View source for 2013 AMS-536 Spring

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|- style="background:white"
! style="width:10%" | '''Instructor''' 
| Dr. William J. Allen  [631-632-8519, william.allen@stonybrook.edu]
Dr. Robert C. Rizzo    [631-632-8519, rizzorc@gmail.com] 
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| '''Course No.''' || AMS-536 / CHE-536
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| '''Location/Time''' || Math Tower, Room S235 (COMPUTER LAB next to SINC site), Mon/Wed 2:20PM - 3:40PM   
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| '''Office Hours''' || Anytime or by appointment, Math Tower, Room 3-129, Dept. of Applied Math & Statistics
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| '''Teaching Assistant''' || Yuchen Zhou, Math Tower, Room 3-129, Dept. of Applied Math & Statistics
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== Project Information ==

'''Project Approval Sheet'''
*[http://rizzo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/projectA.student.info.doc project.student.info.doc]


'''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'''
*[http://rizzo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/project.guidelines.pdf project.guidelines.pdf]
*[http://rizzo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/project.example.dGhyd.pdf project.example.dGhyd.pdf]
*[http://rizzo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/project.example.MMPS.pdf project.example.MMPS.pdf]
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== Tutorials, Software Links, and Other Relevant Class Information==
*[http://ringo.ams.sunysb.edu/index.php/Rizzo_Lab_Information_and_Tutorials Rizzo_Lab_Information_and_Tutorials]
*Cheat Sheet: [[Unix]], [[Vi]], [[C_Shell_Scripting]]

== 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.


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| '''Date'''
| '''Participant'''
| '''Talk'''
|-
| 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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| 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 
|-
| 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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| 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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| 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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| 2013.02.13 || Group Study || Visualization/analysis software, <br> VMD, MOE, Chimera, <br> Seawulf account setups, environments, shell scripting, misc unix
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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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| 2013.02.20 || 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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| 2013.02.27 || Group Study || Tutorials: DOCK <br> individual project discussion
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| 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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| 2013.03.11 || 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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| 2013.03.18 || Spring Recess || Spring Recess
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| 2013.03.20 || Spring Recess || Spring Recess
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| 2013.03.25 || Group Study || Tutorials: AMBER <br> individual project discussion
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| 2013.03.27 || Group Study || Tutorials: AMBER <br> wiki editing
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| 2013.04.01 || Group Study || Project Setups / Troubleshooting
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| 2013.04.03 || Group Study || Project Setups / Troubleshooting
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| 2013.04.08 || TBD || Project Proposal
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| 2013.04.10 || TBD || Project Proposal
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| 2013.04.15 || TBD || Project Proposal
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| 2013.04.17 || '''Preliminary Report Due''' <br> TBD || Project Proposal 
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| 2013.04.22 || TBD || Project Proposal
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| 2013.04.24 || TBD || Progress Report
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| 2013.04.29 || TBD || Progress Report  
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| 2013.05.01 || TBD || Progress Report 
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| 2013.05.06 || TBD || Progress Report 
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| 2013.05.08 || '''Last Day of Class''' <br> TBD || 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 Lingling Jiang (Math Tower room 3-129) and email electronic copy to rizzorc@gmail.com'''
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