Difference between revisions of "2013 AMS-536 Spring"

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! style="width:10%" | '''Instructor'''  
 
! style="width:10%" | '''Instructor'''  
 
| Dr. William J. Allen  [631-632-8519, william.allen@stonybrook.edu]
 
| Dr. William J. Allen  [631-632-8519, william.allen@stonybrook.edu]
−
Dr. Robert C. Rizzo    [631-632-8519, rizzorc@gmail.com]
 
 
|-
 
|-
 
| '''Course No.''' || AMS-536 / CHE-536
 
| '''Course No.''' || AMS-536 / CHE-536
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'''Project Approval Sheet'''
 
'''Project Approval Sheet'''
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*[http://rizzo.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/projectA.student.info.doc project.student.info.doc]
  
  
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'''Final Report Guidelines and Example Final Papers'''
 
'''Final Report Guidelines and Example Final Papers'''
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*[http://rizzo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/project.guidelines.pdf project.guidelines.pdf]
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*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/project.guidelines.pdf project.guidelines.pdf]
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*[http://rizzo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/project.example.dGhyd.pdf project.example.dGhyd.pdf]
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*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/project.example.dGhyd.pdf project.example.dGhyd.pdf]
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*[http://rizzo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/project.example.MMPS.pdf project.example.MMPS.pdf]
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*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/project.example.MMPS.pdf project.example.MMPS.pdf]
 
<br>
 
<br>
  
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| 2013.02.13 || Group Study || Visualization/analysis software <br> VMD, Chimera, and MOE
 
| 2013.02.13 || Group Study || Visualization/analysis software <br> VMD, Chimera, and MOE
 
|-
 
|-
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| 2013.02.18 || Group Study || Tutorials: DOCK <br> individual project discussion [http://rizzo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2013.02.18.ams536.pdf Allen, W.]
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| 2013.02.18 || 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.]
 
|-
 
|-
 
| 2013.02.20 || Group Study || Tutorials: DOCK <br> individual project discussion
 
| 2013.02.20 || Group Study || Tutorials: DOCK <br> individual project discussion
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| 2013.03.04 || Group Study || Tutorials: DOCK <br> wiki editing
 
| 2013.03.04 || Group Study || Tutorials: DOCK <br> wiki editing
 
|-
 
|-
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| 2013.03.06 || Group Study || Tutorials: AMBER <br> individual project discussion [http://rizzo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2012.02.29.ams536.lingling.amber_intro.pdf Jiang L.]
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| 2013.03.06 || 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.]
 
|-
 
|-
 
| 2013.03.11 || Group Study || Tutorials: AMBER <br> individual project discussion  
 
| 2013.03.11 || Group Study || Tutorials: AMBER <br> individual project discussion  
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| 2013.03.27 || Group Study || Tutorials: AMBER <br> wiki editing
 
| 2013.03.27 || Group Study || Tutorials: AMBER <br> wiki editing
 
|-
 
|-
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| 2013.04.01 || '''Deadline for project proposal discussion''' <br> Group Study || Project Setups / Troubleshooting
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| 2013.04.01 || '''Deadline for project proposal discussion''' <br> Foda, Zack and Kasavajhala, Koushik || Project Proposal
 
|-
 
|-
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| 2013.04.03 || Group Study || Project Setups / Troubleshooting
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| 2013.04.03 || Ralph, Brian and Guo, Jiaye || Project Proposal
 
|-
 
|-
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| 2013.04.08 || TBD || Project Proposal
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| 2013.04.08 || Shan, Jiahui and Krantsevich, Nick || Project Proposal
 
|-
 
|-
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| 2013.04.10 || TBD || Project Proposal
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| 2013.04.10 || Xing, Weiliang and Stenzoski, Natalie || Project Proposal
 
|-  
 
|-  
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| 2013.04.15 || TBD || Project Proposal
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| 2013.04.15 || Krantsevich, Artem and Chen, Yuan || Project Proposal
 
|-
 
|-
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| 2013.04.17 || '''Preliminary Report Due''' <br> TBD || Project Proposal  
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| 2013.04.17 || '''Preliminary Report Due''' <br> Huang, He and Chen, Ye || Project Proposal  
 
|-
 
|-
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| 2013.04.22 || TBD || Project Proposal
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| 2013.04.22 || Ralph, Brian and Kasavajhala, Koushik || Progress Report
 
|-
 
|-
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| 2013.04.24 || TBD || Progress Report
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| 2013.04.24 || Guo, Jiaye and Krantsevich, Nick || Progress Report
 
|-
 
|-
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| 2013.04.29 || TBD || Progress Report   
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| 2013.04.29 || Foda, Zach and Shan, Jiahui || Progress Report   
 
|-
 
|-
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| 2013.05.01 || TBD || Progress Report  
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| 2013.05.01 || Xing, Weiliang and Stenzoski, Natalie || Progress Report  
 
|-
 
|-
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| 2013.05.06 || TBD || Progress Report  
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| 2013.05.06 || Chen, Yuan and Krantsevich, Artem || Progress Report  
 
|-
 
|-
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| 2013.05.08 || '''Last Day of Class''' <br> TBD || Progress Report
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| 2013.05.08 || '''Last Day of Class''' <br> Chen, Ye and Huang, He || Progress Report
 
|-
 
|-
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| 2013.05.15 || '''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 Yuchen Zhou (Math Tower room 3-129) and email electronic copy to rizzorc@gmail.com'''
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| 2013.05.15 || '''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 Yuchen Zhou (Math Tower room 3-129) and email electronic copy to Joe'''
 
|-
 
|-
 
|}
 
|}

Latest revision as of 09:18, 7 August 2013


Instructor 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 2:20PM - 3:40PM
Office Hours Anytime or by appointment, Math Tower, Room 3-129, Dept. of Applied Math & Statistics
Teaching Assistant Yuchen Zhou, Math Tower, Room 3-129, Dept. of Applied Math & Statistics


Project Information

Project Approval 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
2013.01.28 First Day of Class and Organizational Meeting
Group Study 		Mathlab account setup
Discuss research paper and presentations
handouts for unix / vim / csh tutorials
2013.01.30 Group Study Confirm Mathlab accounts work
Go over unix / vim / csh tutorials
Seawulf account setup
2013.02.04 Group Study Continue unix / vim / csh tutorials
Logging into Seawulf
2013.02.06 Group Study Finish unix / vim / csh tutorials
Csh scripting exercises
Transfering files to Seawulf
2013.02.11 Group Study Visualization/analysis software
VMD, Chimera, and MOE
2013.02.13 Group Study Visualization/analysis software
VMD, Chimera, and MOE
2013.02.18 Group Study Tutorials: DOCK
individual project discussion Allen, W.
2013.02.20 Group Study Tutorials: DOCK
individual project discussion
2013.02.25 Group Study Tutorials: DOCK
individual project discussion
2013.02.27 Group Study Tutorials: DOCK
individual project discussion
2013.03.04 Group Study Tutorials: DOCK
wiki editing
2013.03.06 Group Study Tutorials: AMBER
individual project discussion Jiang L.
2013.03.11 Group Study Tutorials: AMBER
individual project discussion
2013.03.13 Group Study Tutorials: AMBER
individual project discussion
2013.03.18 Spring Recess Spring Recess
2013.03.20 Spring Recess Spring Recess
2013.03.25 Group Study Tutorials: AMBER
individual project discussion
2013.03.27 Group Study Tutorials: AMBER
wiki editing
2013.04.01 Deadline for project proposal discussion
Foda, Zack and Kasavajhala, Koushik 		Project Proposal
2013.04.03 Ralph, Brian and Guo, Jiaye Project Proposal
2013.04.08 Shan, Jiahui and Krantsevich, Nick Project Proposal
2013.04.10 Xing, Weiliang and Stenzoski, Natalie Project Proposal
2013.04.15 Krantsevich, Artem and Chen, Yuan Project Proposal
2013.04.17 Preliminary Report Due
Huang, He and Chen, Ye 		Project Proposal
2013.04.22 Ralph, Brian and Kasavajhala, Koushik Progress Report
2013.04.24 Guo, Jiaye and Krantsevich, Nick Progress Report
2013.04.29 Foda, Zach and Shan, Jiahui Progress Report
2013.05.01 Xing, Weiliang and Stenzoski, Natalie Progress Report
2013.05.06 Chen, Yuan and Krantsevich, Artem Progress Report
2013.05.08 Last Day of Class
Chen, Ye and Huang, He 		Progress Report
2013.05.15 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 Yuchen Zhou (Math Tower room 3-129) and email electronic copy to Joe
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