Difference between revisions of "2011 AMS-536 Spring"

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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/project.student.info.doc project.student.info.doc]
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*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/project.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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== Schedule ==
 
== Schedule ==
−
Note: Each participant please update the Wiki as required with the title of your talk.
+
* 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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| '''Talk'''
 
| '''Talk'''
 
|-
 
|-
−
| 2011.01.31 || '''First Day of Class''' <br> Group Study || Organizational Meeting / '''Mathlab accounts'''
+
| 2011.01.31 || '''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
 
|-
 
|-
−
| 2011.02.02 || Group Study || Visualization software #1, Misc unix skills <br> VMD, MOE, Chimera, vi, general unix cmds, shell scripting
+
| 2011.02.02 || 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  
 
|-
 
|-
−
| 2011.02.07 || Group Study || Visualization software #2, Misc unix skills <br> VMD, MOE, Chimera, vi, general unix cmds, shell scripting <br> '''Seawulf accounts'''
+
| 2011.02.07 || Group Study || Visualization/analysis software, <br> VMD, MOE, Chimera, <br> Seawulf account setups, environments, shell scripting, misc unix
 
|-
 
|-
−
| 2011.02.09 || Group Study || Visualization software #3, Misc unix skills <br> VMD, MOE, Chimera, vi, general unix cmds, shell scripting <br> '''Seawulf accounts'''
+
| 2011.02.09 || Group Study || Visualization/analysis software, <br> VMD, MOE, Chimera, <br> Seawulf account setups, environments, shell scripting, misc unix
 
|-
 
|-
−
| 2011.02.14 || Group Study || Visualization software #3, Misc unix skills <br> VMD, MOE, Chimera, vi, general unix cmds, shell scripting <br> '''Seawulf accounts''
+
| 2011.02.14 || Group Study || Visualization/analysis software, <br> VMD, MOE, Chimera, <br> Seawulf account setups, environments, shell scripting, misc unix
 
|-
 
|-
−
| 2011.02.16 || Group Study || Tutorials: Group 1=DOCK, Group 2=AMBER <br> project discussion
+
| 2011.02.16 || Group Study || Tutorials: AMBER <br> individual project discussion
 
|-
 
|-
−
| 2011.02.21 || Group Study || Tutorials: Group 1=DOCK, Group 2=AMBER <br> project discussion
+
| 2011.02.21 || Group Study || Tutorials: AMBER <br> individual project discussion
 
|-
 
|-
−
| 2011.02.23 || Group Study || Tutorials: Group 1=DOCK, Group 2=AMBER <br> project discussion
+
| 2011.02.23 || Group Study || Tutorials: AMBER <br> individual project discussion
 
|-
 
|-
−
| 2011.02.28 || Group Study || Tutorials: Group 1=AMBER, Group 2=DOCK <br> project discussion
+
| 2011.02.28 || Group Study || Tutorials: AMBER <br> individual project discussion
 
|-
 
|-
−
| 2011.03.02 || Group Study || Tutorials: Group 1=AMBER, Group 2=DOCK <br> project discussion
+
| 2011.03.02 || Group Study || Tutorials: AMBER <br> individual project discussion
 
|-
 
|-
−
| 2011.03.07 || Group Study || Tutorials: Group 1=AMBER, Group 2=DOCK <br> project discussion
+
| 2011.03.07 || Group Study || Tutorials: DOCK <br> individual project discussion
 
|-
 
|-
−
| 2011.03.09 || Group Study || Tutorials: Group 1=AMBER, Group 2=DOCK <br> project discussion
+
| 2011.03.09 || Group Study || Tutorials: DOCK <br> individual project discussion
 
|-
 
|-
−
| 2011.03.14 || Group Study || Tutorials: Group 1=AMBER, Group 2=DOCK <br> project discussion  
+
| 2011.03.14 || Group Study || Tutorials: DOCK <br> individual project discussion  
 
|-
 
|-
−
| 2011.03.16 || Group Study || Project Setups / Troubleshooting
+
| 2011.03.16 || Group Study || Tutorials: DOCK <br> individual project discussion
 
|-
 
|-
 
| 2011.03.21 || Group Study || Project Setups / Troubleshooting
 
| 2011.03.21 || Group Study || Project Setups / Troubleshooting
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| 2011.03.28 || Group Study || Project Setups / Troubleshooting
 
| 2011.03.28 || Group Study || Project Setups / Troubleshooting
 
|-
 
|-
−
| 2011.03.30 || Group Study || Project Setups / Troubleshooting
+
| 2011.03.30 || Fochtman, Brian; Ashiru-Balogun, Jibril || Talk Title ; Talk Title
 
|-
 
|-
−
| 2011.04.04 || SPRING BREAK || NO CLASS
+
| 2011.04.04 || Martingano, Daniel; Li, Zhu|| Talk Title ; Talk Title
 
|-
 
|-
−
| 2011.04.06 || SPRING BREAK || NO CLASS
+
| 2011.04.06 || Lee, So Jeong; Spagnuolo, Lauren|| Talk Title ; Talk Title
 
|-
 
|-
−
| 2011.04.05 || Adler, Jeremy; Chang, Andrew || Talk Title ; Talk Title
+
| 2011.04.11 || Jee, Jo-Ann; Cao, Yiwei|| Talk Title ; Talk Title
 
|-
 
|-
−
| 2011.04.07 || Cheglikov, Alex; Cheng-Tsung, Eric || The design of novel modulators of actin assembly; Interaction between InhA and it's inhibitors
+
| 2011.04.13 || Liao, Junzhuo; Akter, Rehana|| Talk Title ; Talk Title
 
|-  
 
|-  
−
| 2011.04.12 || Gorgani, Farzan; Hauser, Kevin; || Talk Title ; mTER
+
| 2011.04.18 || Spring Break || Spring Break
 
|-
 
|-
−
| 2011.04.14 || Jiang, Lingling; Kirkup, Colleen|| Pharmacophore modeling based on Docking and MD for the inhibition of Gp41 ; Talk Title
+
| 2011.04.20 || Spring Break || Spring Break
 
|-
 
|-
−
| 2011.04.19 || Li, Haoquan; Neckles, Carla|| Talk Title ; Computational Studies of Thiolactomycin and KasA from the FASII Pathway in Mycobacterium tuberculosis
+
| 2011.04.25 || Gardin, Justin; Fochtman, Brian || Talk Title ; Talk Title
 
|-
 
|-
−
| 2011.04.21 || '''Preliminary Report Due''' <br> Adler, Jeremy; Chang, Andrew || Talk Title ; Talk Title
+
| 2011.04.27 || '''Preliminary Report Due''' <br> Ashiru-Balogun, Jibril; Martingano, Daniel || Talk Title ; Talk Title
 
|-
 
|-
−
| 2011.04.26 || Cheglikov, Alex; Cheng-Tsung, Eric || Talk Title ; Interaction between InhA and it's inhibitors
+
| 2011.05.02 || Li, Zhu; Lee, So Jeong || Talk Title ; Talk Title
 
|-
 
|-
−
| 2011.04.28 || Gorgani, Farzan; Hauser, Kevin; || determining the conformation of changes of hnox ; Mechanics and Dynamics of a Mitochondrial Transcription Terminator
+
| 2011.05.04 || Spagnuolo, Lauren; Jee, Jo-Ann || Talk Title ; Talk Title
 
|-
 
|-
−
| 2011.05.03 || Jiang, Lingling; Kirkup, Colleen|| Pharmacophore modeling based on Docking and MD for the inhibition of Gp41; Talk Title   
+
| 2011.05.09 || Cao, Yiwei; Liao, Junzhuo|| Talk Title ; Talk Title   
 
|-
 
|-
−
| 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
+
| 2011.05.11 || '''Last Day of Class''' <br> Akter, Rehana; Gardin, Justin || 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'''
+
| 2011.05.18 || '''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 Sudipto Mukherjee (Math Tower room 3-129) and email electronic copy to rizzorc@gmail.com'''
 
|-
 
|-
 
|}
 
|}

Latest revision as of 16:23, 5 August 2013


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

  • 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
2011.01.31 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
2011.02.02 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
2011.02.07 Group Study Visualization/analysis software,
VMD, MOE, Chimera,
Seawulf account setups, environments, shell scripting, misc unix
2011.02.09 Group Study Visualization/analysis software,
VMD, MOE, Chimera,
Seawulf account setups, environments, shell scripting, misc unix
2011.02.14 Group Study Visualization/analysis software,
VMD, MOE, Chimera,
Seawulf account setups, environments, shell scripting, misc unix
2011.02.16 Group Study Tutorials: AMBER
individual project discussion
2011.02.21 Group Study Tutorials: AMBER
individual project discussion
2011.02.23 Group Study Tutorials: AMBER
individual project discussion
2011.02.28 Group Study Tutorials: AMBER
individual project discussion
2011.03.02 Group Study Tutorials: AMBER
individual project discussion
2011.03.07 Group Study Tutorials: DOCK
individual project discussion
2011.03.09 Group Study Tutorials: DOCK
individual project discussion
2011.03.14 Group Study Tutorials: DOCK
individual project discussion
2011.03.16 Group Study Tutorials: DOCK
individual project discussion
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 Fochtman, Brian; Ashiru-Balogun, Jibril Talk Title ; Talk Title
2011.04.04 Martingano, Daniel; Li, Zhu Talk Title ; Talk Title
2011.04.06 Lee, So Jeong; Spagnuolo, Lauren Talk Title ; Talk Title
2011.04.11 Jee, Jo-Ann; Cao, Yiwei Talk Title ; Talk Title
2011.04.13 Liao, Junzhuo; Akter, Rehana Talk Title ; Talk Title
2011.04.18 Spring Break Spring Break
2011.04.20 Spring Break Spring Break
2011.04.25 Gardin, Justin; Fochtman, Brian Talk Title ; Talk Title
2011.04.27 Preliminary Report Due
Ashiru-Balogun, Jibril; Martingano, Daniel 		Talk Title ; Talk Title
2011.05.02 Li, Zhu; Lee, So Jeong Talk Title ; Talk Title
2011.05.04 Spagnuolo, Lauren; Jee, Jo-Ann Talk Title ; Talk Title
2011.05.09 Cao, Yiwei; Liao, Junzhuo Talk Title ; Talk Title
2011.05.11 Last Day of Class
Akter, Rehana; Gardin, Justin 		Talk Title ; Talk Title
2011.05.18 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 Sudipto Mukherjee (Math Tower room 3-129) and email electronic copy to rizzorc@gmail.com
Retrieved from "https://ringo.ams.stonybrook.edu/index.php?title=2011_AMS-536_Spring&oldid=8026"