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Computational Biophysics Workshop - Lake Tahoe, May 23-27, 2005

Evaluation of the Theoretical and Computational Biophysics Workshop in Lake Tahoe

Lectures and Tutorials Evaluation

Questionnaire, analysis, and report: David Brandon 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.
• There aren't enough comments to provide a sample size that can be considered representative of the entire workshop population; e.g. for one tutorial there are three comments.  Further, those responding are self-selected, i.e. those who went through with completing the evaluation form may or may not be representative of a 'typical' attendee. 
• 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 1

Day 1 Lecture:  Introduction to Protein Structure and Dynamics (N: r=17, c=13)

Most respondents, 94%, rated the lecture as highly relevant.  Sample comments are:

• "This was an excellent introduction to VMD. It was useful to have the capabilities of the package explained to us; I was not aware of quite how complete the package is."
• "A very nice presentation of theory and practice of MD-simulations and visualization of results."

Overall, those commenting indicate the lecture provided a good overview, was well-presented and informative.  

Day 1 Tutorial:  VMD Tutorial (N: r=17, c=14)

As was the case for the day one lecture, 94% of respondents found the tutorial content highly relevant.  Sample comments are:

• "I like how it is step-by-step so that I can really try things. But also because of this format I can go back later and review items that I don't remember quickly. Also the TA's and Professor Tajkhorshid were extremely helpful."
• "The tutorial is really complete!! Congratulations."

Comments are generally, positive regarding the overall content and organization of the tutorial, with some comments suggesting scripting be discussed in more detail.

Day 2

Day 2 Lecture:  Introduction to Bioinformatics  (N: r=16, c=14)

A majority, 56%, rated the relevance of the lecture as very high.  Sample comments are:

• "Zan did a great job of clearly explaining not only some basic bioinformatics concepts but also how VMD can now be used to trivially do jobs that otherwise would require programming."
• "The lecture was very interesting."

Comments indicate an interest in the topic, with some suggesting more time for the topic or more discussion of some issues, and others indicating a lack of familiarity with some of the terms used.

Day 2 Tutorials:  Evolution of Protein Structure; Aquaporins Tutorial (N: r=15, c=11; r=11, c=7)

The relevance of the tutorials was high, with 93% rating  for Evolution of Protein Structure and 100% rating Aquaporins tutorial relevance as very good to excellent .  Sample comments are:

• Evolution: "Excellent, clear examples. Easy to follow. Made the usefulness of VMD to bioinformaticists very evident."
• Aquaporins: "The tutorial is easy to follow even for a first time user and also gives a lot of biological information and other related background. It should be easier to apply what I have learned to my own system. "

Comments are generally positive regarding the organization and writing of the tutorials.

Day 3

Day 3 Lecture:  Equilibrium/Nonequilibrium Properties of Proteins (N: r=18, c=13)

A clear majority, 89%, found the lecture content to be highly relevant.  Sample comments are:

• "This was an excellent lecture! Klaus reviewed the physical chemistry behind NAMD and showed how textbook results could be recovered from NAMD analyses. A number of statistical mechanical theorems were shown to be satisfied. Temperature echo was explained and the procedure for observing it in MD was elucidated."
• "This was good for me because I have already been running MD simulations using Tinker...today gave me a roadmap for how I do the things I have already been doing but now in this environment."

Overall, the comments are positive, indicating the speech was clearly delivered and informative.

Day 3 Tutorial:  NAMD Tutorial (N: r=18, c=15)

Almost all those responding, 95%, rated the tutorial relevance as very high.  Sample comments are:

• "The handouts were very detailed and everything (files, etc) was prepared. It was very easy to follow all the instructions step-by-step. Excellent for self education. I think that the tutorial needs more interactions between "students" and "instructors"."
• "It is very detailed and quite easy to understand, and to follow. It will not be difficult to transfer what I learned here to my own system. I can understand it is necessary to be as detailed as possible especially for those who have not gone through the previous tutorials. But I am still thinking can we make it a little simpler, e.g. simplifying the part about loading new molecules. The tutorial is quite long even just to read in 4 hours. "

Comments are generally positive about the tutorial, though many respondents indicate needing more time to get through the entire tutorial.

Day 4

Day 4 Lecture:  Determining Classical Force Fields  (N: r=17, c=15)

All respondents - 100% - rate the lecture as highly relevant.  Sample comments are:

• "Dr. Tajkhorshid's lecture was unusually informative. He has a clear grasp of quantum chemistry and an ability to explain the concepts and their application."
• "Excellent lecture. More information on the qm/mm would be nice, time permitting of course. I was instilled with the Importance of forcefield parameters well."

Comments are complimentary regarding the content and delivery of the lecture, with a few suggestions for additional topic, e.g., more on quantum chemistry and quantum mechanics. 

Day 4 Tutorials: Parameterizing a Novel Residue; Topology File Tutorial  (N: r=17, c=14; r=8, c=7)

Respondents indicated a 94% relevance rating for the Parameterizing tutorial, and a 100% rating for the Topology file tutorial.  Sample comments are:

• Parameterizing: "The tutorial is very well done and each step is very well explained."
• Topology: "It is very good and it gives very good tips to change topology files."

The comments offered some praise, but also some constructive criticism for the content and use of the tutorials.

Day 5

Day 5 Lecture:  Simulating Membrane Channels  (N: r=14, c=11)

Of those responding, 86% rated the lecture as highly relevant to their interests.  Sample comments are:

• "Very interesting examples and a very nice presentation of it. It gave a good perspective to see the simulations by opening the VMD."
• "Very interesting and a good case study of what can be done with MD."

The majority of comments about the lecture were very positive.

Day 5 Tutorials:  Simulating Nanotubes; Stretching Deca-Alanine  (N: r=13, c=9; r=6, c=6 )

A majority, 92%, found the nanotubes tutorial relevant, and at a 100% rating, all of the respondents found steered molecular dynamics tutorial highly relevant. Sample comments are:

• Nanotubes: "It is great to see how water behaves when flowing along a channel, in the presence of charges or not... Fabulous tutorial!!"
• Stretching Deca-alanine: "I have seen how extract a lot of information, like free energy of process, etc."

Comments indicate that almost all participants found the tutorials interesting, though some indicate they didn't have time to get to all the tutorial content.

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

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Table 1: Summary of Relevance Statistics

 

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Funded by a grant from
the National Institute of
General Medical Sciences
of the National Institutes
of Health

Beckman Institute for Advanced Science and Technology // National Institutes of Health // National Science Foundation // Physics, Computer Science, and Biophysics at University of Illinois at Urbana-Champaign