2020 AMS-536 Spring (original syllabus)

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THIS IS THE ORIGINAL SYLLABUS, PLEASE REFER TO THE REVISED SYLLABUS
THIS IS THE ORIGINAL SYLLABUS, PLEASE REFER TO THE REVISED SYLLABUS
THIS IS THE ORIGINAL SYLLABUS, PLEASE REFER TO THE REVISED SYLLABUS
THIS IS THE ORIGINAL SYLLABUS, PLEASE REFER TO THE REVISED SYLLABUS


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:

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


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

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


Date Participant Notes
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 DOCK 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 AMBER slides
2020.03.23 Mon Group Study 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



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.

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