2024 AMS-536 Spring

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Please see https://ringo.ams.stonybrook.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 Chris Corbo [631-632-8519, christopher dot corbo - at - stonybrook dot edu]
Teaching Assistant Brock Boysan [631-632-8519, brock dot boysan - at - stonybrook dot edu]
Course No. AMS-536 / CHE-536
Location/Time Math Tower Sinc Site, S235, Monday and Wednesday 2:30PM - 3:50PM
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%)



Syllabus Notes

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 2:30-3:50PM) in person.
  • It is imperative that everyone attend ALL lab classes in person 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.
  • Please note that a doctor's excuse will be required if a student misses any important deadlines because of illness.
  • 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 will be in person, and reviewed by course participants using the 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:

  • Title Slide
  • Talk Outline
  • 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 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

Date Participant Notes
- SECTION 1: COMPUTING INFRASTRUCTURE AND TOOLS
2024.01.22 Mon Group Study First 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
2024.01.24 Wed Group Study Seawulf accounts setup/infrastructure
unix / vim / csh introduction
Visualization demo's Chimera
2024.01.29 Mon Group Study Seawulf accounts setup/infrastructure
unix / vim / csh introduction
Visualization demo's Chimera
2024.01.31 Wed Group Study Seawulf accounts setup/infrastructure
unix / vim / csh introduction
Visualization demo's Chimera
2024.02.05 Mon Group Study Seawulf accounts setup/infrastructure
unix / vim / csh introduction
Visualization demo's Chimera
- SECTION 2: DOCK TUTORIAL see Joe Allen DOCK slides
2024.02.07 Wed Group Study Draft Student Project Proposal OHARE Sheet Due
Tutorials: DOCK virtual screening/de novo design
individual project discussion
2024.02.12 Mon Group Study Tutorials: DOCK virtual screening/de novo designg
individual project discussion
2024.02.14 Wed Group Study Tutorials: DOCK vvirtual screening/de novo design
individual project discussion
2024.02.19 Mon Group Study Final Student Project Proposal OHARE Sheet Due
Tutorials: DOCK virtual screening/de novo design
individual project discussion
2024.02.21 Wed Group Study Tutorials: DOCK virtual screening/de novo design
individual project discussion
2024.02.26 Mon Group Study Tutorials: DOCK virtual screening/de novo design
individual project discussion
2024.02.28 Wed Group Study Tutorials: DOCK virtual screening/de novo design
individual project discussion
2024.03.04 Mon Group Study Tutorials: DOCK virtual screening/de novo design
individual project discussion
- SECTION 3: AMBER TUTORIAL see Lingling Jiang AMBER slides
2024.03.06 Wed Group Study Tutorials: AMBER molecular dynamics and analysis
individual project discussion
2024.03.11 Mon Spring Break Spring Break
2024.03.13 Wed Spring Break Spring Break
2024.03.18 Mon Group Study Tutorials: AMBER molecular dynamics and analysis
individual project discussion
2024.03.20 Wed Group Study Tutorials: AMBER molecular dynamics and analysis
individual project discussion
2024.03.25 Mon Group Study Tutorials: AMBER molecular dynamics and analysis
individual project discussion
2024.03.27 Wed Group Study Tutorials: AMBER molecular dynamics and analysis
individual project discussion
2024.04.01 Mon Group Study Tutorials: AMBER molecular dynamics and analysis
individual project discussion
2024.04.03 Wed Group Study Draft Paper Due
Tutorials: AMBER molecular dynamics and analysis
individual project discussion
- SECTION 4: CLASS PROJECTS
2024.04.08 Mon Group Study solar eclipse
2024.04.10 Wed Group Study Oral presentations
Satya
An
2024.04.15 Mon Group Study Oral presentations
Hoang
Andrew
2024.04.17 Wed Group Study Oral presentations
Zach
Aishwarya
2024.04.22 Mon Group Study Oral presentations/Project Analysis/Troubleshooting
Kathleen - FINISH de novo/genetic tutorial
2024.04.24 Wed Group Study Project Analysis/Troubleshooting
2024.04.29 Mon Group Study Project Analysis/Troubleshooting
2024.05.01 Wed Group Study Last Day Class
Project Analysis/Troubleshooting
2024.05.03 Fri Final Written Report due by 5PM today. Final Written Report due by 5PM today.
Please email electronic copy to ALL Course Instructors using the file name template of "LASTNAME_FIRSTNAME_PAPER.pdf"
2024.05.03 Fri Semester Withdrawal Information Last day students can submit a withdrawal form to the Graduate School/SPD. Petition required after this date.



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 Student Conduct and Community Standards any disruptive behavior that interrupts their ability to teach, compromises the safety of the learning environment, or inhibits students' ability to learn. Until/unless the latest COVID guidance is explicitly amended by SBU, during Fall 2021"disruptive behavior” will include refusal to wear a mask during classes. For the latest COVID guidance, please refer to: https://www.stonybrook.edu/commcms/strongertogether/latest.php

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