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| − | {| align="center" border="2" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:80%"
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| − | || '''Supervisor''' || Dr. Robert C. Rizzo [631-632-9340, robert.rizzo@stonybrook.edu]
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| − | | '''Instructor''' || Dr. Guilherme Duarte Ramos Matos [631-632-8519, guilherme dot duarteramosmatos -at- stonybrook dot edu]
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| − | | '''Teaching Assistant''' || Steve Telehany [631-632-8519, stephen dot telehany - at - stonybrook dot edu]
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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 2:30PM - 3:50PM
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| − | | '''Office Hours''' || By appointment, Math Tower, Room 3-129, Dept. of Applied Math & Statistics
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| − | | '''Acknowledgments''' || The AMS-536 instructors would like to thank: <br>
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| − | (1) Chemical Computing Group at http://www.chemcomp.com for generously providing MOE software teaching licenses <br>
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| − | (2) Firat Coskun and the LI-RED and SEAWULF team for cluster support <br>
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| − | (3) Pat Tonra for Mathlab support
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| − | <br>
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| − | == Project Information ==
| + | *[[2020 AMS-536 Spring (original syllabus)]] |
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| − | '''Student Project Proposal OHARE Sheet'''
| + | *[[2020 AMS-536 Spring (revised syllabus)]] |
| − | *[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/studentproject.OHARE.template.docx studentproject.OHARE.template.docx] | |
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| − | '''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:
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| − | *Introduction/Background (include biological relevance)
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| − | *Specifics of Your System
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| − | *Computational Details (theory)
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| − | *Computational Details (system setup)
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| − | *Results and Discussion (include a critical interpretation of your results)
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| − | *Conclusions
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| − | *Future
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| − | *Acknowledgments
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| − | '''Final Report Guidelines and Example Final Papers'''
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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://ringo.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.MMPS.pdf project.example.MMPS.pdf]
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| − | <br>
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| − | == Tutorials, Software Links, and Other Relevant Class Information==
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| − | *[http://ringo.ams.sunysb.edu/index.php/Rizzo_Lab_Information_and_Tutorials Rizzo_Lab_Information_and_Tutorials]
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| − | *Cheat Sheet: [[Unix]], [[Vi]], [[BASH scripting]], [[C_Shell_Scripting]], [[SLURM]]
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| − | *[http://www.ee.surrey.ac.uk/Teaching/Unix/index.html Unix Command Guide]
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| − | *[https://it.stonybrook.edu/help/kb/seawulf-queues Seawulf Queue Info]
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| − | *[https://en.wikipedia.org/wiki/Help:Cheatsheet Wikitext Cheat Sheet (for preparing tutorial Wiki page)]
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| − | *[https://www.mediawiki.org/wiki/Help:Formatting Wikitext Formatting Tips (for making the tutorial Wiki page pretty)]
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| − | *[https://www.youtube.com/watch?v=hQxKYSUdiD8 Chimera Basics - Video]
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| − | *[https://www.youtube.com/watch?v=eLxhKc7Ljjk Chimera Structure Analysis - Video]
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| − | == Schedule ==
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| − | * Each participant please update the Wiki as required with the title of your talk.
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| − | * Please note that a doctor's excuse will be required if you miss your scheduled oral presentation date because of illness.
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| − | | '''Date'''
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| − | | '''Participant'''
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| − | | '''Talk'''
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| − | | || '''SECTION 1: COMPUTING INFRASTRUCTURE AND TOOLS''' ||
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| − | | 2020.01.27 Mon || '''First Day of Class''' <br> Group Study || Seawulf accounts setup <br> unix / vim / csh introduction <br> Discuss presentations and final projects (OHARE sheets)
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| − | | 2020.01.29 Wed || Group Study || Seawulf accounts setup <br> unix / vim / csh introduction <br> Visualization demo's Chimera and VMD
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| − | | 2020.02.03 Mon ||| Group Study || Seawulf accounts setup <br> unix / vim / csh introduction <br> Visualization demo's Chimera and VMD
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| − | | 2020.02.05 Wed ||| Group Study || Seawulf accounts setup <br> unix / vim / csh introduction <br> Visualization demo's Chimera and VMD
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| − | | 2020.02.10 Mon || Group Study || Seawulf queuing system <br>
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| − | | 2020.02.12 Wed || Group Study || Seawulf queuing system <br> Ethics in Writing (Rob)
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| − | | || '''SECTION 2: DOCK TUTORIAL''' ( [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2013.02.18.ams536.pdf see Joe Allen slides] ) ||
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| − | | 2020.02.17 Mon || '''Draft Student Project Proposal OHARE Sheet Due''' <br> Group Study || Tutorials: DOCK virtual screening <br> individual project discussion
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| − | | 2020.02.19 Wed || Group Study || Tutorials: DOCK virtual screening <br> individual project discussion
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| − | | 2020.02.24 Mon || '''Final Student Project Proposal OHARE Sheet Due''' <br> Group Study || Tutorials: DOCK virtual screening <br> individual project discussion
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| − | | 2020.02.26 Wed || Group Study || Tutorials: DOCK de novo design <br> individual project discussion
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| − | | 2020.03.02 Mon || Group Study || Tutorials: DOCK de novo design <br> individual project discussion
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| − | | 2020.03.04 Wed || Group Study || Tutorials: DOCK de novo design <br> individual project discussion
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| − | | 2020.03.09 Mon || Group Study || Tutorials: DOCK genetic algorithm <br> individual project discussion
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| − | | 2020.03.11 Wed || Group Study || Tutorials: DOCK genetic algorithm <br> individual project discussion
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| − | | 2020.03.16 Mon || '''Spring Recess || Spring Recess'''
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| − | | 2020.03.18 Wed || '''Spring Recess || Spring Recess'''
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| − | | || '''SECTION 3: AMBER TUTORIAL''' ( [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2012.02.29.ams536.lingling.amber_intro.pdf see Lingling Jiang slides] ) ||
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| − | | 2020.03.23 Mon || Group Study || Tutorials: AMBER <br> individual project discussion
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| − | | 2020.03.25 Wed || Group Study || Tutorials: AMBER <br> individual project discussion
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| − | | 2020.03.30 Mon || Group Study || Tutorials: AMBER <br> individual project discussion
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| − | | 2020.04.01 Wed || Group Study || Tutorials: AMBER <br> individual project discussion
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| − | | 2020.04.06 Mon || Group Study || Tutorials: AMBER <br> individual project discussion
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| − | | 2020.04.08 Wed || Group Study || Tutorials: AMBER <br> finalize class wiki
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| − | | || '''SECTION 4: PROJECT PRESENTATIONS''' ||
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| − | | 2020.04.13 Mon || '''Draft Paper Due''' <br> Oral Presentations ||Oral Presentations (Miaomiao H., Chris C., Kalani J.)
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| − | | 2020.04.15 Wed || Oral Presentations || Oral Presentations (Ryan M., Brandon G, Scott L.)
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| − | | 2020.04.20 Mon || Oral Presentations || Oral Presentations (Steven P., Jose G., Yunlei Z.)
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| − | | 2020.04.22 Wed || Group Study || Project Analysis/Troubleshooting
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| − | | 2020.04.27 Mon || '''Draft Paper Due''' <br> Group Study || Project Analysis/Troubleshooting
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| − | | 2020.04.29 Wed || Oral Presentations || Oral Presentations (Kalani J., Brandon G., Yunlei Z.)
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| − | | 2020.05.04 Mon || Oral Presentations || Oral Presentations (Chris C., Scott L., Jose G.)
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| − | | 2020.05.06 Wed || '''Last Day Class'''<br> Oral Presentations || Oral Presentations (Miaomaio H., Ryan M., Steven P.)
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| − | | 2020.05.08 Fri || '''Final Written Report due by 5PM today.'''<br> || Give hard copy printout to Dr. Robert Rizzo (Math Tower room 1-111), Dr. Guilherme Matos (Math Tower room 3-129) or Steve Telehany (Math Tower room 3-129) and email electronic copy to rizzorc -at- gmail dot com and guilherme.duarteramosmatos -at- stonybrook dot edu
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| − | |}
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