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Computational Biophysics Workshop - Pittsburgh, Nov. 28 - Dec. 1, 2005

Evaluation of the Theoretical and Computational Biophysics Workshop at the Pittsburgh Supercomputing Center

Lectures and Tutorials Evaluation

Questionnaire, analysis, and report: David Brandon, Kathryn Walsh 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 1

Day 1 Lecture: Molecular Graphics and Molecular Dynamics (N: r=18, c=17)

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

• "Excellent overall introduction about molecular graphics and dynamics.  Totally very useful."
• "Great introduction.  What a great teacher."

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. more time on MD, or statistical physics.

Day 1 Tutorial: VMD/Molecular Graphics (N: r=18, c=17)

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

• "I have used VMD before, but was not familiar with the newer features and other ones.  The hands-on session was an excellent way to learn and practice the theory.  I would go back and recommend it to everyone to learn from this."
• "The tutorial followed introductory lecture very good.  Easy to follow, detailed instructions, very useful."

There are also various suggestions, such as adding a membrane protein setup system example, and covering more advanced aspects of VMD.

Day 2

Day 2 Lecture: Equilibrium/Nonequilibrium Properties of Proteins (N: r=20, c=16)

At a 85% relevance rating, most respondents found the lecture content to be highly relevant.  Sample comments are:

• "A very informative and entertaining lecture – perhaps one of the best I’ve attended on the subject.  Again, his ability to focus on the physical relevance of the equations and how simulations succeed and fail at representing the physics of biomolecules and ensembles was exemplary.  I was especially impressed by his enthusiasm when discussing the temp. echoes observed in simulations, prior to detection in experimental methods.  AWESOME."
• "Excellent overall intro about equilibrium/ non-equilibrium proteins."

Some suggestions from respondents include requests for more background on statistical physics, and use of more biology-orientated examples.

Day 2 Tutorial: NAMD/Molecular Dynamics Tutorial (N: r=20, c=18)

All respondents, 100%, rated the tutorial relevance as very high.  Sample comments are:

• "Very thorough examples and exercises."
• "Awesome tutorial.  Truly hands-on.  We appreciate your hard work!  Minor suggestion: One example showing protein-ligand system setup and MD."

Some respondents indicate wanting more time to work on the tutorial.

Day 3

Day 3 Lecture:  Introduction to Bioinformatics (N: r=16, 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

Day 3 Lecture: Determining Classical Force Fields (N: r=16, c=11)

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

• "Incredible morning session.  I learned very much.  The morning put me over “the mountain (or at least the first foot hill)”.  I came to the workshop hoping to leave with an understanding of what can and can’t be done currently – what are limits.  After this morning, I think I can do this.  A diagram of steps and files with definitions for inputs/ outputs would be great.  Maybe I missed it."
• "The lecture was very good both in terms of material and the way it was presented."

There are some suggestions. e.g., for spending less time on the basics of molecular dynamics, or to have less intensive theory.

Day 3 Tutorial: Parameterizing a Novel Residue; Topology Files (N: r=16, c=8; r=13, c=11)

Respondents generated an 94% relevance rating for the parameterization tutorial, and an 77% rating for the topology files tutorial.  Sample comments are:

• Novel residue: "I’ve had to do this before, and this is a very good overview.  Tutorial handbook has references I actually want to read."
• Topology: "Excellent explanation."

Comments are generally complimentary of the parameterization tutorial, with some specific suggestions made for improvement, such as how the content can be carried out in GAMESS or Gaussian, a section in which participants add a found parameter, and providing study material beforehand.  For the topology tutorial, many comments indicate respondents did not have time to get to or all the way through the tutorial.

Day 4

Day 4 Lecture: Simulating Membrane Channels (N: r=10, c=8)

Nearly all respondents - 90% - rated the lecture as highly relevant to their interests.  Sample comments are:

• "Great stuff – very relevant to what I want to do.  Wish it were longer!"
• "Very good!  Clear and inspiring."

Comments are uniformly positive, with some suggestions such as soliciting questions before the workshop to discuss when on site and more time for the lecture subject.

Day 4 Tutorial: Simulating Nanotubes; Stretching Deca-Alanine (N: r=10, c=8; r=3, c=5)

The Nanotubes tutorial received a relevance rating of 90%, and Deca-alanine 100%. Sample comments are:

• Nanotubes: "Highly interesting, liked the IMD part."
• Deca-alanine: Comments indicate participants ran out of time before they could do this tutorial.

Comments are uniformly complimentary of the nanotubes tutorial, except for one suggestion that more physics be included.  As for the Deca-alanine tutorial, most comments indicate that respondents ran out of time before they could evaluate the tutorial.

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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