Difference between revisions of "2018 AMS-536 Spring"
From Rizzo_Lab
| (4 intermediate revisions by the same user not shown) | |||
| Line 76: | Line 76: | ||
| || '''SECTION 2: DOCK TUTORIAL''' ( [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2013.02.18.ams536.pdf see Joe Allen slides] ) || | | || '''SECTION 2: DOCK TUTORIAL''' ( [http://ringo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2013.02.18.ams536.pdf see Joe Allen slides] ) || | ||
|- | |- | ||
| − | | 2018.02.12 Mon || '''Draft Student Project Proposal OHARE Sheet Due''' <br> Group Study || Tutorials: DOCK <br> individual project discussion | + | | 2018.02.12 Mon || '''Draft Student Project Proposal OHARE Sheet Due''' <br> Group Study || Tutorials: DOCK virtual screening <br> individual project discussion |
|- | |- | ||
| − | | 2018.02.14 Wed || Group Study || Tutorials: DOCK <br> individual project discussion | + | | 2018.02.14 Wed || Group Study || Tutorials: DOCK virtual screening <br> individual project discussion |
|- | |- | ||
| − | | 2018.02.19 Mon || Group Study || Tutorials: DOCK <br> individual project discussion | + | | 2018.02.19 Mon || Group Study || Tutorials: DOCK virtual screening <br> individual project discussion |
|- | |- | ||
| − | | 2018.02.21 Wed || Group Study || Tutorials: DOCK <br> individual project discussion | + | | 2018.02.21 Wed || Group Study || Tutorials: DOCK de novo design <br> individual project discussion |
|- | |- | ||
| − | | 2018.02.26 Mon || '''Final Student Project Proposal OHARE Sheet Due''' <br> Group Study || Tutorials: DOCK <br> individual project discussion | + | | 2018.02.26 Mon || '''Final Student Project Proposal OHARE Sheet Due''' <br> Group Study || Tutorials: DOCK de novo design <br> individual project discussion |
|- | |- | ||
| − | | 2018.02.28 Wed || Group Study || Tutorials: DOCK <br> individual project discussion | + | | 2018.02.28 Wed || Group Study || Tutorials: DOCK de novo design (NOVA) <br> individual project discussion |
|- | |- | ||
| − | | 2018.03.05 Mon || Group Study || Tutorials: DOCK <br> individual project discussion | + | | 2018.03.05 Mon || Group Study || Tutorials: DOCK genetic algorithm (CONGA) <br> individual project discussion |
|- | |- | ||
| − | | 2018.03.07 Wed || | + | | 2018.03.07 Wed || SNOW DAY || SNOW DAY |
|- | |- | ||
| 2018.03.12 Mon || '''Spring Recess || Spring Recess''' | | 2018.03.12 Mon || '''Spring Recess || Spring Recess''' | ||
| Line 100: | Line 100: | ||
| 2018.03.19 Mon || Group Study || Tutorials: AMBER <br> individual project discussion | | 2018.03.19 Mon || Group Study || Tutorials: AMBER <br> individual project discussion | ||
|- | |- | ||
| − | | 2018.03.21 Wed || | + | | 2018.03.21 Wed || SNOW DAY || SNOW DAY |
|- | |- | ||
| 2018.03.26 Mon || Group Study || Tutorials: AMBER <br> individual project discussion | | 2018.03.26 Mon || Group Study || Tutorials: AMBER <br> individual project discussion | ||
| Line 112: | Line 112: | ||
| || '''SECTION 4: PROJECT PRESENTATIONS''' || | | || '''SECTION 4: PROJECT PRESENTATIONS''' || | ||
|- | |- | ||
| − | | 2018.04.9 Mon || | + | | 2018.04.9 Mon || Group Study ||Project Analysis/Troubleshooting |
|- | |- | ||
| − | | 2018.04.11 Wed || '''Draft Paper Due''' <br> | + | | 2018.04.11 Wed || '''Draft Paper Due''' <br> Group Study || Project Analysis/Troubleshooting |
|- | |- | ||
| − | | 2018.04.16 Mon || | + | | 2018.04.16 Mon || Oral Presentations || Oral Presentations (Adam, Seungyoun) |
|- | |- | ||
| − | | 2018.04.18 Wed || | + | | 2018.04.18 Wed || Oral Presentations || Oral Presentations (Lakshan, Lauren) |
|- | |- | ||
| 2018.04.23 Mon || '''Draft Paper Due''' <br> Group Study || Project Analysis/Troubleshooting | | 2018.04.23 Mon || '''Draft Paper Due''' <br> Group Study || Project Analysis/Troubleshooting | ||
| Line 124: | Line 124: | ||
| 2018.04.25 Wed || Group Study || Project Analysis/Troubleshooting | | 2018.04.25 Wed || Group Study || Project Analysis/Troubleshooting | ||
|- | |- | ||
| − | | 2018.04.30 Mon || | + | | 2018.04.30 Mon || Oral Presentations || Oral Presentations (Adam, Seungyoun) |
|- | |- | ||
| − | | 2018.05.02 Wed || '''Last Day Class'''<br> | + | | 2018.05.02 Wed || '''Last Day Class'''<br> Oral Presentations || Oral Presentations (Lakshan, Lauren) |
|- | |- | ||
| 2018.05.03 Thur || '''Final Written Report due by 1PM today.'''<br> || 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 | | 2018.05.03 Thur || '''Final Written Report due by 1PM today.'''<br> || 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 | ||
|- | |- | ||
|} | |} | ||
Latest revision as of 14:24, 26 March 2018
| 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
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 | ||
| 2018.01.22 Mon | First Day of Class Group Study |
Mathlab/LI-RED accounts setup unix / vim / csh introduction Discuss presentations and final projects |
| 2018.01.24 Wed | Group Study | Mathlab/Seawulf accounts setup unix / vim / csh introduction Visualization demo's |
| 2018.01.29 Mon | Group Study | Mathlab/Seawulf accounts setup unix / vim / csh introduction Visualization demo's |
| 2018.01.31 Wed | Group Study | Mathlab/Seawulf accounts setup unix / vim / csh introduction Visualization demo's |
| 2018.02.05 Mon | Group Study | Unix / Vim Challenges |
| 2018.02.07 Wed | Group Study | Seawulf queuing system Chimera demo VMD demo Class Project Expectation: Ethics in Writing (Rob) |
| SECTION 2: DOCK TUTORIAL ( see Joe Allen slides ) | ||
| 2018.02.12 Mon | Draft Student Project Proposal OHARE Sheet Due Group Study |
Tutorials: DOCK virtual screening individual project discussion |
| 2018.02.14 Wed | Group Study | Tutorials: DOCK virtual screening individual project discussion |
| 2018.02.19 Mon | Group Study | Tutorials: DOCK virtual screening individual project discussion |
| 2018.02.21 Wed | Group Study | Tutorials: DOCK de novo design individual project discussion |
| 2018.02.26 Mon | Final Student Project Proposal OHARE Sheet Due Group Study |
Tutorials: DOCK de novo design individual project discussion |
| 2018.02.28 Wed | Group Study | Tutorials: DOCK de novo design (NOVA) individual project discussion |
| 2018.03.05 Mon | Group Study | Tutorials: DOCK genetic algorithm (CONGA) individual project discussion |
| 2018.03.07 Wed | SNOW DAY | SNOW DAY |
| 2018.03.12 Mon | Spring Recess | Spring Recess |
| 2018.03.14 Wed | Spring Recess | Spring Recess |
| SECTION 3: AMBER TUTORIAL ( see Lingling Jiang slides ) | ||
| 2018.03.19 Mon | Group Study | Tutorials: AMBER individual project discussion |
| 2018.03.21 Wed | SNOW DAY | SNOW DAY |
| 2018.03.26 Mon | Group Study | Tutorials: AMBER individual project discussion |
| 2018.03.28 Wed | Group Study | Tutorials: AMBER individual project discussion |
| 2018.04.02 Mon | Group Study | Tutorials: AMBER individual project discussion |
| 2018.04.04 Wed | Group Study | Tutorials: AMBER finalize class wiki |
| SECTION 4: PROJECT PRESENTATIONS | ||
| 2018.04.9 Mon | Group Study | Project Analysis/Troubleshooting |
| 2018.04.11 Wed | Draft Paper Due Group Study |
Project Analysis/Troubleshooting |
| 2018.04.16 Mon | Oral Presentations | Oral Presentations (Adam, Seungyoun) |
| 2018.04.18 Wed | Oral Presentations | Oral Presentations (Lakshan, Lauren) |
| 2018.04.23 Mon | Draft Paper Due Group Study |
Project Analysis/Troubleshooting |
| 2018.04.25 Wed | Group Study | Project Analysis/Troubleshooting |
| 2018.04.30 Mon | Oral Presentations | Oral Presentations (Adam, Seungyoun) |
| 2018.05.02 Wed | Last Day Class Oral Presentations |
Oral Presentations (Lakshan, Lauren) |
| 2018.05.03 Thur | Final Written Report due by 1PM 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 |
