Computational Biophysics Workshop - Boston, Dec. 5-9, 2004

TCB Hands-on Workshop in Boston

Evaluation of the Theoretical and Computational Biophysics Workshop held at the Colonnade Hotel, Boston

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), 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 Tutorial
Day 5 Simulating Membrane Channels
 Simulating Nanotubes

Day 1

Day 1 Lecture:  Introduction to Protein Structure and Dynamics (N: r=19, c=15)

All respondents rated the lecture as highly relevant.  Sample comments are:

  • "Excellent overview of some salient features relating to biolmolecular MD.."
  • "I was amazed by how pedagogical the lecture was: there was not a single fact unexplained, yet it was interesting."

Overall, those commenting indicate the lecture provided a good overview, and also helped frame how VMD could be used for MD.  

Day 1 Tutorial:  VMD Tutorial (N: r=19, c=15)

As was the case for the day one lecture, 89.5% found the tutorial content highly relevant.  Sample comments are:

  • "The tutorials give an insight in the possibilities and offer a couple of easy solutions to problems!!"
  • "Really easy after the lecture. everything perfectly organized.  All assistants were very very kind and helpful"

Comments are positive regarding the overall content and organization of the tutorial.  

Day 2

Day 2 Lecture:  Statistical Mechanics of Proteins (N: r=16, c=7)

A clear majority, 87.5%, found the lecture content to be highly relevant.  Sample comments are:

  • "It was very interesting to learn a different aspect of the MD, which can be very useful if we are looking for errors in our own MD simulations."
  • "Very good!!  I would like to see more protein analysis!!"

Overall, the comments are positive, and provided some constructive criticism.

Day 2 Tutorial:  NAMD Tutorial (N: r=17, c=11)

Almost all those responding, 88.2%, rated the tutorial relevance as very high.  Sample comments are:

  • "The instructors patiently answered my many questions.  They were extremely helpful."
  • "Helpful to do the tutorial.  Assistants were easily accessible."

As was the case with the day three lecture, comments are positive about the tutorial.  Many express a desire for more time to absorb the material from both the lecture and tutorial.The teaching assistants were praised for their assistance and patience.

Day 3

Day 3 Lecture:  Introduction to Bioinformatics  (N: r=17, c=12)

A clear majority, 82.4%, rated the relevance of the lecture as very high.  Sample comments are:

  • "The new sequences/ structure bioinformatics tools being added to VMD are great!  They will encourage simulationists to think about bioinformatics, a topic they might otherwise neglect."
  • "Excellent.  Very interesting!!  I came for this part of the workshop!!  I would like to see more DNA examples of MD in the future."

Comments are generally positive regarding the lecture.  A couple of suggestions recommended using different examples (i.e. DNA). 

Day 3 Tutorial:  Evolution of Protein Structure and Aquaporins Tutorial (N: r=17, c=12)

The relevance of the lecture was high, with 88.3% rating relevance as very good to excellent.  Sample comments are:

  • "Short, sweet, and to the point – I liked these tutorials."
  • "Excellent tutorials, great tools."

Comments are generally positive regarding the organization and writing of the tutorial; however participants point out redundancies between the two tutorials, and a few comments seeking more information on selected technical details. 

Day 4

Day 4 Lecture:  Parameters of Classical Force Fields  (N: r=17, c=11)

A very high proportion, 94.1%, rate the lecture as highly relevant.  Sample comments are:

  • "Excellent introduction by Emad to the CHARMM.  Force field parameters and how one goes about adapting it to specific problems."
  • "A+ overview of top four par files."

Comments are complimentary regarding the content of the lecture. 

Day 4 Tutorial: Parameterizing a Novel Residue Tutorial  (N: r=16, c=12)

With 87.6% rating relevance as very good to excellent, the majority of respondents found this topic of interest.  Sample comments are:

  • "Very helpful part of the workshop!"
  • "Great examples in the tutorial!"

Across the majority of responses, the tutorial is well-regarded.  A handful of comments provide constructive criticism.

Day 5

Day 5 Lecture:  Simulating Membrane Channels  (N: r=17, c=7)

Of those responding, 88.2% rated the lecture as highly relevant to their interests.  Sample comments are:

  • "One of my favorite of the series.  Good application of info learned during the week."
  • "Very interesting!  This has been the best lecture yet!"

The majority of comments about the lecture were very positive.

Day 5 Tutorial:  Simulating Nanotubes Tutorial   (N: r=, c=8)

A majority, 93.8%, of respondents found this tutorial highly relevant. Sample comments are:

  • "The tutorial was instructive and fun.  Playing with the parameters especially helped my understanding. "
  • "Was very interesting.  Gave a good background in the use of AutoImD"

Comments also indicate that almost all participants found the tutorial interesting and informative.


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: Introduction to Protein Structure and Dynamics 19


42.1
 57.9
Day 1 Tutorial: VMD Tutorial 19

10.5
 26.3
 63.2
Day 2 Lecture: Statistical Mechanics of Proteins
 16

12.5
 37.5
 50.0
Day 2 Tutorial: NAMDTutorials
 17

11.8
 23.5
 64.7
Day 3 Lecture: Introduction to Bioinformatics 17

17.6
 35.3
 47.1
Day 3 Tutorial: Evolution of Protein Structure and Aquaporins Tutorial
 17

11.8
 47.1
 41.2
Day 4 Lecture: Parameters for Classical Force Fields 17

5.9
 23.5
 70.6
Day 4 Tutorial: Parametirizing a Novel Residue Tutorial
 16

12.5
 18.8
 68.8
Day 5 Lecture: Simulating Membrane Channels
 17

11.5
 17.6
 70.6
Day 5 Tutorial: Nanotubes Tutorial
 16
6.3
31.3
 62.5