BELOW ARE EXAMPLES OF THE FEEDBACK YOU MAY GET ON YOUR PRESENTATION. Names have been changed. Topics are from a different graduate-level class. ----------------------------------------------------------- Jane. 03.25 Crisp presentation. Further examples. Good graphics. Take Home message(s). Missing: Intro, Motivation. ----------------------------------------- Joe. Fast Maltipoles. Good Motivation. Nice, intuitive graphics in the actual algorithm. Good idea to illustrate on "easier" implementation. Missing: Brief Table of Content. Take home message is missing. First graphics too small. The 1st slide was somewhat confusing. It is always a good idea to get the main idea across as clear as possible. Then, once people got the gist of it, go to specific implementation. Accuracy? Which parameter(s) control it? (Remember: speed and accuracy are key properties of any method). Small point: I would talk about computational complexity towards the end. I would also briefly discuss why it is NlogN. Very small point: Give enough information for a cited paper so that people can look it up. E.g. Onufriev et. al. Proteins, 55, 383-394 (2004). or Alexey Onufriev, D. Bashford and D.A. Case, "Exploring native states and large-scale conformational changes with a modified Generalized Born model.", Proteins, (2004). ========================== Mar 27 ========================== Jane: "Ewald Summation" Good beginning. Summary. Critiques: Motivational slide: mismatch between the slide and what you have said. Why previosly existing algorithms were bad? Main critique: more time needed to explain the key concept. Graphics would have really helped. ------------------------- Joe: "Different Molecular Surface Definitions. Good general motivation. Good outline. Good intro into surfaces, but one key element missing: water size = probe. Good use of graphics. Critique: connection between hard math and graphics is not very clear in some case. Suggestion: work out just one example in detail. Missing motivation: why you need smooth surface? Why are discontinuities bad? Generally, too many details in some parts. ============================================================= April 3. Jane: "Mutiple Conformational States..." Outline: Ok. Motivation: OK, but woild not hurt to throw in a picture of myoglobin. Serious critique: need to spend more time explaining key concepts/definitions. Perhaps give very simple examples illustrating the more complex real picture. Critique: do not present material you do not understand. Critique: Take home message? ---------------------- Joe: the "Contact order paper" Outline: Ok. Motivation: Ok. Great use of graphics to introduce the key concept (local contacts). Take home message: OK. Critique: define terms where first used (local vs. non-local). You don't need to dive into a rigorous definition right away, but you want to give people a qualitative, intuitive explanation. Use illustration. One way to do it would be to present your defining slides first, and then formulate the problem. Critique: Define axes labels. ln(folding rate) is better than just ln(k). Critique: Make sure each quantity is defined: e.g. dG = [(L-S)/L]^CO*L. ---------------------------------------- April 8. (2nd presentation) Jane: "Folding at Home". Outline. Ok. Motivation. OK. Critique: never show graphics that can't be seen. Critique: needed to spend a bit more time on the science of it. ----------------------------- Joe: CAVER. Outline: OK. Motivation: OK. Good use of graphics from a separate paper to support the concepts. Good description of the algorithm. Pictures. Take Home. Small critique: would make sense to discuss how multiple tunnels are found? ===================================================================== April 15. Jane: MD on Anton. Outline. Ok. Motivation. OK. Critique: any molecular dynamics can not simulate milliseconds? That's not true.Need to be more specific: atomistic. Critique: what is determinism? Time-reversibility? Why are these important? Critique: make sure you understand how things are done (e.g. errors computed relative to what? ) OR do not talk about it. You do not have to talk about everything. Conclusion: OK. April 17. -------------------------------------------------------------- Joe: Millisecond folding. Outline OK. Motivation OK. Critique: introduce unknown terminiology (GROMACS). Especially key ones: RMSD. A movie: good idea. Conclusions OK. ----------------------------------------------------- Jane: The top7 paper. Good motivation. Critique: focus on the key part (simultaneous optimization ofsequence and structure). Critique: this is the type of paper where you want to use graphics to describe what was done. Too many numbers/details. Small critique: should have mentioned unusually high stability of the protein. --------------------------------------- April 22. Joe: DE Saws folding paper. Outline. OK. Motivation Ok. Pictures nicely labelled. Notable: Researched "around" the paper, even contacted the authors. Suggestion: you are talking after Anton was introduced in this class, a good idea to mention previous speaker, as a courtsey. Very good talk over-all.