View source for 2023 AMS-536 Spring

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=== <center> Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage (Research and Teaching) </center> ===
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| '''Instructor''' || Dr. Robert C. Rizzo  [631-632-9340, robert dot rizzo -at- stonybrook.edu]
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| '''Teaching Assistant''' || Steve Pak  [631-632-8519, steven dot pak - at - stonybrook dot edu]
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| '''Teaching Assistant''' || John Bickel  [631-632-8519, john dot bickel - at - stonybrook dot edu]
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| '''Course No.''' || AMS-536 / CHE-536
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| '''Location/Time''' || Online, Monday and Wednesday 2:40PM - 4:00PM
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| '''Office Hours''' || Anytime or 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>
(1) Chemical Computing Group at http://www.chemcomp.com for generously providing MOE software teaching licenses <br>
(2) Firat Coskun and the LI-RED and SEAWULF team for cluster support <br>
(3) Pat Tonra for Mathlab support <br>
(4) Victor Poon for other computational support<br>
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| '''Grading''' ||  Grades will be based on the quality of: <br>
(1) attendance, participation in class discussion, wiki tutorial construction, assisting others (25%) <br>
(2) oral presentations (25%) <br>
(3) final written report (50%)
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== '''Online Syllabus Notes''' ==
As a result of the COVID-19 outbreak this computational lab-based course is being offered online. This is a mixed course meaning that there will be both synchronous and asynchronous aspects. Note that course grading criteria has been modified from previous years (see grading breakdown above). Other details for this semester are as follows:

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== General Information == 
* This is a lab based class that will be held at the regularly scheduled time (M/W 2:40-4:00PM) online via [https://it.stonybrook.edu/services/zoom ZOOM].
* It is imperative that everyone attend ALL lab classes since we will be providing critical material and going over computational tutorials and examples in "real time".  
* Based on prior experience, students that miss lab class quickly fall behind and it is difficult to catch up.
* All class correspondence should be addressed to ALL TA's/course Instructors.
* Please consult the Schedule below prior to coming to each each class.
* Oral Presentations of Class Projects will be recorded by each participant individually (see Recording Your Oral Presentation Using Zoom section below), at home, and then emailed to the Instructors (see Video Presentation due date below).
* Oral Presentations will be reviewed based on the Reviewer Assignments listed in the Schedule using a [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021_ams.536.presentation.assessment.docx Reviewer Assessment Sheet] .
* A key component of the course is a Final Written Report, based on an independent class project, which will be written in the format of a peer-reviewed journal article. 

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== Class Project Information ==
'''Student Project Proposal OHARE Sheet:''' OHARE stands for '''O'''bjective, '''H'''ypothesis, '''A'''pproach, '''R'''ational, and '''E'''xpected outcomes.  All students will submit (and revise as necessary) an OHARE sheet to help them clearly define and outline their independent projects. 
*[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 Guidelines:''' These presentations should be formal and your chance to tell a complete story. Talks should be presented in PPT format and be between 20 and 25 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. Check our guidelines on [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/how_not_to_make_a_presentation.pdf how not to make a presentation]. 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

<br>
'''Recording Your Oral Presentation Using Zoom:''' It is very straightforward to create a video of yourself giving a PPT presentation using Zoom:
*Download the Zoom app ( https://it.stonybrook.edu/services/zoom )
*Open the Zoom app
*Create a new Zoom meeting with only yourself (make sure audio and video are turned on)
*Share your screen
*Open your presentation in PPT and put in presentation mode
*Start recording and give a short test presentation to make sure that everything is working smoothly (use mouse as necessary to highlight specific regions of your slides)
*Stop recording and quit the meeting 
*Open the newly created video (using QuickTime or some other video player) to make sure that your test presentation has both audio and video and looks good
*Follow the above steps to create your "full-length" video presentation (videos should not exceed 20-25 minutes)
*Email your video to the Instructors who will make it available to the class (please name your Zoom video Lastname.mp4)

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'''Final Written Report Guidelines and Example Final Papers:''' Written project guidelines and example papers to use as a guide are provided below.
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/project.guidelines.pdf project.guidelines.pdf]
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/project.example.dGhyd.pdf project.example.dGhyd.pdf]
*[http://ringo.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]] 
**[[BASH scripting]] 
**[[C_Shell_Scripting]] 
**[[SLURM]]
*[http://www.ee.surrey.ac.uk/Teaching/Unix/index.html Unix Command Guide]
*[https://it.stonybrook.edu/help/kb/seawulf-queues Seawulf Queue Info]
*[https://en.wikipedia.org/wiki/Help:Cheatsheet Wikitext Cheat Sheet (for preparing tutorial Wiki page)]
*[https://www.mediawiki.org/wiki/Help:Formatting Wikitext Formatting Tips (for making the tutorial Wiki page pretty)]
*[https://www.youtube.com/watch?v=hQxKYSUdiD8 Chimera Basics - Video]
*[https://www.youtube.com/watch?v=eLxhKc7Ljjk Chimera Structure Analysis - Video]
*[https://njardarson.lab.arizona.edu/content/top-pharmaceuticals-poster Top Pharmaceutical Posters]
*[http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm DOCK6.9 User Manual]
*[http://ambermd.org/doc12/Amber16.pdf AMBER 16 User Manual]
*[http://www.alchemistry.org/wiki/Main_Page Free Energy Calculations]

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<br>
== Schedule ==
* Please note that a doctor's excuse will be required if a student miss any important deadlines because of illness.

{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:95%"
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| '''Date'''
| '''Participant'''
| '''Notes'''
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| - || '''SECTION 1: COMPUTING INFRASTRUCTURE AND TOOLS''' || Please make sure that the Zoom program is up and running on your home computer prior to the first class <br> https://it.stonybrook.edu/services/zoom
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| 2023.01.23 Mon || Group Study || '''First Day of Class''' <br> Seawulf accounts setup <br> unix / vim / csh introduction <br> Discuss class objectives and syllabus, OHARE sheets, wiki page creation, oral presentations, final written reports 
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| 2023.01.25 Wed || Group Study || Seawulf accounts setup/infrastructure <br> unix / vim / csh introduction <br> Visualization demo's Chimera 
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| 2023.01.30 Mon ||| Group Study || Seawulf accounts setup/infrastructure <br> unix / vim / csh introduction <br> Visualization demo's Chimera 
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| 2023.02.01 Wed ||| Group Study || Seawulf accounts setup/infrastructure <br> unix / vim / csh introduction <br> Visualization demo's Chimera 
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| 2023.02.06 Mon || Group Study || Seawulf accounts setup/infrastructure <br> unix / vim / csh introduction <br> Visualization demo's Chimera 
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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 DOCK slides] 
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| 2023.02.08 Wed || Group Study || Tutorials: DOCK virtual screening/de novo design <br> individual project discussion  
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| 2023.02.13 Mon || Group Study || '''Draft Student Project Proposal OHARE Sheet Due''' <br> Tutorials: DOCK virtual screening/de novo designg <br> individual project discussion 
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| 2023.02.15 Wed || Group Study || Tutorials: DOCK vvirtual screening/de novo design <br> individual project discussion
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| 2023.02.20 Mon || Group Study || '''Final Student Project Proposal OHARE Sheet Due''' <br> Tutorials: DOCK virtual screening/de novo design <br> individual project discussion
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| 2023.02.22 Wed || Group Study || Tutorials: DOCK virtual screening/de novo design <br> individual project discussion
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| 2023.02.27 Mon || Group Study || Tutorials: DOCK virtual screening/de novo design <br> individual project discussion
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| 2023.03.01 Wed || Group Study || Tutorials: DOCK virtual screening/de novo design <br> individual project discussion
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| 2023.03.06 Mon || Group Study || Tutorials: DOCK virtual screening/de novo design <br> individual project discussion
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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 AMBER slides ]
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| 2023.03.08 Wed || Group Study || Tutorials: AMBER molecular dynamics and analysis <br> individual project discussion
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| 2023.03.13 Mon || Spring Break || Spring Break
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| 2023.03.15 Wed || Spring Break || Spring Break
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| 2023.03.20 Mon || Group Study || Tutorials: AMBER molecular dynamics and analysis <br> individual project discussion
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| 2023.03.22 Wed || Group Study || Tutorials: AMBER molecular dynamics and analysis <br> individual project discussion
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| 2023.03.27 Mon || Group Study || Tutorials: AMBER molecular dynamics and analysis <br> individual project discussion
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| 2023.03.29 Wed || Group Study || Tutorials: AMBER molecular dynamics and analysis <br> individual project discussion
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| 2023.04.03 Mon || Group Study  || Tutorials: AMBER molecular dynamics and analysis <br> individual project discussion 
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| 2023.04.05 Wed || Group Study  || '''Draft Paper Due''' <br> Tutorials: AMBER molecular dynamics and analysis <br> individual project discussion 
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| - || '''SECTION 4: CLASS PROJECTS''' ||
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| 2023.04.10 Mon || Group Study  || Project Analysis/Troubleshooting 
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| 2023.04.12 Wed || Group Study  || Project Analysis/Troubleshooting 
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| 2023.04.17 Mon || Group Study  || Project Analysis/Troubleshooting
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| 2023.04.19 Wed || Group Study  || 

'''Class Project Videos Due''' (email videos to Steve Pak by 2:30PM today, please name files Lastname.mp4) <br>
<br>
'''(1) [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022_ams536_videos/2022_ams536_alcantara.mp4 alcantara.mp4]'''<br>
'''(2) [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022_ams536_videos/2022_ams536_sillato.mp4 sillato.mp4]'''<br>
'''(3) [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022_ams536_videos/2022_ams536_hall.mp4 hall.mp4]'''<br>
'''(4) [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022_ams536_videos/2022_ams536_takemura.mp4 takemura.mp4]'''<br>
'''(5) [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022_ams536_videos/2022_ams536_kochert.mp4 kochert.mp4]'''<br>
'''(6) [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022_ams536_videos/2022_ams536_boysan.mp4 boysan.mp4]'''<br>
'''(7) [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2022_ams536_videos/2022_ams536_dean.mp4 dean.mp4]'''<br>

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'''Reviewer Assignments for Class Project Videos''' (use video links above) <br> 
'''[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021_ams.536.presentation.assessment.docx Reviewer Assessment Sheets] are due 1 week from today''' <br>
<br>
(1) Alcantara will review
* Dean, Sillato
<br>
(2) Sillato will review
* Alcantara, Boysan
<br>
(3) Hall will review
* Sillato, Alcantara
<br>
(4) Takemura will review
* Hall, Dean
<br>
(5) Kochert will review
* Takemura, Hall
<br>
(6) Boysan will review
* Kochert, Takemura
<br>
(7) Dean will review
* Boysan, Kochert

<br>
Pak reviews
* Alcantara, Sillato, Hall
<br>
Bickel reviews
* Takemura, Kochert, Boysan
<br> 
Rizzo reviews
* Dean
<br>
<br>
Project Analysis/Troubleshooting
<br>
|-
| 2023.04.24 Mon || Group Study  || Project Analysis/Troubleshooting
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| 2023.04.26 Wed || Group Study || '''[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021_ams.536.presentation.assessment.docx Reviewer Assessment Sheets] Must Be Emailed to Steve Pak, John Bickel, and Rob Rizzo by 11:00PM based on your Reviewer Assignments from above''' <br> Project Analysis/Troubleshooting
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| 2023.05.01 Mon || Group Study  || Project Analysis/Troubleshooting 
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| 2023.05.03 Wed || Group Study  || '''Last Day Class'''<br> Project Analysis/Troubleshooting 
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| 2023.05.05 Fri || '''Final Written Report due by 5PM today.''' || '''Final Written Report due by 5PM today.''' <br> Please email electronic copy to rizzorc -at- gmail dot com and steven dot pak - at - stonybrook dot eduu and john dot bickel - at - stonybrook dot eduu using the file name template of "LASTNAME_FIRSTNAME_PAPER.pdf" 
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| 2023.05.05 Fri || '''Semester Withdrawal Information'''  || ''Last day students can submit a withdrawal form to the Graduate School/SPD. Petition required after this date.'' 
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|}
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'''GENERAL INFORMATION:''' AMS-536 is designed for students who wish to gain hands-on experience modeling biological molecules at the atomic level. In conjunction with the participants' interest, Molecular Mechanics, molecular dynamics, Monte Carlo, Docking (virtual screening), or Quantum Mechanics software packages will be used. Projects will include setup, execution, and analysis. Students will work on individual projects outside of class. Course participants will give presentations relevant to the simulations being performed and a final project report will be required. Grades will be based on the quality of the talks, participation in class discussion, attendance, and the final written report. Familiarity with working in a Unix (Linux) environment is desirable.


'''Learning Obectives:'''
*(1) Gain hands-on experience modeling biological molecules at the atomic level.  
*(2) Learn to navigate linx/unix operating system 
*(3) Learn shell scripting and text-based editing (vim program)
*(4) Learn to use a linux-based computing cluster that has a queuing system
*(5) Learn to use visualization software (Chimera, MOE, and VMD programs)
*(6) Setup, execute, and analyze docking (DOCK) and molecular dynamics (AMBER) tutorials.  
*(7) Give oral presentations on individual research projects which includes:
**(i) Introduction/Background (include biological relevance)
**(ii) Specifics of Your System
**(iii) Computational Details (theory)
**(iv) Computational Details (system setup)
**(v) Results and Discussion (include a critical interpretation of your results)
**(vi) Conclusions
**(vii) Future
**(viii) Acknowledgments
*(8) Write a polished well-referenced manuscript in the format of a peer-reviewed Journal Article.



'''LITERATURE DISCLAIMER:''' Hyperlinks and manuscripts accessed through Stony Brook University's electronic journal subscriptions are provided below for educational purposes only.


'''PRESENTATION DISCLAIMER:''' Presentations may contain slides from a variety of online sources for educational and illustrative purposes only, and use here does not imply that the presenter is claiming that the contents are their own original work or research.

== '''Required Syllabi Statements:''' ==
 The University Senate Undergraduate and Graduate Councils have authorized that the following required statements appear in all teaching syllabi (graduate and undergraduate courses) on the Stony Brook Campus.. This information is also located on the Provost’s website: https://www.stonybrook.edu/commcms/provost/faculty/handbook/academic_policies/syllabus_statement.php


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