Lectures and Tutorials Evaluation of the Computational Biophysics Workshop at Champaign, Illinois

July 6-10, 2009

Questionnaire: Klaus Schulten, TCB Group, UIUC, and modified by David Brandon, TCB Group, UIUC
Analysis and report: David Brandon, TCB Group, UIUC

The NIH Resource for Macromolecular Modeling and Bioinformatics is headed by Klaus Schulten, and Co-PIs Z. Luthey-Schulten, L. Kale, E. Tajkhorshid, and A. Aksimentiev. As part of its outreach, the Resource offers workshops to introduce and transfer its programs and technological solutions to the biomedical community. The Resource presented a five-day (July 6-10, 2009) workshop at the iHotel and Conference Center in Champaign, Illinois. Resource faculty provided morning lectures, and teaching assistants and faculty led afternoon hands-on sessions using Resource software, and tutorials consisting of text and computer files.

Workshop lectures were provided by K. Schulten, E. Tajkhorshid, and Z. Luthey-Schulten. Teaching assistants were graduate students from TCBG and the Luthey-Schulten group. Tutorials and preparation of the laptops was provided by the graduate students and by other Resource staff, and on-site the tutorial sessions were led by the graduate students.  The program of the workshop consisted of lectures and hands-on sessions, with an emphasis on the latter. At the end of each day of the workshop participants were asked to evaluate the workshop's lectures and tutorials, via forms customized for each day; a copy of the forms used is available here.

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.
  • 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 Lecture Tutorial
Day 1 Introduction to Protein Structure and Dynamics Using VMD
Day 2 Statistical Mechanics of Proteins NAMD Tutorial
Day 3 Parameters for Classical Force Fields Parameterizing a Novel Residue; Topology File Tutorial; Stretching Deca-alanine Tutorial
Day 4 Simulating Membrane Channels Membrane Proteins Tutorial; Simulation of Water Permeation Through Nanotubes
Day 5 Introduction to Bioinformatics Evolution of Translation Tutorials: Class I Aminoacyl-tRNA Synthetase; Elongation Factor Tu; tRNA and the Ribosome; or, Bioinformatics of Aquaporins

Day 1

Day 1 Lecture:  Introduction to Protein Structure and Dynamics (N: r=19, c=16)

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

  • Great lecture emphasizing the need to visualize systems accurately to investigate important biological phenomena. Dr. Schulten has great passion for this subject and communicates it in an excellent heartfelt and sincere way.
  • Very good introduction. Good depth and breadth coverage of MD.

Overall, those commenting indicate the lecture provided a good overview, with some indicating due to their experience with VMD before the workshop that some material was review for them. 

Day 1 Tutorial:  Using VMD (N: r=19, c=18)

As was the case for the day one lecture, at 89% a majority found the tutorial content highly relevant.  Sample comments are:

  • The tutorials are easy going and very clear. Every thing was explained step by step.
  • The tutorial materials are great. Perfect to start out with. Very long day!

Comments are positive regarding the overall content and organization of the tutorial, and the contributions of the teaching assistants, with a few specific suggestions for improvements to various sections of the tutorial content.

Day 2

Day 2 Lecture:  Statistical Mechanics of Proteins (N: r=15, c=11)

A clear majority, 93%, found the lecture content to be highly relevant.  Sample comments are:

  • Enjoyed combination of theory and specific examples
  • Very motivating as well as humbling to see the power of NAMD.

Overall, the comments are positive, with some comments suggesting improvements, such as more time spent on guiding biologists through the math, or that the breadth of topics covered was challenging.

Day 2 Tutorial:  NAMD Tutorial (N: r=15, c=12)

Almost all those responding, 73%, rated the tutorial relevance as very high.  Sample comments are:

  • Wonderfully planned and informative and easy to use
  • Absolutely amazing. The tutorials are extremely well organized, written very clearly in a simple language making it a really enjoyable learning experience. I used to be skeptical about simulations and it amazes me how easily Ive begun to appreciate simulations and the entire area of theoretical/computational biology.

Comments are generally positive regarding the tutorial, but there is a common theme that more time is needed to complete the tutorial than provided in the workshop schedule.

Day 3

Day 3 Lecture:  Parameters for Classical Force Fields (N: r=20, c=13)

Nearly all participants, 95%, rated the relevance of the lecture as very high.  Sample comments are:

  • Lecture was clearly presented and very well organized. Interesting theory and background presented in a concise manner. Loved it.
  • Very good.

The majority of comments compliment the lecture, indicating the lecture kept lively material which would otherwise be dry.

Day 3 Tutorials:  Parameterizing a Novel Residue; Topology File Tutorial; Stretching Deca-alanine Tutorial (N: r=20, c=16)

The relevance of the lecture was high, with 75% of participants rating relevance as very good to excellent.  Sample comments are:

  • Very well-organized tutorials.
  • Very interesting exercises.

While appreciative of the tutorial content, many express a desire for more time to work through and absorb tutorial content.

Day 4

Day 4 Lecture:  Simulating Membrane Channels  (N: r=20, c=13)

At 100% participant agreement, the consensus was that the lecture was highly relevant.  Sample comments are:

  • I liked the bits of practical advice in the talk, like coarse graining is better when atomic interactions like hydrogen bonding are less important.
  • Very informative, good amount of useful content covered. Thanks.

Overall, comments are complimentary regarding the content of the lecture; some suggestions were to cover the examples provided later in tutorials, and to have fewer topics.

Day 4 Tutorial: Membrane Proteins Tutorial; Simulation of Water Permeation Through Nanotubes (N: r=19, c=16)

With 84% rating relevance as very good to excellent, the majority of respondents found this topic of interest.  Sample comments are:

  • Best tutorial challenging, difficult and most relevant to my research.
  • Nice to step through a multi-step problem.

While indicating more time was desired to complete tutorials by some participants, overall the tutorials are viewed positively.

Day 5

Day 5 Lecture:  Introduction to Bioinformatics (N: r=14, c=9)

Of those responding, 64% rated the lecture as highly relevant to their interests.  Sample comments are:

  • Very informative and interesting lecture covering wide rage of key concepts and ideas.
  • Good example but a little bit more overview would have been very helpful.

Comments are positive overall, though a common theme is that more overview or a slower pace would help those new to the field to follow the lecture.

Day 5 Tutorial:  Evolution of Translation Tutorials I & II: Class I Aminoacyl-tRNA Synthetases and the Elongation Factor Tu (EF-Tu:tRNA)'Evolution of Translation Tutorial III: tRNA and the Ribosome, or Bioinformatics Study of Aquaporins (N: r=13, c=8)

A majority, 62%, of respondents found this tutorial highly relevant. Sample comments are:

  • Interesting and well prepared.
  • Thanx. Very relevant to my research.

Comments overall are positive, with some comments suggesting improvements or other areas for the tutorials to cover.

 

The complete set of comments is available.  To request the comments, e-mail brandon@ks.uiuc.edu.


 

Table 1: Summary of Relevance Statistics


  Poor Fair Good Very Good Excellent
N % % % % %
Day 1: Introduction to Protein Structure and Dynamics
 
19 0 5 0 53 42
Day 1 Tutorial: Using VMD
 
19 5 0 5 21 68
Day 2: Statistical Mechanics of Proteins
 
15 0 0 7 53 40
Day 2 Tutorial: NAMD Tutorial
15 0 0 27 40 33
Day 3 Tutorial: Parameters for Classical Force Fields
20 0 0 5 35 60
Day 3 Tutorials:  Parameterizing a Novel Residue; Topology File
Tutorial;
Stretching Deca-alanine Tutorial
20 0 10 15 30 45
Day 4 Lecture: Day 4: Simulating Membrane Channels 20 0 0 0 40 60
Day 4 Tutorials: Membrane Proteins Tutorial; Simulation of Water
Permeation Through Nanotubes
19 0 0 16 32 53
Day 5 Lecture: Introduction to Bioinformatics
14 7 0 29 21 43
Day 5 Tutorials:  Evolution of Translation Tutorials I & II: Class I
Aminoacyl-tRNA Synthetases and the Elongation Factor Tu
(EF-Tu:tRNA);
Evolution of Translation Tutorial III: tRNA and the
Ribosome, or Bioinformatics Study of Aquaporins
13 0 8 31 8 54