Computational Biophysics Workshop - Champaign, Aug. 10-14, 2009
Lectures and Tutorials Evaluation of the Computational Biophysics Workshop at Champaign, Illinois
August 10-14, 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 (August 10-14, 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 faculty members K. Schulten, E. Tajkhorshid, and Z. Luthey-Schulten, who provided the first lecture of each day, and by Resource staff members J. Stone, C. Harrison, K. Vandivort, J. Phillips, and R. Brunner, who provided the second lecture of each day. 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 two 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. 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 1 Lecture 1: Introduction to Protein Structure and Dynamics (N: r=15, c=13)
A majority of respondents, 87%, rated the lecture as highly relevant. Sample comments are:
- Having no prior experience with MD, I was more than a little intimidated by this workshop. However, the introduction & subsequent lectures gentle enough to put me at ease while still being very informative.
- Lecture was very clear, easy to follow/adopt into VMD world.
Day 1 Lecture 2: VMD 1.8.7 - Key features of recent release (N: r=15, c=11)
A majority of respondents, 87%, rated the lecture as highly relevant. Sample comments are:
- I got a feel for what you can do in the graphics in VMD and that there is a much broader range of features than I had previously thought.
- Excellent lecture with nice new features.
Day 1 Tutorial: Using VMD; NAMD Tutorial (N: r=15, c=15)
Almost all participants, 93%, found the tutorial content highly relevant. Sample comments are:
- Basic but complete---I’ve learned a lot so far. I worked both tutorials VMD & NAMD.
- (VMD & NAMD) Scripting is little tough for me, but TA’s explanation helped a lot. THANKS!!
Day 2 Lecture 1: Statistical Mechanics of Proteins (N: r=13 c=9)
A clear majority, 92%, found the lecture content to be highly relevant. Sample comments are:
- Loved it, the lecture helped e a lot to understand NAMD tutorial trial. Very good organization and order.
- Very good lecture covering basics of NAMD/MD.
Day 2 Lecture 2: NAMD 2.7 - Key features of Upcoming Release (N: r=13, c=8)
Over three quarters of respondents, 77%, found the lecture content to be highly relevant. Sample comments are:
- Very interesting – I am excited to hear more about Chris’s work with the helicase.
- I think there should have been a little more time for this lecture, but the subject was very interesting.
Day 2 Tutorial: NAMD Tutorial & Stetching Deca-Alanine; or, Expert NAMD Set; or Free Energy Set (N: r=13, c=11)
Almost all those responding, 92%, rated the tutorial relevance as very high. Sample comments are:
- NAMD tutorial – I didn’t make it as far as I had hoped, but NAMD tutorial, I got a lot out of what I did get done. The TA’s were super patient & helpful.
- Free energy. I think you know why? TA’s are great.
Day 3 Lecture 1: Introduction to Bioinformatics (N: r=18, c=11)
A majority of participants, 83%, rated the relevance of the lecture as very high. Sample comments are:
- I don’t really do anything involving sequences & what not, but it was super interesting & impressive to see what VMD & MultiSeq can do & the information you can gain.
- Very informative – I am a very frequent user of VMD but had never used multiseq before and today I learned what I had been missing out on. I’m very excited to start using this feature of VMD.
Day 3 Lecture 2: Sequence Analysis in VMD 1.8.7 - Key Features (N: r=18, c=6)
At 89%, most participants agreed that the relevance of the lecture was very high. Sample comments are:
- It was straightforward and the talk was very clear.
- I’ve got more familiar with VMD and felt it also a powerful tool in solving biomformatics problems.
Day 3 Tutorials: Basic Sequence Analysis; or, Expert Sequence Analysis; or, work on own projects (N: r=17, c=14)
The relevance of the tutorial was high, with 94% of participants rating tutorial relevance as very good to excellent. Sample comments are:
- Tutorials are as before very informative thorough & interesting. The tutors are very helpful & patient. This specific set of tutorials are not as difficult to figure out on ones own, but offer a lot of real examples.
- Topology tutorial & Evolution of translation. All the TAs were very helpful..I learned a ton and got some great feedback. Thanks you guys!
Day 4 Lecture 1: Parameters for Classical Force Fields (N: r=, c=11)
At 93% participant agreement, ratings indicate the lecture was viewed as highly relevant. Sample comments are:
- Great lecturer! Pace of the presentation was very good. Knowledge of the speaker was amazing esp. b/c he did not shy away from basic questions as well as complex questions. Very approachable lecture placement was perfect for me esp. I struggled w/top para files working on my project on the previous day. Speaker installed appreciation for building of top-files as well as what’s contained in them. Great explanations of theoretical concepts as well as execution of protocols.
- Very interesting and it was good to get a repetition of how molecular dynamics work. I could have listened to it for a lot longer.
Day 4 Lecture 2: GPU Accelerated NAMD 2.7 (N: r=, c=8)
At 73% participant agreement, a majority indicate that the lecture was highly relevant. Sample comments are:
- Great and very relevant lectures, explained parameterizing theoretical background clearly & in detail. GPU lecture gave a good understanding on the technical aspects on how the GPU works.
- The contribution of NAMD to the MD simulation community is huge and Jim’s talk clarifies what are the performance of different version of NAMD.
Day 4 Tutorial: Parameterizing a Novel Residue; Topology File Tutorial; Simulation of Water Permeation through Nanotubes (N: r=, c=11)
With 85% rating relevance as very good to excellent, the majority of respondents found the tutorials relevant. Sample comments are:
- Nanotubes tutorial was very good & pertinent to my work!
- I tried to learn all of them, I think those tutorials are useful and helped me to make new topology and parameter files by myself
Day 5 Lecture: Simulating Membrane Channels (N: r=, c=8)
Of those responding, 92% rated the lecture as highly relevant to their interests. Sample comments are:
- Very interesting lectures, with great examples of applications of NAMD, lecturer kept asking us challenging questions to make sure we understood the concepts which is very enjoyable.
- Very helpful and informative – I was not previously very familiar with the capabilities of NAMD & VMD to generate & simulate membranes, and I am excited about using these new found tools in the future.
Day 5 Lecture: Highlights of VMD Plugins (N: r=, c=7)
At 100% agreement, all rated the lecture as highly relevant to their interests. Sample comments are:
- Demos worked great! So many plugins, WOW! I am looking forward to trying out a lot of them, esp. molefacture.
- I am very excited about these new plugins and am looking forward to using them.
Day 5 Tutorial: Membrane Proteins Tutorial; or, Expert NAMD Set; or, Free Energy Set (N: r=, c=8)
A modest majority, 67%, of respondents found these tutorials as highly relevant. Sample comments are:
- Membrane proteins – There were a couple of problems with the tutorial, but maybe it was just me that made some mistakes. Otherwise it was a good model that can easily be altered to fit your own protein.
- Worked on my own project and TAs were very helpful.
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 Lecture: Introduction to Protein Structure and Dynamics | 15 | 0 | 0 | 13 | 47 | 60 |
| Day 1 Lecture: VMD 1.8.7 - Key Features of Recent Release | 15 | 0 | 0 | 13 | 47 | 60 |
| Day 1 Tutorial: Using VMD; NAMD Tutorial | 15 | 0 | 0 | 7 | 40 | 53 |
| Day 2 Lecture: Statistical Mechanics of Proteins | 13 | 0 | 8 | 0 | 31 | 62 |
| Day 2 Lecture: NAMD 2.7 - Key Features of Upcoming Release | 13 | 0 | 0 | 23 | 38 | 38 |
| Day 2 Tutorial: NAMD Tutorial & Stetching Deca-Alanine; or, Expert NAMD Set; or, Free Energy Set |
13 | 8 | 0 | 0 | 54 | 38 |
| Day 3 Lecture: Introduction to Bioinformatics | 18 | 0 | 0 | 11 | 44 | 39 |
| Day 3 Lecture: Sequence Analysis in VMD 1.8.7 | 18 | 0 | 0 | 11 | 50 | 39 |
| Day 3 Tutorials: Evolution of Translation Tutorials:
Class I Aminoacyl-tRNA Synthetase; Elongation Factor Tu; tRNA and the Ribosome; or, Bioinformatics of Aquaporins |
17 | 0 | 0 | 6 | 41 | 53 |
| Day 4 Lecture: Parameters for Classical Force Fields | 15 | 0 | 0 | 7 | 20 | 73 |
| Day 4 Lecture: GPU accelerated NAMD 2.7 | 15 | 0 | 13 | 13 | 47 | 27 |
| Day 4 Tutorials: Parameterizing a Novel Residue;
Topology File Tutorial; Stretching Deca-alanine Tutorial |
13 | 0 | 0 | 15 | 38 | 46 |
| Day 5 Lecture: Simulating Membrane Channels |
13 |
0 | 8 | 0 | 8 | 85 |
| Day 5 Lecture: Highlights of VMD lugins | 13 | 0 | 0 | 0 | 31 | 69 |
| Day 5 Tutorials: Membrane Proteins Tutorial; Simulation
of Water Permeation Through Nanotubes |
12 | 0 | 0 | 33 | 17 | 50 |
