Difference between revisions of "2014 AMS-536 Spring"

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== Project Information ==
 
== Project Information ==
  
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'''Project Approval Sheet'''
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'''Project Proposal Sheet'''
 
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/projectA.student.info.doc project.student.info.doc]
 
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/projectA.student.info.doc project.student.info.doc]
  
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| '''Talk'''
 
| '''Talk'''
 
|-
 
|-
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| || '''SECTION 1: COMPUTING INTERFACES AND TOOLS''' ||
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| || '''SECTION 1: COMPUTING INFRASTRUCTURE AND TOOLS''' ||
 
|-
 
|-
−
| 2014.01.27 Mon || '''First Day of Class and Organizational Meeting''' <br> Group Study || Mathlab account setup <br> Discuss research paper and presentations <br> handouts for unix / vim / csh tutorials
+
| 2014.01.27 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
 
|-
 
|-
 
| 2014.01.29 Wed || Group Study || Confirm Mathlab accounts work <br> Go over unix / vim / csh tutorials <br> Seawulf account setup  
 
| 2014.01.29 Wed || Group Study || Confirm Mathlab accounts work <br> Go over unix / vim / csh tutorials <br> Seawulf account setup  
 
|-
 
|-
−
| 2014.02.03 Mon || Group Study || Continue unix / vim / csh tutorials <br> Logging into Seawulf
+
| 2014.02.03 Mon || Group Study || SNOW STORM, CLASS CANCELLED
 
|-
 
|-
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| 2014.02.05 Wed || Group Study || Finish unix / vim / csh tutorials <br> Csh scripting exercises <br> Transfering files to Seawulf
+
| 2014.02.05 Wed || Group Study || SNOW STORM, CLASS CANCELLED
 
|-
 
|-
 
| 2014.02.10 Mon || Group Study || Visualization/analysis software <br> VMD, Chimera, and MOE
 
| 2014.02.10 Mon || Group Study || Visualization/analysis software <br> VMD, Chimera, and MOE
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| 2014.02.26 Wed || Group Study || Tutorials: DOCK <br> individual project discussion
 
| 2014.02.26 Wed || Group Study || Tutorials: DOCK <br> individual project discussion
 
|-
 
|-
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| 2014.03.03 Mon || Group Study || Tutorials: DOCK <br> wiki editing
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| 2014.03.03 Mon || Group Study || Tutorials: DOCK <br> finalize class wiki tutorial
 +
|-
 +
| || '''SECTION 3: AMBER TUTORIAL''' ||
 
|-
 
|-
 
| 2014.03.05 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.]
 
| 2014.03.05 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.]
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| 2014.03.24 Mon || Group Study || Tutorials: AMBER <br> individual project discussion
 
| 2014.03.24 Mon || Group Study || Tutorials: AMBER <br> individual project discussion
 
|-
 
|-
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| 2014.03.26 Wed || Group Study || Tutorials: AMBER <br> wiki editing
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| 2014.03.26 Wed || '''Approved Project Proposal Sheet Due''' <br> Group Study || Tutorials: AMBER <br> finalize class wiki tutorial
 
|-
 
|-
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| 2014.03.31 Mon || '''Deadline for project proposal discussion''' <br> Foda, Zack and Kasavajhala, Koushik || Project Proposal
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| || '''SECTION 4: PROJECT PRESENTATIONS''' ||
 
|-
 
|-
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| 2014.04.02 Wed || Ralph, Brian and Guo, Jiaye || Project Proposal
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| 2014.03.31 Mon || Lu Bai and Mike || Oral Presentations: Project Proposal
 
|-
 
|-
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| 2014.04.07 Mon || Shan, Jiahui and Krantsevich, Nick || Project Proposal
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| 2014.04.02 Wed || Ivan and Arkin || Oral Presentations: Project Proposal
 
|-
 
|-
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| 2014.04.09 Wed || Xing, Weiliang and Stenzoski, Natalie || Project Proposal
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| 2014.04.07 Mon || Tianao and Junjie || Oral Presentations: Project Proposal
 +
|-
 +
| 2014.04.09 Wed || Mosavverul and Jessica || Oral Presentations: Project Proposal
 
|-  
 
|-  
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| 2014.04.14 Mon || Krantsevich, Artem and Chen, Yuan || Project Proposal
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| 2014.04.14 Mon || Kai and Fangfei || Oral Presentations: Project Proposal
 +
|-
 +
| 2014.04.16 Wed || '''Preliminary Written Report Due''' <br> Yan and Yao || Oral Presentations: Project Proposal
 
|-
 
|-
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| 2014.04.16 Wed || '''Preliminary Report Due''' <br> Huang, He and Chen, Ye || Project Proposal
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| 2014.04.21 Mon || Lu Bai and Ivan || Oral Presentations: Progress Report
 
|-
 
|-
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| 2014.04.21 Mon || Ralph, Brian and Kasavajhala, Koushik || Progress Report
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| 2014.04.23 Wed || Mike and Arkin || Oral Presentations: Progress Report
 
|-
 
|-
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| 2014.04.23 Wed || Guo, Jiaye and Krantsevich, Nick || Progress Report
+
| 2014.04.28 Mon || Tianao and Junjie || Oral Presentations: Progress Report
 
|-
 
|-
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| 2014.04.28 Mon || Foda, Zach and Shan, Jiahui || Progress Report
+
| 2014.04.30 Wed || Mosavverul and Jessica || Oral Presentations: Progress Report
 
|-
 
|-
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| 2014.04.30 Wed || Xing, Weiliang and Stenzoski, Natalie || Progress Report  
+
| 2014.05.05 Mon || Kai and Fangfei || Oral Presentations: Progress Report
 
|-
 
|-
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| 2014.05.05 Mon || Chen, Yuan and Krantsevich, Artem || Progress Report  
+
| 2014.05.07 Wed || Yan and Yao || Oral Presentations: Progress Report
 
|-
 
|-
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| 2014.05.07 Wed || '''Last Day of Class''' <br> Chen, Ye and Huang, He || Progress Report
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| 2014.05.12 Mon || '''Last Day of Class''' || Class Make-Up Day
 
|-
 
|-
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| 2014.05.14 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'''
+
| 2014.05.14 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'''
 
|-
 
|-
 
|}
 
|}

Latest revision as of 14:18, 11 March 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
2014.01.27 Mon First Day of Class
Group Study 		Mathlab account setup
Discuss oral presentations and written report
handouts for unix / vim / csh tutorials
2014.01.29 Wed Group Study Confirm Mathlab accounts work
Go over unix / vim / csh tutorials
Seawulf account setup
2014.02.03 Mon Group Study SNOW STORM, CLASS CANCELLED
2014.02.05 Wed Group Study SNOW STORM, CLASS CANCELLED
2014.02.10 Mon Group Study Visualization/analysis software
VMD, Chimera, and MOE
2014.02.12 Wed Group Study Visualization/analysis software
VMD, Chimera, and MOE
SECTION 2: DOCK TUTORIAL
2014.02.17 Mon Group Study Tutorials: DOCK
individual project discussion Allen, W.
2014.02.19 Wed Group Study Tutorials: DOCK
individual project discussion
2014.02.24 Mon Group Study Tutorials: DOCK
individual project discussion
2014.02.26 Wed Group Study Tutorials: DOCK
individual project discussion
2014.03.03 Mon Group Study Tutorials: DOCK
finalize class wiki tutorial
SECTION 3: AMBER TUTORIAL
2014.03.05 Wed Group Study Tutorials: AMBER
individual project discussion Jiang L.
2014.03.10 Mon Group Study Tutorials: AMBER
individual project discussion
2014.03.12 Wed Group Study Tutorials: AMBER
individual project discussion
2014.03.17 Mon Spring Recess Spring Recess
2014.03.19 Wed Spring Recess Spring Recess
2014.03.24 Mon Group Study Tutorials: AMBER
individual project discussion
2014.03.26 Wed Approved Project Proposal Sheet Due
Group Study 		Tutorials: AMBER
finalize class wiki tutorial
SECTION 4: PROJECT PRESENTATIONS
2014.03.31 Mon Lu Bai and Mike Oral Presentations: Project Proposal
2014.04.02 Wed Ivan and Arkin Oral Presentations: Project Proposal
2014.04.07 Mon Tianao and Junjie Oral Presentations: Project Proposal
2014.04.09 Wed Mosavverul and Jessica Oral Presentations: Project Proposal
2014.04.14 Mon Kai and Fangfei Oral Presentations: Project Proposal
2014.04.16 Wed Preliminary Written Report Due
Yan and Yao 		Oral Presentations: Project Proposal
2014.04.21 Mon Lu Bai and Ivan Oral Presentations: Progress Report
2014.04.23 Wed Mike and Arkin Oral Presentations: Progress Report
2014.04.28 Mon Tianao and Junjie Oral Presentations: Progress Report
2014.04.30 Wed Mosavverul and Jessica Oral Presentations: Progress Report
2014.05.05 Mon Kai and Fangfei Oral Presentations: Progress Report
2014.05.07 Wed Yan and Yao Oral Presentations: Progress Report
2014.05.12 Mon Last Day of Class Class Make-Up Day
2014.05.14 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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