Difference between revisions of "2021 AMS-536 Spring"

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'''Class Project Videos Due''' (email videos to Steve Pak by 2:30PM today, please name files Lastname.mp4) <br>
 
'''Class Project Videos Due''' (email videos to Steve Pak by 2:30PM today, please name files Lastname.mp4) <br>
 
<br>
 
<br>
'''(1) [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/videos/Lastname.mp4 Dovedytis.mp4]'''<br>
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'''(1) [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021_ams536_videos/2021_ams536_Dovedytis.mp4 Dovedytis.mp4]'''<br>
'''(2) [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/videos/Lastname.mp4 Foran.mp4]'''<br>
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'''(2) [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021_ams536_videos/2021_ams536_Foran.mp4 Foran.mp4]'''<br>
'''(3) [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/videos/Lastname.mp4 Kochath.mp4]'''<br>
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'''(3) [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021_ams536_videos/2021_ams536_Kochath.mp4 Kochath.mp4]'''<br>
'''(4) [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/videos/Lastname.mp4 Rangwala.mp4]'''<br>
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'''(4) [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021_ams536_videos/2021_ams536_Rangwala.mp4 Rangwala.mp4]'''<br>
'''(5) [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/videos/Lastname.mp4 Steier.mp4]'''<br>
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'''(5) [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021_ams536_videos/2021_ams536_Steier.mp4 Steier.mp4]'''<br>
'''(6) [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/videos/Lastname.mp4 Cuomo.mp4]'''<br>
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'''(6) [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021_ams536_videos/2021_ams536_Cuomo.mp4 Cuomo.mp4]'''<br>
'''(7) [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/videos/Lastname.mp4 He.mp4]'''<br>
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'''(7) [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021_ams536_videos/2021_ams536_He.mp4 He.mp4]'''<br>
'''(8) [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/videos/Lastname.mp4 Koller.mp4]'''<br>
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'''(8) [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2021_ams536_videos/2021_ams536_Koller.mp4 Koller.mp4]'''<br>
  
 
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| 2021.04.28 Wed || Group Study  || Project Analysis/Troubleshooting  
 
| 2021.04.28 Wed || Group Study  || Project Analysis/Troubleshooting  
 
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| 2021.05.03 Mon || 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 by 2:30PM based on your Reviewer Assignments from above''' <br> Project Analysis/Troubleshooting
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| 2021.05.03 Mon || 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 by 11:00PM based on your Reviewer Assignments from above''' <br> Project Analysis/Troubleshooting
 
|-
 
|-
 
| 2021.05.05 Wed || Group Study || '''Last Day Class'''<br> Project Analysis/Troubleshooting
 
| 2021.05.05 Wed || Group Study || '''Last Day Class'''<br> Project Analysis/Troubleshooting
 
|-
 
|-
| 2021.05.07 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
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| 2021.05.07 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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Revision as of 15:08, 3 May 2021

Please see http://ringo.ams.sunysb.edu/~rizzo for Rizzo Group Homepage (Research and Teaching)

Instructor Dr. Robert C. Rizzo [631-632-9340, robert dot rizzo -at- stonybrook.edu]
Teaching Assistant Steve Pak [631-632-8519, steven dot pak - at - stonybrook dot edu]
Teaching Assistant John Bickel [631-632-8519, john dot bickel - at - stonybrook dot edu]
Course No. AMS-536 / CHE-536
Location/Time Online, Monday and Wednesday 2:40PM - 4:00PM
Office Hours Anytime or by appointment, Math Tower, Room 3-129, Dept. of Applied Math & Statistics
Acknowledgments The AMS-536 instructors would like to thank:

(1) Chemical Computing Group at http://www.chemcomp.com for generously providing MOE software teaching licenses
(2) Firat Coskun and the LI-RED and SEAWULF team for cluster support
(3) Pat Tonra for Mathlab support
(4) Victor Poon for other computational support

Grading Grades will be based on the quality of:

(1) attendance, participation in class discussion, wiki tutorial construction, assisting others (25%)
(2) oral presentations (25%)
(3) final written report (50%)



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:


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 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 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.


Class Project Information

Student Project Proposal OHARE Sheet: OHARE stands for Objective, Hypothesis, Approach, Rational, and Expected outcomes. All students will submit (and revise as necessary) an OHARE sheet to help them clearly define and outline their independent projects.


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 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


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)


Final Written Report Guidelines and Example Final Papers: Written project guidelines and example papers to use as a guide are provided below.


Tutorials, Software Links, and Other Relevant Class Information



Schedule

  • Please note that a doctor's excuse will be required if a student miss any important deadlines because of illness.
Date Participant Notes
- 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
https://it.stonybrook.edu/services/zoom
2021.02.01 Mon Group Study First Day of Class -- SNOW DAY --
2021.02.03 Wed Group Study First Real Day of Class
Seawulf accounts setup
unix / vim / csh introduction
Discuss class objectives and syllabus, OHARE sheets, wiki page creation, oral presentations, final written reports, etc
Lecture Video
2021.02.08 Mon Group Study Seawulf accounts setup
unix / vim / csh introduction
Visualization demo's Chimera and VMD
Lecture Video
2021.02.10 Wed Group Study Seawulf accounts setup
unix / vim / csh introduction
Visualization demo's Chimera and VMD
Lecture Video
2021.02.15 Mon Group Study Seawulf queuing system

Lecture Video

2021.02.17 Wed Group Study Seawulf queuing system
Ethics in Writing (Rob)

Lecture Video

- SECTION 2: DOCK TUTORIAL see Joe Allen DOCK slides
2021.02.22 Mon Group Study Draft Student Project Proposal OHARE Sheet Due
Tutorials: DOCK virtual screening
individual project discussion
2021.02.24 Wed Group Study Tutorials: DOCK virtual screening
individual project discussion
2021.03.01 Mon Group Study Final Student Project Proposal OHARE Sheet Due
Tutorials: DOCK virtual screening
individual project discussion
2021.03.03 Wed Group Study Tutorials: DOCK virtual screening
individual project discussion
2021.03.08 Mon Group Study Tutorials: DOCK virtual screening
individual project discussion
2021.03.10 Wed Group Study Tutorials: DOCK virtual screening
individual project discussion
2021.03.15 Mon Group Study Tutorials: DOCK de novo design
individual project discussion
2021.03.17 Wed Group Study Tutorials: DOCK de novo design
individual project discussion
- SECTION 3: AMBER TUTORIAL see Lingling Jiang AMBER slides
2021.03.22 Mon Group Study Tutorials: AMBER molecular dynamics
individual project discussion
2021.03.24 Wed Group Study Tutorials: AMBER molecular dynamics
individual project discussion
2021.03.29 Mon Group Study Tutorials: AMBER molecular dynamics
individual project discussion
2021.03.31 Wed Group Study Tutorials: AMBER molecular dynamics
individual project discussion
2021.04.05 Mon Group Study Tutorials: AMBER molecular dynamics
individual project discussion
2021.04.07 Wed Group Study Tutorials: AMBER molecular dynamics
individual project discussion
- SECTION 4: CLASS PROJECTS
2021.04.12 Mon Group Study Draft Paper Due
Project Analysis/Troubleshooting
2021.04.14 Wed Group Study Project Analysis/Troubleshooting
2021.04.19 Mon Group Study Project Analysis/Troubleshooting
2021.04.21 Wed Group Study Project Analysis/Troubleshooting
2021.04.26 Mon Group Study

Class Project Videos Due (email videos to Steve Pak by 2:30PM today, please name files Lastname.mp4)

(1) Dovedytis.mp4
(2) Foran.mp4
(3) Kochath.mp4
(4) Rangwala.mp4
(5) Steier.mp4
(6) Cuomo.mp4
(7) He.mp4
(8) Koller.mp4


Reviewer Assignments for Class Project Videos (use video links above)
Reviewer Assessment Sheets are due 1 week from today

(1) Dovedytis will review

  • Foran, Kochath, Rangwala


(2) Foran will review

  • Dovedytis, Cuomo, He


(3) Kochath will review

  • Cuomo, He, Steier


(4) Rangwala will review

  • Foran, Kochath, Koller


(5) Steier will review

  • He, Koller, Rangwala


(6) Cuomo will review

  • Dovedytis, Foran, Koller


(7) He will review

  • Steier, Cuomo, Kochath


(8) Koller will review

  • Dovedytis, Steier, Rangwala


Pak reviews

  • Dovedytis, Steier, Kochath, Rangwala


Bickel reviews

  • He, Foran, Koller, Coumo



Project Analysis/Troubleshooting

2021.04.28 Wed Group Study Project Analysis/Troubleshooting
2021.05.03 Mon Group Study Reviewer Assessment Sheets Must Be Emailed to Steve Pak by 11:00PM based on your Reviewer Assignments from above
Project Analysis/Troubleshooting
2021.05.05 Wed Group Study Last Day Class
Project Analysis/Troubleshooting
2021.05.07 Fri Final Written Report due by 5PM today. Final Written Report due by 5PM today.
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"



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


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.