Computational Biophysics Workshop - Chicago, Jun. 9-13, 2005

TCB Hands-on Workshop in Chicago  

Evaluation of the Theoretical and Computational Biophysics Workshop in Chicago

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 Introduction to Bioinformatics Evolution of Protein Structure and Aquaporins Tutorials
Day 3 Statistical Mechanics of Proteins NAMD Tutorial
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=20, c=18)

Nearly all respondents, 95%, rated the lecture as highly relevant.  Sample comments are:

  • "I thought both lecture and tutorial were excellent."
  • "The Molecular Graphics lecture was a nice blend of theory and VMD examples, mixing biomolecular structure background w/ the theoretical basis of VMD and how to apply it to the question at hand."

The corpus of the comments suggest respondents found the lecture a good introduction to the topic at hand, and clearly presented.

Day 1 Tutorial: VMD/Molecular Graphics (N: r=20, c=18)

All respondents, 100%,  found the tutorial content highly relevant.  Sample comments are:

  • "The documents are really good, the tutorial is clear, thanks!!!"
  • "Very detailed.  Though I have used before there were a lot of new things I learnt.  Keep up the good work!  Teaching assistants are very helpful and patient in answering the questions."

Comments are generally complimentary of the tutorial, with occasional specific suggestions, such as more time to work on the tutorial, or how VMD might work on other platforms.

Day 2

Day 2 Lecture: Introduction to Bioinformatics (N: r=17, c=16)

A majority of respondents, 81%, rated the relevance of the lecture as very high.  Sample comments are:

  • "The presentation is very straightforward and clear.  It’s important to know that the structural alignment help us to relate protein in a more meaningful way."
  • "Very nice blend of motivation, application and algorithm details."

Overall, respondents appreciated the lecture, though there were some language/terminology barriers experienced by some respondents.

Day 2 Tutorial: Evolution of Protein Structure; Bioinformatics Study of Aquaporins (N: r=17, c=15)

The relevance of the tutorials was high, with a relevance rating from respondents of 87%.  Sample comments are:

  • "The tutorials were straightforward and easy. May want to add some more complexity to highlight more features."
  • "Nice that two examples given, and split into two clear parts. Here it really became clear Tcl/Tk is very useful to allow modification."

Comments indicate that respondents found the tutorials easy to follow, with some respondents indicating they felt the tutorials overlapped each other significantly.

Day 3

Day 3 Lecture: Equilibrium/Nonequilibrium Properties of Proteins (N: r=18, c=17)

All respondents, 100%, found the lecture content to be highly relevant.  Sample comments are:

  • "Very interesting lecture.  Has the right balance between computational part and physics."
  • "Excellent lecture, even though I’m a biologist I could follow the idea, and took out the information that I need."

Comment are generally highly complimentary and appreciative; a few respondents indicated some problems following math in the lecture.

Day 3 Tutorial: NAMD/Molecular Dynamics Tutorial (N: r=18, c=16)

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

  • "Excellently designed tutorial! Very interesting; great learning experience. Thoroughly enjoyed working through the tutorial. Teaching assistants are simply wonderful people as are the excellent faculty members. Keep up the great service to education!"
  • "This is a really good tutorial. I really learned a lot from this tutorial. There are lots of things in it and I think it is served also as a quick reference to NAMD in the future."

Comments are generally complimentary, with several respondents indicating they need more time to complete the tutorial.

Day 4

Day 4 Lecture: Determining Classical Force Fields (N: r=18, c=13)

A majority of respondents - 94% - rate the lecture as highly relevant.  Sample comments are:

  • "Excellent presentation with detailed explanation. Thoroughly enjoyed the lecture and learnt a lot."
  • "Very good, very practical lecture."

Comments are generally appreciative, with some varying suggestions about the level of detail presented in the lecture.

Day 4 Tutorial: Parameterizing a Novel Residue; Topology Files (N: r=18, c=15)

Respondents provided a 100% relevance rating for the tutorials.  Sample comments are:

  • "It helps a lot in understanding the outline of topology and parameter files. Makes me realize it is not easy to modify it, let alone building the file itself."
  • "Very well written and very interesting. A great illustration of modern comp chem power."

Generally, comments are complimentary of the tutorials, along with some suggestions for more time to finish the tutorials, and suggestions that non-commercial software be used.

Day 5

Day 5 Lecture: Simulating Membrane Channels (N: r=19, c=17)

Of those responding, 94% rated the lecture as highly relevant to their interests.  Sample comments are:

  • "Very good – real world examples of methods of analysis was probably the most helpful part of the workshop."
  • "Excellent lecture – good examples.  Nice exposure to computational philosophy, driven by examples (i.e. make changes to system to test hypothesis, how to look at system to gain understanding)."

Overall, comments are uniformly positive.

Day 5 Tutorial: Simulating Nanotubes; Stretching Deca-Alanine (N: r=19, c=15)

At a 100% relevance rating, all of the respondents found the tutorials relevant. Sample comments are:

  • "Extremely well-thought out – great to see IMD and SMD.  No big problems – useful to see our own improvements by our facility w/ these tutorials."
  • "Very interesting: nice look at how to simplify systems. Great end place – as these tutorials were shorter, allowing us to finish up and be encouraged for the future!"

Again, comments are generally complimentary, with some suggestions for more detail in some areas of the tutorials.

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     5.6 38.9 55.6
Day 1 Tutorial: VMD/Molecular Graphics 18       33.3 66.7
Day 2 Lecture: Bioinformatics 16   6.3 12.5 43.8 37.5
Day 2 Tutorial: Evolution of Protein Structure; Bioinformatics Study of Aquaporins 15     13.3 33.3 53.3
Day 3 Lecture: Equilibrium/Nonequilibrium Properties of Proteins 18       33.3 66.7
Day 3 Tutorial: NAMD/Molecular Dynamics Tutorial 18       33.3 66.7
Day 4 Lecture: Determining Classical Force Fields 18   5.6   33.3 61.1
Day 4 Tutorial: Parameterizing a Novel Residue; Topology Files 17       47.1 52.9
Day 5 Lecture: Simulating Membranes 18     5.6 11.1 83.3
Day 5 Tutorial: Nanotubes; Stretching Deca-Alanine 16       25 75