Difference between revisions of "2013 AMS-536 Spring"

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| '''Talk'''
 
| '''Talk'''
 
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| 2012.01.28 || '''First Day of Class and Organizational Meeting''' <br> Group Study || Mathlab account setups, Unix and vi tutorials <br> (1) http://www.ee.surrey.ac.uk/Teaching/Unix <br> (2) At Linux command prompt type "vimtutor" (without the quotes) to start a built in tutorial for the text editor program called vi
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| 2013.01.28 || '''First Day of Class and Organizational Meeting''' <br> Group Study || Mathlab account setups, Unix and vi tutorials <br> (1) http://www.ee.surrey.ac.uk/Teaching/Unix <br> (2) At Linux command prompt type "vimtutor" (without the quotes) to start a built in tutorial for the text editor program called vi
 
|-
 
|-
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| 2012.01.30 || Group Study || Continue Mathlab account setups, Unix and vi tutorials <br> (1) http://www.ee.surrey.ac.uk/Teaching/Unix <br> (2) At Linux command prompt type "vimtutor" (without the quotes) to start a built in tutorial for the text editor program called vi  
+
| 2013.01.30 || Group Study || Continue Mathlab account setups, Unix and vi tutorials <br> (1) http://www.ee.surrey.ac.uk/Teaching/Unix <br> (2) At Linux command prompt type "vimtutor" (without the quotes) to start a built in tutorial for the text editor program called vi  
 
|-
 
|-
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| 2012.02.04 || Group Study || Visualization/analysis software, <br> VMD, MOE, Chimera, <br> Seawulf account setups, environments, shell scripting, misc unix
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| 2013.02.04 || Group Study || Visualization/analysis software, <br> VMD, MOE, Chimera, <br> Seawulf account setups, environments, shell scripting, misc unix
 
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|-
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| 2012.02.06 || Group Study || Visualization/analysis software, <br> VMD, MOE, Chimera, <br> Seawulf account setups, environments, shell scripting, misc unix
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| 2013.02.06 || Group Study || Visualization/analysis software, <br> VMD, MOE, Chimera, <br> Seawulf account setups, environments, shell scripting, misc unix
 
|-
 
|-
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| 2012.02.11 || Group Study || Visualization/analysis software, <br> VMD, MOE, Chimera, <br> Seawulf account setups, environments, shell scripting, misc unix
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| 2013.02.11 || Group Study || Visualization/analysis software, <br> VMD, MOE, Chimera, <br> Seawulf account setups, environments, shell scripting, misc unix
 
|-
 
|-
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| 2012.02.13 || Group Study || Cheat Sheet: [[Unix]], [[Vi]], [[C_Shell_Scripting]]
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| 2013.02.13 || Group Study || Cheat Sheet: [[Unix]], [[Vi]], [[C_Shell_Scripting]]
 
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| 2012.02.18 || Group Study || Tutorials: DOCK <br> individual project discussion [http://rizzo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2012.02.13.ams536.joe.docking_intro.pdf Allen, W.]
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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/2012.02.13.ams536.joe.docking_intro.pdf Allen, W.]
 
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| 2012.02.20 || Group Study || Tutorials: DOCK <br> individual project discussion
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| 2013.02.20 || Group Study || Tutorials: DOCK <br> individual project discussion
 
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| 2012.02.25 || Group Study || Tutorials: DOCK <br> individual project discussion
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| 2013.02.25 || Group Study || Tutorials: DOCK <br> individual project discussion
 
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| 2012.02.27 || Group Study || Tutorials: DOCK <br> individual project discussion
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| 2013.02.27 || Group Study || Tutorials: DOCK <br> individual project discussion
 
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| 2012.03.04 || Group Study || Tutorials: DOCK <br> wiki editing
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| 2013.03.04 || Group Study || Tutorials: DOCK <br> wiki editing
 
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| 2012.03.06 || 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://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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| 2012.03.11 || Group Study || Tutorials: AMBER <br> individual project discussion  
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| 2013.03.11 || Group Study || Tutorials: AMBER <br> individual project discussion  
 
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| 2012.03.13 || Group Study || Tutorials: AMBER <br> individual project discussion  
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| 2013.03.13 || Group Study || Tutorials: AMBER <br> individual project discussion  
 
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| 2012.03.18 || Spring Recess || Spring Recess
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| 2013.03.18 || Spring Recess || Spring Recess
 
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| 2012.03.20 || Spring Recess || Spring Recess
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| 2013.03.20 || Spring Recess || Spring Recess
 
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| 2012.03.25 || Group Study || Tutorials: AMBER <br> individual project discussion
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| 2013.03.25 || Group Study || Tutorials: AMBER <br> individual project discussion
 
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| 2012.03.27 || Group Study || Tutorials: AMBER <br> wiki editing
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| 2013.03.27 || Group Study || Tutorials: AMBER <br> wiki editing
 
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| 2012.04.01 || Group Study || Project Setups / Troubleshooting
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| 2013.04.01 || Group Study || Project Setups / Troubleshooting
 
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| 2012.04.03 || Group Study || Project Setups / Troubleshooting
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| 2013.04.03 || Group Study || Project Setups / Troubleshooting
 
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| 2012.04.08 || TBD || Project Proposal
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| 2013.04.08 || TBD || Project Proposal
 
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| 2012.04.10 || TBD || Project Proposal
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| 2013.04.10 || TBD || Project Proposal
 
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| 2012.04.15 || TBD || Project Proposal
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| 2013.04.15 || TBD || Project Proposal
 
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| 2012.04.17 || '''Preliminary Report Due''' <br> TBD || Project Proposal  
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| 2013.04.17 || '''Preliminary Report Due''' <br> TBD || Project Proposal  
 
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| 2012.04.22 || TBD || Project Proposal
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| 2013.04.22 || TBD || Project Proposal
 
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| 2012.04.24 || TBD || Progress Report
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| 2013.04.24 || TBD || Progress Report
 
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| 2012.04.29 || TBD || Progress Report   
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| 2013.04.29 || TBD || Progress Report   
 
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| 2012.05.01 || TBD || Progress Report  
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| 2013.05.01 || TBD || Progress Report  
 
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|-
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| 2012.05.06 || TBD || Progress Report  
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| 2013.05.06 || TBD || Progress Report  
 
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|-
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| 2012.05.08 || '''Last Day of Class''' <br> TBD || Progress Report
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| 2013.05.08 || '''Last Day of Class''' <br> TBD || Progress Report
 
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| 2012.05.15 || '''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 Lingling Jiang (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 Lingling Jiang (Math Tower room 3-129) and email electronic copy to rizzorc@gmail.com'''
 
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Revision as of 15:36, 15 January 2013


Instructor 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
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 Lingling Jiang, 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 setups, Unix and vi tutorials
(1) http://www.ee.surrey.ac.uk/Teaching/Unix
(2) At Linux command prompt type "vimtutor" (without the quotes) to start a built in tutorial for the text editor program called vi
2013.01.30 Group Study Continue Mathlab account setups, Unix and vi tutorials
(1) http://www.ee.surrey.ac.uk/Teaching/Unix
(2) At Linux command prompt type "vimtutor" (without the quotes) to start a built in tutorial for the text editor program called vi
2013.02.04 Group Study Visualization/analysis software,
VMD, MOE, Chimera,
Seawulf account setups, environments, shell scripting, misc unix
2013.02.06 Group Study Visualization/analysis software,
VMD, MOE, Chimera,
Seawulf account setups, environments, shell scripting, misc unix
2013.02.11 Group Study Visualization/analysis software,
VMD, MOE, Chimera,
Seawulf account setups, environments, shell scripting, misc unix
2013.02.13 Group Study Cheat Sheet: Unix, Vi, C_Shell_Scripting
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 Group Study Project Setups / Troubleshooting
2013.04.03 Group Study Project Setups / Troubleshooting
2013.04.08 TBD Project Proposal
2013.04.10 TBD Project Proposal
2013.04.15 TBD Project Proposal
2013.04.17 Preliminary Report Due
TBD 		Project Proposal
2013.04.22 TBD Project Proposal
2013.04.24 TBD Progress Report
2013.04.29 TBD Progress Report
2013.05.01 TBD Progress Report
2013.05.06 TBD Progress Report
2013.05.08 Last Day of Class
TBD 		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 Lingling Jiang (Math Tower room 3-129) and email electronic copy to rizzorc@gmail.com
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