BUT FOLLOWS MON SCHEDULE''' || Tutorials: AMBER <br> individual project discussion
 
|-
 
|-
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| 2014.03.11 Wed || Group Study || Tutorials: AMBER <br> individual project discussion  
+
| 2015.03.09 Mon || Group Study || Tutorials: AMBER <br> individual project discussion  
 
|-
 
|-
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| 2014.03.16 Mon || Spring Recess || Spring Recess
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| 2015.03.11 Wed || '''Final Student Project Proposal OHARE Sheet Due''' <br> Group Study || Tutorials: AMBER <br> individual project discussion
 
|-
 
|-
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| 2014.03.18 Wed || Spring Recess || Spring Recess
+
| 2015.03.16 Mon || Spring Recess || Spring Recess
 
|-
 
|-
−
| 2014.03.23 Mon || Group Study || Tutorials: AMBER <br> individual project discussion
+
| 2015.03.18 Wed || Spring Recess || Spring Recess
 
|-
 
|-
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| 2014.03.25 Wed || '''Approved Project Proposal Sheet Due''' <br> Group Study || Tutorials: AMBER <br> finalize class wiki tutorial
+
| 2015.03.23 Mon || Group Study || Tutorials: AMBER <br> individual project discussion
 +
|-
 +
| 2015.03.25 Wed || Group Study || Tutorials: AMBER <br> individual project discussion
 +
|-
 +
| 2015.03.27 Fri || Group Study <br> '''NOTE: TODAY IS FRIDAY BUT FOLLOWS MON SCHEDULE''' || Tutorials: AMBER <br> finalize class wiki tutorial
 
|-
 
|-
 
| || '''SECTION 4: PROJECT PRESENTATIONS''' ||
 
| || '''SECTION 4: PROJECT PRESENTATIONS''' ||
 
|-
 
|-
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| 2014.03.30 Mon || X and X || Oral Presentations: Project Proposal
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| 2015.03.30 Mon || Cortes, Michael and Elmes, Matthew || Oral Presentations: Project Proposal
 
|-
 
|-
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| 2014.04.01 Wed || X and X || Oral Presentations: Project Proposal
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| 2015.04.01 Wed || Shanbhoque, Prajna and Singleton, Courtney  || Oral Presentations: Project Proposal
 
|-
 
|-
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| 2014.04.06 Mon || X and X || Oral Presentations: Project Proposal
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| 2015.04.06 Mon || Yin, Xingyu and Zhang, Beibei  || Oral Presentations: Project Proposal
 
|-
 
|-
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| 2014.04.08 Wed || X and X || Oral Presentations: Project Proposal
+
| 2015.04.08 Wed || Belfon, Kellon and Chiappone, Sam  || Oral Presentations: Project Proposal
 
|-  
 
|-  
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| 2014.04.13 Mon || X and X || Oral Presentations: Project Proposal
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| 2015.04.13 Mon || Jones, George and Liu, Cong  || Oral Presentations: Project Proposal
 
|-
 
|-
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| 2014.04.15 Wed || '''Preliminary Written Report Due''' <br> Yan and Yao || Oral Presentations: Project Proposal
+
| 2015.04.15 Wed || '''Preliminary Written Report Due''' <br> Tian, Chuan and Cortes, Michael || Oral Presentations: Project Proposal
 
|-
 
|-
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| 2014.04.20 Mon || X and X || Oral Presentations: Progress Report
+
| 2015.04.20 Mon || Elmes, Matthew and Shanbhoque, Prajna  || Oral Presentations: Progress Report
 
|-
 
|-
−
| 2014.04.22 Wed || X and X || Oral Presentations: Progress Report
+
| 2015.04.22 Wed || Belfon, Kellon and Yin, Xingyu || Oral Presentations: Progress Report
 
|-
 
|-
−
| 2014.04.27 Mon || X and X || Oral Presentations: Progress Report
+
| 2015.04.27 Mon || Jiaye Guo || '''Virtual Screening Post-processing'''
 
|-
 
|-
−
| 2014.04.29 Wed || X and X || Oral Presentations: Progress Report
+
| 2015.04.29 Wed || Zhang, Beibei and Singleton, Courtney  || Oral Presentations: Progress Report
 
|-
 
|-
−
| 2014.05.04 Mon || X and X || Oral Presentations: Progress Report
+
| 2015.05.04 Mon || Chiappone, Sam and Jones, George  || Oral Presentations: Progress Report
 
|-
 
|-
−
| 2014.05.06 Wed || X and X || || '''Last Day of Class''' ||
+
| 2015.05.06 Wed || Liu, Cong and Tian, Chuan || Oral Presentations: Progress Report
 
|-
 
|-
−
| 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'''
+
| 2015.05.13 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'''
 
|-
 
|-
 
|}
 
|}

Latest revision as of 13:55, 4 May 2015


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) Yan Yu and the 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
2015.01.26 Mon Snow Day Hot Cocoa
Sledding
Snowball fights
2015.01.28 Wed First Day of Class
Group Study 		Mathlab/Seawulf accounts setup
unix / vim / csh introduction
Discuss presentations and final projects
2015.02.02 Mon Snow Day Shoveling and such
2015.02.04 Wed Group Study Confirm Mathlab accounts
Set up Seawulf accounts
Set up ssh connection on personal laptops
2015.02.09 Mon Group Study Unix / Vim Challenges
2015.02.11 Wed Group Study Seawulf queuing system
Chimera demo (Jiaye)
VMD demo (Brian)
Class Project Expectation: Ethics in Writing (Rob)
SECTION 2: DOCK TUTORIAL ( Joe Allen Presentation )
2015.02.16 Mon Group Study Tutorials: DOCK
individual project discussion
2015.02.18 Wed Group Study Tutorials: DOCK
individual project discussion
2015.02.23 Mon Group Study Tutorials: DOCK
individual project discussion
2015.02.25 Wed Draft Student Project Proposal OHARE Sheet Due
Group Study 		Tutorials: DOCK
individual project discussion
2015.03.02 Mon Group Study Tutorials: DOCK
individual project discussion
2015.03.04 Wed Group Study Tutorials: DOCK
finalize class wiki tutorial
SECTION 3: AMBER TUTORIAL ( Lingling Jiang presentation )
2015.03.06 Fri Group Study
NOTE: TODAY IS FRIDAY BUT FOLLOWS MON SCHEDULE 		Tutorials: AMBER
individual project discussion
2015.03.09 Mon Group Study Tutorials: AMBER
individual project discussion
2015.03.11 Wed Final Student Project Proposal OHARE Sheet Due
Group Study 		Tutorials: AMBER
individual project discussion
2015.03.16 Mon Spring Recess Spring Recess
2015.03.18 Wed Spring Recess Spring Recess
2015.03.23 Mon Group Study Tutorials: AMBER
individual project discussion
2015.03.25 Wed Group Study Tutorials: AMBER
individual project discussion
2015.03.27 Fri Group Study
NOTE: TODAY IS FRIDAY BUT FOLLOWS MON SCHEDULE 		Tutorials: AMBER
finalize class wiki tutorial
SECTION 4: PROJECT PRESENTATIONS
2015.03.30 Mon Cortes, Michael and Elmes, Matthew Oral Presentations: Project Proposal
2015.04.01 Wed Shanbhoque, Prajna and Singleton, Courtney Oral Presentations: Project Proposal
2015.04.06 Mon Yin, Xingyu and Zhang, Beibei Oral Presentations: Project Proposal
2015.04.08 Wed Belfon, Kellon and Chiappone, Sam Oral Presentations: Project Proposal
2015.04.13 Mon Jones, George and Liu, Cong Oral Presentations: Project Proposal
2015.04.15 Wed Preliminary Written Report Due
Tian, Chuan and Cortes, Michael 		Oral Presentations: Project Proposal
2015.04.20 Mon Elmes, Matthew and Shanbhoque, Prajna Oral Presentations: Progress Report
2015.04.22 Wed Belfon, Kellon and Yin, Xingyu Oral Presentations: Progress Report
2015.04.27 Mon Jiaye Guo Virtual Screening Post-processing
2015.04.29 Wed Zhang, Beibei and Singleton, Courtney Oral Presentations: Progress Report
2015.05.04 Mon Chiappone, Sam and Jones, George Oral Presentations: Progress Report
2015.05.06 Wed Liu, Cong and Tian, Chuan Oral Presentations: Progress Report
2015.05.13 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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