TCB Hands-on Workshop in San Francisco

 

Evaluation of the Theoretical and Computational Biophysics Workshop in San Francisco

Lectures and Tutorials Evaluation

Questionnaire, analysis, and report: David Brandon, Molly Punke and Klaus Schulten, TCB group, UIUC

At the end of each day of the workshop participants were asked to evaluate the workshop's lectures and tutorials.  Rankings of the relevance of the lectures and tutorials were solicited, as were open comments about each lecture and tutorial. Participation in the evaluation was voluntary. 

Click here for the Lectures & Tutorials Feedback Form.

Summaries for the lectures and tutorials are comprised of three elements, 1) the proportion rating the relevance of the lecture or tutorial as highly relevant (i.e. 'very good' + 'excellent' ratings; see Table 1: Summary of Relevance Statistics below) and 2) select comments considered illustrative of respondent opinion, and 3) text summarizing the main points of the total body of comments for a lecture or tutorial.  As is frequently the case with surveys, not all respondents answered all questions; the number of responses for the relevance ratings (r=) and comments (c=) are listed next to the name of each lecture and tutorial summary, e.g. (N: r=34, c=8).

Some issues to consider when reading the comments: 

  • Written comments, particularly when comments are extreme in one direction or the other, tend to stick in one's head more so than statistics that may present a more accurate summary of opinion.
  • Attendees appear to have been somewhat heterogeneous in scientific background, training, interests, and to an extent language; so, for any lecture or tutorial there was likely always someone new to the topic who needed more time, help and explanation, and at the same time someone very experienced who wanted more breadth and/or depth on the topic.

Summaries are organized below by day, lecture, and tutorial, and can be located using the navigation table below or by scrolling down the page.

Day Lecture Tutorial
Day 1 Introduction to Protein Structure and Dynamics VMD Tutorial
Day 2 Statistical Mechanics of Proteins NAMD Tutorial
Day 3 Introduction to Bioinformatics Evolution of Protein Structure and Aquaporins Tutorials
Day 4 Parameters for Classical Force Fields Parameterizing a Novel Residue and Topology File Tutorialsl
Day 5 Simulating Membrane Channels Simulating Nanotubes and Stretching Deca-alanine Tutorials

Day 1

Day 1 Lecture: Molecular Graphics and Molecular Dynamics (N: r=19, c=15)

Most respondents, 89%, rated the lecture as highly relevant.  Sample comments are:

  • "Excellent lecture.  It really gave a good justification for molecular graphics-based analysis."

  • "This was really great. I didn’t really know about the capabilities of Molecular Dynamics. It was both exciting and informative."

While comments tend to have in common an appreciation of the introductory aspects of the lecture, there were suggestions for other topics to cover as well, e.g. the history of VMD, and strategies for effective graphic representations of proteins.

Day 1 Tutorial: VMD/Molecular Graphics (N: r=19, c=17)

A majority of respondents, 89%,  found the tutorial content highly relevant.  Sample comments are:

  • "Very useful to know all capabilities of VMD."
  • "Excellent tutorial – no ideas for improvement. The laptops, portable mice, and wireless internet were all great. The tutorial was well-written and informative."

Compliments on the tutorials are mixed with various suggestions, such as for more background/material on Tcl scripting.

Day 2

Day 2 Lecture: Equilibrium/Nonequilibrium Properties of Proteins (N: r=19, c=14)

At a 89% relevance rating, most respondents found the lecture content to be highly relevant.  Sample comments are:

  • "This is the best lecture in statistical mechanics I have ever had. Dr. Schulten explained complex ideas or problems by simple examples/analogies the best I’ve seen. Not only did I learn the concepts, but also the better ways to teach in the future. Thanks!"
  • "Excellent introduction! I learned a lot about what issues I should think about when using MD-making sure I’m doing something reasonable. “If you don’t have a hypothesis, don’t use the computer!” –KS. So true!"

Complimentary comments are mixed with comments debating the amount of mathematics and theory appropriate for the lecture.

Day 2 Tutorial: NAMD/Molecular Dynamics Tutorial (N: r=19, c=18)

Nearly all respondents, 89%, rated the tutorial relevance as very high.  Sample comments are:

  • "Very thorough examples and exercises."
  • "A nice concise explanation of the use of the package."

Respondents indicate wanting more time to work on the tutorial, and more background or in-depth exploration of some topics.

Day 3

Day 3 Lecture:  Introduction to Bioinformatics (N: r=17, c=15)

A majority of respondents, 70%, rated the relevance of the lecture as very high.  Sample comments are:

  • "Nobody teaches bioinformatics the way Zan does. Often you find people in biology with some computer science training, or vice versa. Zan knows it all: quantum chemistry, physics, biology and computer skills. Thanks for showing us what’s possible with VMD! And answering many questions! My impression of the UIUC group is that they offer service after sale, except that NAMD + VMD is 100% free. I won’t hesitate to ask questions after the workshop. They’re heroes."
  • "This was my favorite section. I really needed this material. I didn’t know that VMD was so powerful. Well done!"

Suggestions mixed in with appreciation for the lecture indicate some respondents needed more background in the topic to be able to understand some of the terminology used in the lecture.

Day 3 Tutorial: Evolution of Protein Structure; Bioinformatics Study of Aquaporins (N: r=17, c=15; r=17, c=10)

The rated relevance of the tutorials was high, with a relevance rating from respondents of 82% for the evolution of protein structure tutorial, and 90% for the aquaporins tutorial.  Sample comments are:

  • Evolution: "I learned a lot about the structural basis of how tRNA works. VMD seems to be powerful tool for doing structure-based sequence alignments."
  • Aquaporins: "Very good. Maybe for Q values a “zoom” on the Q values range could help to study in detail specific areas."

Respondent comments are appreciative of the tutorials and the topics they cover, though many suggest there is overlap in the content of the two tutorials.

Day 4

Day 4 Lecture: Determining Classical Force Fields (N: r=16, c=13)

Almost all respondents - 94% - rate the lecture as highly relevant.  Sample comments are:

  • "This lecture was extremely useful and informative! Emad just did an awesome job with this material."
  • "He was really very thorough in his explanations about the methods for doing the classical force field simulations etc. Dr T was really marvelous."

There are some suggestions for topics the lecture cover or directions to explore, but overall respondents are appreciative the lecture and lecturer.

Day 4 Tutorial: Parameterizing a Novel Residue; Topology Files (N: r=16, c=9; r=16, c=6)

Respondents generated an 87% relevance rating for the parameterization tutorial, and an 81% rating for the topology files tutorial.  Sample comments are:

  • Novel residue: "I really liked this tutorial! Watching the minimization was really cool. It was also great to use Spartan and see where the parameters actually come from (I previously thought they were just determined empirically from crystal structures)."
  • Topology: "Well done overall. I like the planned derailment of the calculation in the Parameterizing tutorial above, and think we could benefit greatly from such pedagogy here. Change a section of the parameter file, run, fail, explain why, repeat. It would be valuable in general to be exposed to every possible VMD + NAMD error over the course of the workshop!"

Comments are generally complimentary of the parameterization tutorial, with some specific suggestions made for improvement; for the topology tutorial, there are suggestions that less typing be required of tutorial users.

Day 5

Day 5 Lecture: Simulating Membrane Channels (N: r=16, c=11)

All respondents - 100% - rated the lecture as highly relevant to their interests.  Sample comments are:

  • "Speaker very knowledgeable, and lecture examples chosen were very interesting (aquaporin in particular). Learned a great deal that will help in my own work."
  • "Very good. Great intro to the area with nice examples. Details to analyze simulations were great, but the best part was to have the science as the main point and not the nice drawings."

Comments are uniformly positive, regarding the quality of the lecture presented and the amount respondents felt they learned.

Day 5 Tutorial: Simulating Nanotubes; Stretching Deca-Alanine (N: r=16, c=8; r=16, c=10)

With each tutorial earning a relevance rating of 100%, results indicate all of the respondents found the tutorials highly relevant. Sample comments are:

  • Nanotubes: "Yet another fantastic tutorial!"
  • Deca-alanine: "I now see the value in IMD and AutoIMD."

Again, comments are generally complimentary for both tutorials, with some suggestions that the deca-alanine tutorial provide more information on those aspects that involve Matlab.


The complete set of comments is available by e-mailing brandon@ks.uiuc.edu to request the comments.  


Table 1: Summary of Relevance Statistics

    Poor Fair Good Very Good Excellent
N % % % % %
Day 1 Lecture: Molecular Graphics and Molecular Dynamics 18     11 22 67
Day 1 Tutorial: VMD/Molecular Graphics 18     11 28 61
Day 2 Lecture: Equilibrium/Nonequilibrium Properties of Proteins 17     12 24 65
Day 2 Tutorial: NAMD/Molecular Dynamics Tutorial 18     11 44 44
Day 3 Lecture: Bioinformatics 17   6 24 29 41
Day 3 Tutorial: Evolution of Protein Structure 17     18 29 53
Day 3 Tutorial: Bioinformatics Study of Aquaporins 10     10 10 80
Day 4 Lecture: Determining Classical Force Fields 15     7 27 67
Day 4 Tutorial: Parameterizing a Novel Residue 15     13 40 47
Day 4 Tutorial: Topology Files 11   9 9 36 45
Day 5 Lecture: Simulating Membranes 16       13 88
Day 5 Tutorial: Nanotubes 15       27 73
Day 5 Tutorial: Stretching Deca-Alanine 12       42 58