2019 AMS-536 Spring
From Rizzo_Lab
| Instructor | Dr. Robert C. Rizzo [631-632-9340, robert.rizzo@stonybrook.edu] |
|---|---|
| Teaching Assistant | Lauren Prentis [631-632-8519, lep213 -at- gmail dot com] and 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 | 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 |
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
- Rizzo_Lab_Information_and_Tutorials
- Cheat Sheet: Unix, Vi, C_Shell_Scripting
- Unix Command Guide
- Seawulf Queue Info
- Example PBS Submission Script
- Useful PBS commands
- Wikitext Cheat Sheet (for preparing tutorial Wiki page)
- Wikitext Formatting Tips (for making the tutorial Wiki page pretty)
- Chimera Basics - Video
- Chimera Structure Analysis - Video
Schedule
- Each participant please update the Wiki as required with the title of your talk.
- Please note that a doctors excuse will be required if you miss your scheduled oral presentation date because of illness.
| Date | Participant | Talk |
| SECTION 1: COMPUTING INFRASTRUCTURE AND TOOLS | ||
| 2019.01.28 Mon | First Day of Class Group Study |
Seawulf accounts setup unix / vim / csh introduction Discuss presentations and final projects (OHARE sheets) |
| 2019.01.30 Wed | Group Study | Seawulf accounts setup unix / vim / csh introduction Visualization demo's Chimera and VMD |
| 2019.02.04 Mon | Group Study | Seawulf accounts setup unix / vim / csh introduction Visualization demo's Chimera and VMD |
| 2019.02.06 Wed | Group Study | Seawulf accounts setup unix / vim / csh introduction Visualization demo's Chimera and VMD |
| 2019.02.11 Mon | Group Study | Seawulf queuing system |
| 2019.02.13 Wed | Group Study | Seawulf queuing system Ethics in Writing (Rob) |
| SECTION 2: DOCK TUTORIAL ( see Joe Allen slides ) | ||
| 2019.02.18 Mon | Draft Student Project Proposal OHARE Sheet Due Group Study |
Tutorials: DOCK virtual screening individual project discussion |
| 2019.02.20 Wed | Group Study | Tutorials: DOCK virtual screening individual project discussion |
| 2019.02.25 Mon | Final Student Project Proposal OHARE Sheet Due Group Study |
Tutorials: DOCK virtual screening individual project discussion |
| 2019.02.27 Wed | Group Study | Tutorials: DOCK de novo design individual project discussion |
| 2019.03.04 Mon | Group Study | Tutorials: DOCK de novo design individual project discussion |
| 2019.03.06 Wed | Group Study | Tutorials: DOCK de novo design individual project discussion |
| 2019.03.11 Mon | Group Study | Tutorials: DOCK genetic algorithm individual project discussion |
| 2019.03.13 Wed | Group Study | Tutorials: DOCK genetic algorithm individual project discussion |
| 2019.03.18 Mon | Spring Recess | Spring Recess |
| 2019.03.20 Wed | Spring Recess | Spring Recess |
| SECTION 3: AMBER TUTORIAL ( see Lingling Jiang slides ) | ||
| 2019.03.25 Mon | Group Study | Tutorials: AMBER individual project discussion |
| 2019.03.27 Wed | Group Study | Tutorials: AMBER individual project discussion |
| 2019.04.01 Mon | Group Study | Tutorials: AMBER individual project discussion |
| 2019.04.03 Wed | Group Study | Tutorials: AMBER individual project discussion |
| 2019.04.08 Mon | Group Study | Tutorials: AMBER individual project discussion |
| 2019.04.10 Wed | Group Study | Tutorials: AMBER finalize class wiki |
| SECTION 4: PROJECT PRESENTATIONS | ||
| 2019.04.15 Mon | Draft Paper Due Oral Presentations |
Oral Presentations (John, Yuzhang) |
| 2019.04.17 Wed | Oral Presentations | Oral Presentations (Ryota, Amie) |
| 2019.04.22 Mon | Oral Presentations | Oral Presentations (Yong Mi, Niven) |
| 2019.04.24 Wed | Group Study | Project Analysis/Troubleshooting |
| 2019.04.29 Mon | Draft Paper Due Group Study |
Project Analysis/Troubleshooting |
| 2019.05.01 Wed | Oral Presentations | Oral Presentations (John, Yuzhang) |
| 2019.05.06 Mon | Oral Presentations | Oral Presentations (Ryota, Yong Mi) |
| 2019.05.08 Wed | Last Day Class Oral Presentations |
Oral Presentations (Amie, Niven) |
| 2019.05.10 Fri | Final Written Report due by 5PM today. |
Give hard copy printout to Robert Rizzo (Math Tower room 1-111) or Lauren Prentis/Steve Telehany (Math Tower room 3-129) and email electronic copy to rizzorc -at- gmail dot com |
