2020 AMS-536 Spring (revised syllabus)

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THIS IS A REVISED SYLLABUS (see notes below)
THIS IS A REVISED SYLLABUS (see notes below)
THIS IS A REVISED SYLLABUS (see notes below)
THIS IS A REVISED SYLLABUS (see notes below)


Supervisor Dr. Robert C. Rizzo [631-632-9340, robert.rizzo@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:

(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

Grading Grades will be based on the quality of:

(1) the oral presentations (15%);
(2) attendance, participation in class discussion, and wiki tutorial construction (15%); and
(3) the final written report (70%).



Revised Syllabus Notes

As a result of the COVID-19 outbreak the course syllabus has been revised per University Instructions to address the semester being shortened by one week and document changes necessary to teach the course online for the rest of the semester. A brief summary of the items that will remain the same or be modified include:


(1) The schedule has been revised starting March 16 2020.
(2) We will continue to hold class (online) via the Zoom program at the regularly scheduled time.
(3) Class tutorials will be prerecorded and uploaded as online videos (these tutorials should be viewed before our regular class time).
(4) Project presentations will be recorded by each participant individually, at home, and then emailed to the instructors for dissemination to the entire class (these presentations should be viewed our before regular class time).


Project Information

Student Project Proposal OHARE Sheet


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 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


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 doctor's excuse will be required if you miss your scheduled oral presentation date because of illness.


Date Participant Talk
SECTION 1: COMPUTING INFRASTRUCTURE AND TOOLS
2020.01.27 Mon First Day of Class
Group Study 		Seawulf accounts setup
unix / vim / csh introduction
Discuss presentations and final projects (OHARE sheets)
2020.01.29 Wed Group Study Seawulf accounts setup
unix / vim / csh introduction
Visualization demo's Chimera and VMD
2020.02.03 Mon Group Study Seawulf accounts setup
unix / vim / csh introduction
Visualization demo's Chimera and VMD
2020.02.05 Wed Group Study Seawulf accounts setup
unix / vim / csh introduction
Visualization demo's Chimera and VMD
2020.02.10 Mon Group Study Seawulf queuing system
2020.02.12 Wed Group Study Seawulf queuing system
Ethics in Writing (Rob)
SECTION 2: DOCK TUTORIAL ( see Joe Allen slides )
2020.02.17 Mon Draft Student Project Proposal OHARE Sheet Due
Group Study 		Tutorials: DOCK virtual screening
individual project discussion
2020.02.19 Wed Group Study Tutorials: DOCK virtual screening
individual project discussion
2020.02.24 Mon Final Student Project Proposal OHARE Sheet Due
Group Study 		Tutorials: DOCK virtual screening
individual project discussion
2020.02.26 Wed Group Study Tutorials: DOCK virtual screening
individual project discussion
2020.03.02 Mon Group Study Tutorials: DOCK virtual screening
individual project discussion
2020.03.04 Wed Group Study Tutorials: DOCK virtual screening
individual project discussion
2020.03.09 Mon Group Study Tutorials: DOCK de novo design
individual project discussion
2020.03.11 Wed Group Study Tutorials: DOCK de novo design
individual project discussion
2020.03.16 Mon Spring Recess Spring Recess
2020.03.18 Wed Spring Recess Spring Recess
SECTION 3: AMBER TUTORIAL ( see Lingling Jiang slides )
2020.03.23 Mon AMBER prep video
Video discussion forum		 Tutorials: AMBER
individual project discussion
2020.03.25 Wed Group Study Tutorials: AMBER
individual project discussion
2020.03.30 Mon Group Study Tutorials: AMBER
individual project discussion
2020.04.01 Wed Group Study Tutorials: AMBER
individual project discussion
2020.04.06 Mon Group Study Tutorials: AMBER
individual project discussion
2020.04.08 Wed Group Study Tutorials: AMBER
finalize class wiki
SECTION 4: PROJECT PRESENTATIONS
2020.04.13 Mon Draft Paper Due
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
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
Oral Presentations 		Oral Presentations
2020.05.08 Fri Final Written Report due by 5PM today.
 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

Academic Integrity

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 [1]

Student Accessibility

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: [2] and search Fire Safety and Evacuation and Disabilities.

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.

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