Computational Biophysics Workshop - Urbana, Feb. 11-15, 2012
Lectures and Tutorials Evaulation of the Theoretical and Computational Biophysics Workshop Urbana
February 11-15, 2012
Questionnaire: Klaus Schulten, TCB Group,
UIUC, and modified by David Brandon, TCB Group, UIUC
Analysis and report: David
Brandon, TCB group, UIUC
The UIUC's Theoretical and Computational Biophysics Group (TCBG), the NIH Center 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 Center offers workshops to introduce and transfer its programs and technological solutions to the biomedical community. The Center organized a one-week (February 11-15, 2012) workshop at the Center's home offices in the Beckman Institute, on the University of Illinois at Urbana-Champaign campus, in Urbana, Illinois. The Center provided all workshop cotent, as well as the classroom, housing, catering, and printing costs.
The program of the workshop consisted of lectures and hands-on sessions. Workshop lectures were given by K. Schulten (UIUC), Z. Schulten (UIUC), and E. Tajkhorshid (UIUC); teaching assistants helped participants during the hands-on tutorial sessions. 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=17, c=13).
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: Introduction to Protein Structure and Dynamics (N: r=17, c=13)
All respondents, 100%, rated the lecture as highly relevant. Sample comments are:
- Very stimulating and interesting. I especially enjoyed hearing about various model systems that VMD/NAMD has been applied to. The discussion at the end was also excellent.
- Loved Klaus's talk - very informative and relevant. Especially good question and answer session!
Day 1 Tutorial: Using VMD; NAMD Tutorial (N: r=16, c=16)
All respondents, 100%, found the tutorial content highly relevant. Sample comments are:
- Tutorials I worked on: Using VMD & (portion of) NAMD tutorial. The tutorials are very easy to follow. All steps described in detail. I really appreiciate help of (very patient) staff! The VMD tutorial introduces a vast part of the software capabilities and encourages 'playing' with options.
- I had completed VMD and ~1/3 of NAMD tutorial before arriving. Both are quite straight-forward to complete on your own.
Day 2 Lecture: Statistical Mechanics of Proteins (N: r=15, c=15)
A majority, 93%, of those responding found the lecture content to be highly relevant. Sample comments are:
- "I really like Prof. Schulten's lecture in which he explains the logic/reasoning/physics behind the numerical simulations. The lectures are helpful. In addtion, the recent advances in MD are very interesting and exciting."
- "Very informative and understandable to an experimentalist."
Day 2 Tutorial: NAMD Tutorial & Stetching Deca-Alanine; or, Expert NAMD Set; or Free Energy Set (N: r=15, c=15)
Most of those responding, 93%, rated tutorial relevance as very high. Sample comments are:
- "Successfully completed the Decan-Alanine tutorial; interesting insights into steered MD."
- "Finished NAMD tutorial, started deca-ala unfolding. Interested in applying the SMD technique to my own system."
Day 3
Day 3 Lecture: Parameters for Classical Force Fields (N: r=8, c=)
At 100% respondent agreement, ratings indicate the lecture was viewed as highly relevant. Sample comments are:
- "Excellent, detailed and clear explanations."
- "A very detailed and useful lecture on the parameterization of force fields. It gave a good taste of how to approach the problem."
Day 3 Tutorial: Parameterizing a Novel Residue; Topology File Tutorial; Simulation of Water Permeation through Nanotubes (N: r=6, c=)
With 100% rating relevance as very good to excellent, all respondents found the tutorials relevant. Sample comments are:
- "Topology Files - gave a good flavor of the challenges and of the strategies to use."
- "Regarding the parameterization tutorials, I believe more time could have been given to the ffTK software."
Day 4 Lecture: Simulating Membrane Channels (N: r=12, c=)
All of those responding, 100% rated the lecture as highly relevant to their interests. Sample comments are:
- "Excellent lecture. Very plain language regarding esoteric hurdles in complex systems."
- "Emad is an excellent lecturer! He keeps us on our toes by asking questions and leaves plenty of room for asking questions ourselves. The aquaporin example was a nice way to illustrate how both just looking at results then quantifying values of interest is powerful in analyzing simulations to extract science."
Day 4 Tutorial: Membrane Proteins Tutorial; or, Expert NAMD Set; or, Free Energy Set (N: r=11, c=)
A majority of respondents - 82% - found these tutorials as highly relevant. Sample comments are:
- "Membrane Protein tutorial (immersing protein in bilayer & solvation) - really good flow of information on how to setup the calculations. The explanation of scripts is really useful; makes it easier to learn the language and write on programs/scripts."
- "Free Energy: the methodology is very useful!"
Day 5
Day 5 Lecture 1: Introduction to Bioinformatics (N: r=11, c=7)
A majority of respondents, 81%, rated the relevance of the lecture as very high. Sample comments are:
- "Very lively overview of a variety of topics - very interesting."
- "For me this was the best day. I learned a lot about the possibilities of VMD. These bioinformatic tools of VMD will be very useful."
Day 5 Tutorials: Basic Sequence Analysis; or, Expert Sequence Analysis; or, work on own projects (N: r=4, c=7)
The relevance of the tutorial was high, with 100% of respondents rating tutorial relevance as very good to excellent. Sample comments are:
- "Sequence analysis - very useful tutorial."
- "The expert sequence analysis is an excellent set of tutorials but are too large for the time devoted to tutorials during the hands-on. Maybe one could be chosen and expanded for the hands on."
The complete set of comments is available by e-mailing workshop+urbana2012@ks.uiuc.edu.
Table 1: Summary of Relevance Statistics
| N | Poor | Fair | Good | Very Good | Excellent | |
| Day 1 Lecture: Introduction to Protein Structure and Dynamics | 17 | 29% | 71% | |||
| Day 1 Tutorial: Using VMD; NAMD Tutorial | 16 | 38% | 63% | |||
| Day 2 Lecture: Statistical Mechanics of Proteins | 15 | 7% | 13% | 80% | ||
| Day 2 Tutorial: NAMD Tutorial & Stetching Deca-Alanine; or, Expert NAMD Set; or, Free Energy Set |
15 | 7% | 40% | 53% | ||
| Day 3 Lecture: Parameters for Classical Force Fields | 8 | 100% | ||||
| Day 3 Tutorials: Parameterizing a Novel Residue; Topology Files | 6 | 100% | ||||
| Day 4 Lecture: Simulating Membrane Channels | 12 | 8% | 92% | |||
| Day 4 Tutorials: Membrane Proteins & Water Permeation Through Nanotubes; or, Expert NAMD Set; or, Free Energy Set |
11 | 18% | 18% | 64% | ||
| Day 5 Lecture: Introduction to Bioinformatics | 11 | 9% | 9% | 45% | 36% | |
| Day 5 Tutorials: Evolution of Translation Tutorials:
Class I br Aminoacyl-tRNA Synthetase; Elongation Factor Tu; tRNAand the Ribosome; or, Bioinformatics of Aquaporins |
4 | 25% | 75% |
