Computational Biophysics Workshop - Pittsburgh, Nov. 6-9, 2006

Evaluation of the Theoretical and Computational Biophysics Workshop at Pittsburgh

Lectures and Tutorials Evaluation

Questionnaire, analysis, and report: David Brandon, 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 NAMD Tutorial
Day 2 Parameters for Classical Force Fields Topology Files, Parameterizing a Novel Residue
Day 3 Introduction to Bioinformatics Evolution of Protein Structure: tRNA Synthetase
Day 4 Simulating Membrane Channels Simulating Nanotubes, Stretching Deca-alanine

Day 1

Day 1 Lecture: Molecular Graphics and Molecular Dynamics (N: r=15, c=11)

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

  • "Very nice lecture, good way of covering basic concepts. Thanks to Dr. Schulten & the group for such a workshop. It’s really great.."
  • "Excellent. Simple, well explained. Highly useful for experimentalists!"

All comments were positive, with some suggestions that lecture slides be provided or available at the start of the lecture for notation purposes, or before the lecture for review.

Day 1 Tutorial: NAMD/Molecular Dynamics Tutorial (N: r=15, c=11)

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

  • "It was a good idea to use VMD before working on NAMD; the paper on NAMD was also very well written."
  • "Nice tutorial to start working w/ NAMD."

Other comments indicate the tutorial is too long for the time provided, and that the TAs were helpful.

Day 2

Day 2 Lecture: Parameters for Classical Force Fields (N: r=14, c=8)

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

  • "I really liked the step-by-step derivations of the math formula presented in the first few slides of the lecture (force field for bonding & non-bonding interactions)."
  • "Well organized lectures. Any question, any time, great answers!"

Further comments again compliment the lecture, with again a suggestion that slides be copied and given to participants for study.

Day 2 Tutorials: Topology Files and Parameterization of a Novel Residue (N: r=14, c=9; r=14, c=9)

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

  • "All the tutorial material has covered details in such a way that helps us to do or prepare files if we need to do something different in the future or to incorporate changes that we may need to look at. The TA’s are really patient and helpful."
  • "Learned a lot about topology files, parameter files, etc. Well organized."

Respondents indicate some parts of the parameterization tutorial were less interesting than prior tutorials, with others complimenting the teaching assistants and the tutorials in general.

Day 3

Day 3 Lecture:  Introduction to Bioinformatics (N: r=12, c=9)

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

  • "A very clearly presented lecture; quite easy to follow even though I have never taken any computer science courses."
  • "Great lecture, which give me a new perspective of bioinformatics."

While appreciative of the lecture, other comments indicate that some participants didn't have a sufficient background in bioinformatics to keep up with the content of the lecture.

Day 3 Tutorial: Evolution of Protein Structure: tRNA Synthetase (N: r=12, c=8)

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:

  • "Very nice tutorial, actually explains how you can look at things if you have a particular question in mind. To my knowledge I definitely think multiseq is a good tool & user friendly combining many things for your analysis at fingertips. “I wish best of luck.”"
  • "Nice tutorial. Nice multiseq."

Other comments are a mix of compliments for the tutorial and teaching assistants, along with pointing to some edits needed in the tutorial text.

Day 4

Day 4 Lecture: Simulating Membrane Channels (N: r=7, c=1)

Only one comment was collected for this lecture:

  • "I like the lecture very much."

Day 4 Tutorials: Simulating Nanotubes; Stretching Deca-Alanine (N: r=7, c=4; r=7, c=4)

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

  • Nanotubes: "Perfect."
  • Deca-alanine: "It was good. Liked the IMD of deca-alanine."

Remaining comments are complimentary for both tutorials; a suggestion for the nanotubes tutorial is to point out some tcl scripts participants can use in their own work.

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

Table 1: Summary of Relevance Statistics

    Poor Fair Good Very Good Excellent
N % % % % %
Day 1 Lecture: Molecular Graphics and Molecular Dynamics 15       40 60
Day 1 Tutorial: NAMD/Molecular Dynamics Tutorial 15       27 73
Day 2 Lecture: Parameters for Classical Force Fields 14       29 71
Day 2 Tutorial: Parameterizing a Novel Residue 14       43 57
Day 2 Tutorial: Topology Files 14       43 57
Day 3 Lecture: Introduction to Bioinformatics 12   8 8 42 42
Day 3 Tutorial: Evolution of Protein Structure: tRNA Synthetase 12     25 17 58
Day 4 Lecture: Simulating Membrane Channels 7       14 86
Day 4 Tutorial: Simulating Nanotubes 7       14 86
Day 4 Tutorial: Stretching Deca-Alanine 7       14 86