2020 AMS-536 Spring

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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%).


Project Information

Student Project Proposal OHARE Sheet


Oral Presentation Guidlines: These meetings should be formal and your chance to tell a complete story. Talks should be presented in PPT format and be 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. 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 de novo design
individual project discussion
2020.03.02 Mon Group Study Tutorials: DOCK de novo design
individual project discussion
2020.03.04 Wed Group Study Tutorials: DOCK de novo design
individual project discussion
2020.03.09 Mon Group Study Tutorials: DOCK genetic algorithm
individual project discussion
2020.03.11 Wed Group Study Tutorials: DOCK genetic algorithm
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 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 (Miaomiao H., Chris C., Kalani J.)
2020.04.15 Wed Oral Presentations Oral Presentations (Ryan M., Brandon G, Scott L.)
2020.04.20 Mon Oral Presentations Oral Presentations (Steven P., Jose G., Yunlei Z.)
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 (Kalani J., Brandon G., Yunlei Z.)
2020.05.04 Mon Oral Presentations Oral Presentations (Chris C., Scott L., Jose G.)
2020.05.06 Wed Last Day Class
Oral Presentations 		Oral Presentations (Miaomaio H., Ryan M., Steven P.)
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
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