View source for 2020 AMS-536 Spring (original syllabus)


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'''PLEASE REFER TO THE REVISED SYLLABUS'''<br>
'''PLEASE REFER TO THE REVISED SYLLABUS'''<br>
'''PLEASE REFER TO THE REVISED SYLLABUS'''<br>
'''PLEASE REFER TO THE REVISED SYLLABUS'''<br>
</div>

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{| align="center" border="2" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:80%"
|- style="background:white" ! style="width:10%" 
| '''Supervisor''' || Dr. Robert C. Rizzo  [631-632-9340, robert dot rizzo -at- stonybrook.edu]
|-
| '''Instructor''' || Dr. Guilherme Duarte Ramos Matos [631-632-8519, guilherme dot duarteramosmatos -at- stonybrook dot edu]
|-
| '''Teaching Assistant''' || Steve Telehany  [631-632-8519, stephen dot telehany - at - stonybrook dot edu]
|-
| '''Course No.''' || AMS-536 / CHE-536
|-
| '''Location/Time''' || Math Tower, Room S235 (COMPUTER LAB next to SINC site), Mon/Wed 2:30PM - 3:50PM   
|-
| '''Office Hours''' || By appointment, Math Tower, Room 3-129, Dept. of Applied Math & Statistics
|-
| '''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>
|-
| '''Grading''' ||  Grades will be based on the quality of: <br>
(1) the oral presentations (15%); <br>
(2) attendance, participation in class discussion, and wiki tutorial construction (15%); and <br>
(3) the final written report (70%).
|-
|}
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== Project Information ==

'''Student Project Proposal OHARE Sheet'''
*[http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Projects/studentproject.OHARE.template.docx studentproject.OHARE.template.docx]


'''Oral Presentation Guidelines:''' These meetings should be formal and your chance to tell a complete story. Talks should be presented in PPT format and be between 20 and 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. 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


'''Final Report Guidelines and Example Final Papers'''
*[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]

== Schedule ==
* Please note that a doctor's excuse will be required if you miss your scheduled oral presentation date because of illness.


{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:95%"
|- style="background:lightblue"
| '''Date'''
| '''Participant'''
| '''Notes'''
|-
| || '''SECTION 1: COMPUTING INFRASTRUCTURE AND TOOLS''' ||
|-
| 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)
|-
| 2020.01.29 Wed || Group Study || Seawulf accounts setup <br> unix / vim / csh introduction <br> Visualization demo's Chimera and VMD
|-
| 2020.02.03 Mon ||| Group Study || Seawulf accounts setup <br> unix / vim / csh introduction <br> Visualization demo's Chimera and VMD
|-
| 2020.02.05 Wed ||| Group Study || Seawulf accounts setup <br> unix / vim / csh introduction <br> Visualization demo's Chimera and VMD
|-
| 2020.02.10 Mon || Group Study || Seawulf queuing system <br> 
|-
| 2020.02.12 Wed || Group Study ||  Seawulf queuing system <br>  Ethics in Writing (Rob)
|-
| || '''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] 
|-
| 2020.02.17 Mon || '''Draft Student Project Proposal OHARE Sheet Due''' <br> Group Study || Tutorials: DOCK virtual screening <br> individual project discussion 
|-
| 2020.02.19 Wed || Group Study || Tutorials: DOCK virtual screening <br> individual project discussion
|-
| 2020.02.24 Mon || '''Final Student Project Proposal OHARE Sheet Due''' <br> Group Study || Tutorials: DOCK virtual screening <br> individual project discussion
|-
| 2020.02.26 Wed || Group Study || Tutorials: DOCK virtual screening <br> individual project discussion
|-
| 2020.03.02 Mon || Group Study || Tutorials: DOCK virtual screening <br> individual project discussion
|-
| 2020.03.04 Wed || Group Study || Tutorials: DOCK virtual screening <br> individual project discussion
|-
| 2020.03.09 Mon || Group Study || Tutorials: DOCK de novo design <br> individual project discussion
|-
| 2020.03.11 Wed || Group Study || Tutorials: DOCK de novo design  <br> individual project discussion 
|-
| 2020.03.16 Mon || '''Spring Recess || Spring Recess'''
|-
| 2020.03.18 Wed || '''Spring Recess || Spring Recess'''
|-
| || '''REVISED SCHEDULE BEGINS HERE''' || ''REVISED SCHEDULE BEGINS HERE''
|-
| 2020.03.23 Mon || '''Extended Spring Recess || Extended Spring Recess'''
|-
| 2020.03.25 Wed || '''Extended Spring Recess || Extended Spring Recess'''
|-
| || '''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 ]
|-
| 2020.03.30 Mon || Group Study || Tutorials: AMBER <br> individual project discussion
|-
| 2020.04.01 Wed || Group Study || Tutorials: AMBER <br> individual project discussion
|-
| 2020.04.06 Mon || Group Study || Tutorials: AMBER <br> individual project discussion
|-
| 2020.04.08 Wed || Group Study || Tutorials: AMBER <br> finalize class wiki
|-
| || '''SECTION 4: PROJECT PRESENTATIONS''' ||
|-
| 2020.04.13 Mon || '''Draft Paper Due''' <br> Oral Presentations  ||Oral Presentations 
|- 
| 2020.04.15 Wed || Oral Presentations  || Oral Presentations 
|-
| 2020.04.20 Mon || Oral Presentations || Oral Presentations 
|-
| 2020.04.22 Wed || Group Study  || Project Analysis/Troubleshooting
|-
| 2020.04.27 Mon || '''Draft Paper Due''' <br> Group Study  || Project Analysis/Troubleshooting
|-
| 2020.04.29 Wed || Oral Presentations  || Oral Presentations 
|-
| 2020.05.04 Mon || Oral Presentations || Oral Presentations 
|-
| 2020.05.06 Wed || '''Last Day Class'''<br> Oral Presentations || Oral Presentations 
|-
| 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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<br>
'''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 has authorized that the following required statements appear in all teaching syllabi 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


'''Student Accessibility Support Center Statement:''' If you have a physical, psychological, medical, or learning disability that may impact your course work, please contact the Student Accessibility Support Center, 128 ECC Building, (631) 632-6748, or at sasc@stonybrook.edu. They will determine with you what accommodations are necessary and appropriate. All information and documentation is confidential.

Students who require assistance during emergency evacuation are encouraged to discuss their needs with their professors and the Student Accessibility Support Center. For procedures and information go to the following website: https://ehs.stonybrook.edu/programs/fire-safety/emergency-evacuation/evacuation-guide-people-physical-disabilities  and search Fire Safety and Evacuation and Disabilities. 


'''Academic Integrity Statement:''' Each student must pursue his or her academic goals honestly and be personally accountable for all submitted work. Representing another person's work as your own is always wrong. Faculty is required to report any suspected instances of academic dishonesty to the Academic Judiciary. Faculty in the Health Sciences Center (School of Health Technology & Management, Nursing, Social Welfare, Dental Medicine) and School of Medicine are required to follow their school-specific procedures. For more comprehensive information on academic integrity, including categories of academic dishonesty please refer to the academic judiciary website at http://www.stonybrook.edu/commcms/academic_integrity/index.html


'''Critical Incident Management:''' Stony Brook University expects students to respect the rights, privileges, and property of other people. Faculty are required to report to the Office of University Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn. Faculty in the HSC Schools and the School of Medicine are required to follow their school-specific procedures. Further information about most academic matters can be found in the Undergraduate Bulletin, the Undergraduate Class Schedule, and the Faculty-Employee Handbook.