Difference between revisions of "2011 AMS-536 Spring"

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| 2011.01.31 || '''First Day of Class''' <br> Group Study || Organizational Meeting / '''Mathlab accounts'''
 
| 2011.01.31 || '''First Day of Class''' <br> Group Study || Organizational Meeting / '''Mathlab accounts'''
 
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| 2011.02.02 || Group Study || Visualization software #1, Misc unix skills <br> VMD, MOE, Chimera, vi, general unix cmds, shell scripting  
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| 2011.02.02 || Group Study || Visualization software #1, Misc unix skills <br> VMD, MOE, Chimera, vi, general unix cmds, shell scripting, Seawulf accounts
 
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| 2011.02.07 || Group Study || Visualization software #2, Misc unix skills <br> VMD, MOE, Chimera, vi, general unix cmds, shell scripting <br> '''Seawulf accounts'''
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| 2011.02.07 || Group Study || Visualization software #2, Misc unix skills <br> VMD, MOE, Chimera, vi, general unix cmds, shell scripting, Seawulf accounts
 
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| 2011.02.09 || Group Study || Visualization software #3, Misc unix skills <br> VMD, MOE, Chimera, vi, general unix cmds, shell scripting <br> '''Seawulf accounts'''
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| 2011.02.09 || Group Study || Visualization software #3, Misc unix skills <br> VMD, MOE, Chimera, vi, general unix cmds, shell scripting, Seawulf accounts
 
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| 2011.02.14 || Group Study || Visualization software #3, Misc unix skills <br> VMD, MOE, Chimera, vi, general unix cmds, shell scripting <br> '''Seawulf accounts''
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| 2011.02.14 || Group Study || Visualization software #3, Misc unix skills <br> VMD, MOE, Chimera, vi, general unix cmds, shell scripting, Seawulf accounts
 
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| 2011.02.16 || Group Study || Tutorials: Group 1=DOCK, Group 2=AMBER <br> project discussion
 
| 2011.02.16 || Group Study || Tutorials: Group 1=DOCK, Group 2=AMBER <br> project discussion
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| 2011.03.30 || Group Study || Project Setups / Troubleshooting
 
| 2011.03.30 || Group Study || Project Setups / Troubleshooting
 
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| 2011.04.04 || SPRING BREAK || NO CLASS
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| 2011.04.04 || Group Study || Project Setups / Troubleshooting
 
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| 2011.04.06 || SPRING BREAK || NO CLASS
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| 2011.04.06 || Last, First; Last, First|| Talk Title ; Talk Title
 
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| 2011.04.05 || Adler, Jeremy; Chang, Andrew || Talk Title ; Talk Title
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| 2011.04.05 || Last, First; Last, First|| Talk Title ; Talk Title
 
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| 2011.04.07 || Cheglikov, Alex; Cheng-Tsung, Eric || The design of novel modulators of actin assembly; Interaction between InhA and it's inhibitors
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| 2011.04.07 || Last, First; Last, First|| Talk Title ; Talk Title
 
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| 2011.04.12 || Gorgani, Farzan; Hauser, Kevin; || Talk Title ; mTER
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| 2011.04.12 || Last, First; Last, First|| Talk Title ; Talk Title
 
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| 2011.04.14 || Jiang, Lingling; Kirkup, Colleen|| Pharmacophore modeling based on Docking and MD for the inhibition of Gp41 ; Talk Title  
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| 2011.04.14 || Last, First; Last, First|| Talk Title ; Talk Title  
 
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| 2011.04.19 || Li, Haoquan; Neckles, Carla|| Talk Title ; Computational Studies of Thiolactomycin and KasA from the FASII Pathway in Mycobacterium tuberculosis
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| 2011.04.19 || Last, First; Last, First|| Talk Title ; Talk Title
 
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| 2011.04.21 || '''Preliminary Report Due''' <br> Adler, Jeremy; Chang, Andrew || Talk Title ; Talk Title
 
| 2011.04.21 || '''Preliminary Report Due''' <br> Adler, Jeremy; Chang, Andrew || Talk Title ; Talk Title
 
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| 2011.04.26 || Cheglikov, Alex; Cheng-Tsung, Eric || Talk Title ; Interaction between InhA and it's inhibitors
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| 2011.04.26 || Last, First; Last, First|| Talk Title ; Talk Title
 
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| 2011.04.28 || Gorgani, Farzan; Hauser, Kevin; || determining the conformation of changes of hnox ; Mechanics and Dynamics of a Mitochondrial Transcription Terminator
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| 2011.04.28 || Last, First; Last, First|| Talk Title ; Talk Title
 
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| 2011.05.03 || Jiang, Lingling; Kirkup, Colleen|| Pharmacophore modeling based on Docking and MD for the inhibition of Gp41; Talk Title   
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| 2011.05.03 || Last, First; Last, First|| Talk Title ; Talk Title   
 
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| 2011.05.05 || '''Last Day of Class''' <br> Li, Haoquan; Neckles, Carla|| Early Stages of Damage Recognition of human 8-oxoguanine glycosylase; Computational Studies of Thiolactomycin and KasA from the FASII Pathway in Mycobacterium tuberculosis
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| 2011.05.05 || '''Last Day of Class''' <br> Last, First; Last, First|| Talk Title ; Talk Title
 
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| 2011.05.12 || '''Final written report due by 5PM, May 12, 2010. Late papers will not be accepted.  See above for sample reports and detailed guidelines.''' || '''Give hard copy to Sudipto Mukherjee (Math Tower room 3-129) and email electronic copy to rizzorc@gmail.com'''
 
| 2011.05.12 || '''Final written report due by 5PM, May 12, 2010. Late papers will not be accepted.  See above for sample reports and detailed guidelines.''' || '''Give hard copy to Sudipto Mukherjee (Math Tower room 3-129) and email electronic copy to rizzorc@gmail.com'''
 
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Revision as of 12:38, 4 January 2011


Instructor 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 3:50PM - 5:10PM
Office Hours Anytime or by appointment, Room 1-101, Dept. of Applied Math & Statistics
Teaching Assistant Sudipto Mukherjee, Room 3-129, 2-8519, 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

Note: Each participant please update the Wiki as required with the title of your talk.


Date Participant Talk
2011.01.31 First Day of Class
Group Study 		Organizational Meeting / Mathlab accounts
2011.02.02 Group Study Visualization software #1, Misc unix skills
VMD, MOE, Chimera, vi, general unix cmds, shell scripting, Seawulf accounts
2011.02.07 Group Study Visualization software #2, Misc unix skills
VMD, MOE, Chimera, vi, general unix cmds, shell scripting, Seawulf accounts
2011.02.09 Group Study Visualization software #3, Misc unix skills
VMD, MOE, Chimera, vi, general unix cmds, shell scripting, Seawulf accounts
2011.02.14 Group Study Visualization software #3, Misc unix skills
VMD, MOE, Chimera, vi, general unix cmds, shell scripting, Seawulf accounts
2011.02.16 Group Study Tutorials: Group 1=DOCK, Group 2=AMBER
project discussion
2011.02.21 Group Study Tutorials: Group 1=DOCK, Group 2=AMBER
project discussion
2011.02.23 Group Study Tutorials: Group 1=DOCK, Group 2=AMBER
project discussion
2011.02.28 Group Study Tutorials: Group 1=AMBER, Group 2=DOCK
project discussion
2011.03.02 Group Study Tutorials: Group 1=AMBER, Group 2=DOCK
project discussion
2011.03.07 Group Study Tutorials: Group 1=AMBER, Group 2=DOCK
project discussion
2011.03.09 Group Study Tutorials: Group 1=AMBER, Group 2=DOCK
project discussion
2011.03.14 Group Study Tutorials: Group 1=AMBER, Group 2=DOCK
project discussion
2011.03.16 Group Study Project Setups / Troubleshooting
2011.03.21 Group Study Project Setups / Troubleshooting
2011.03.23 Group Study Project Setups / Troubleshooting
2011.03.28 Group Study Project Setups / Troubleshooting
2011.03.30 Group Study Project Setups / Troubleshooting
2011.04.04 Group Study Project Setups / Troubleshooting
2011.04.06 Last, First; Last, First Talk Title ; Talk Title
2011.04.05 Last, First; Last, First Talk Title ; Talk Title
2011.04.07 Last, First; Last, First Talk Title ; Talk Title
2011.04.12 Last, First; Last, First Talk Title ; Talk Title
2011.04.14 Last, First; Last, First Talk Title ; Talk Title
2011.04.19 Last, First; Last, First Talk Title ; Talk Title
2011.04.21 Preliminary Report Due
Adler, Jeremy; Chang, Andrew 		Talk Title ; Talk Title
2011.04.26 Last, First; Last, First Talk Title ; Talk Title
2011.04.28 Last, First; Last, First Talk Title ; Talk Title
2011.05.03 Last, First; Last, First Talk Title ; Talk Title
2011.05.05 Last Day of Class
Last, First; Last, First		 Talk Title ; Talk Title
2011.05.12 Final written report due by 5PM, May 12, 2010. Late papers will not be accepted. See above for sample reports and detailed guidelines. Give hard copy to Sudipto Mukherjee (Math Tower room 3-129) and email electronic copy to rizzorc@gmail.com
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