Computational Biophysics Workshop - Pittsburgh, May 10-14, 2010
Lectures and Tutorials Evaulation of the Theoretical and Computational Biophysics Workshop held at the Pittsburgh Supercomputing Center
May 10-14, 2010
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 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 participated in a one-week (May 10-14, 2010) workshop sponsored by the National Resource for Biomedical Supercomputing (NRBSC) at the Pittsburgh Supercomputing Center at Pittsburgh, Pennsylvania. The NRBSC provided the classroom, and computer lab used for the workshop, as well as covering hotel, honorarium, travel, and printing costs; TCBG provided lectures and tutorials, and covered some 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=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: Introduction to Protein Structure and Dynamics (N: r=26, c=22)
Almost all respondents, 92%, rated the lecture as highly relevant. Sample comments are:
- Great introduction MD. I liked the review of the details of MD as well as the incorporation of NAMD/VMD tips/instruction throughout.
- Excellent lecture and it gives me a better understanding of the VMD tool and the basic principle of MD simulation.
Day 1 Tutorial: Using VMD; NAMD Tutorial (N: r=25, c=25)
A majority of participants, 84%, found the tutorial content highly relevant. Sample comments are:
- I used the VMD, NAMD tutorial and found it very lucid and self-explanatory. The staff was extremely helpful as well.
- The tutorials are excellent for beginners. (using VMD and NAMD)
Day 2 Lecture: Statistical Mechanics of Proteins (N: r=26 c= 21)
A majority, 85%, found the lecture content to be highly relevant. Sample comments are:
- Excellent lecture. It reminds me of the importance of statistical mechanics in the analysis of MD simulation.
- I really enjoyed this material. MD movies are of course fun to watch, but I more appreciated the Q&A session, stat-mech validations and overall foils of why we do MD and what questions/problems should we address with it. Don’t change this content.
Day 2 Tutorial: NAMD Tutorial & Stetching Deca-Alanine; or, Expert NAMD Set; or Free Energy Set (N: r=24, c=22)
Most of those responding, 83%, rated the tutorial relevance as very high. Sample comments are:
- Used NAMD tutorial and was satisfied with the scripts and the explanation given for each command.
- “User-defined forces” and “stretching deca-alanine”. It was great to have experts on hand for questions, and I liked that the tutorials are contained and as useful as references for questions down the road.
Day 3
Day 3 Lecture: Parameters for Classical Force Fields (N: r=16, c=17)
At 94% participant agreement, ratings indicate the lecture was viewed as highly relevant. Sample comments are:
- Very insightful lecture. Many practical tips. Learned a lot on a topic I always found scary.
- Insightful and in-depth discussion of parameterization and topology files.
Day 3 Tutorial: Parameterizing a Novel Residue; Topology File Tutorial; Simulation of Water Permeation through Nanotubes (N: r=15, c=16)
With 93% rating relevance as very good to excellent, the majority of respondents found the tutorials relevant. Sample comments are:
- Topology file and Parameterization tutorials. I’m excited about applying these techniques to my research system. These tutorials are very explanatory and helpful. No suggestions.
- Very nice tutorial for people who want to learn how to get top and coordinate file from common macromolecules and novel residues.
Day 4 Lecture: Simulating Membrane Channels (N: r=18, c=16)
Of those responding, 100% rated the lecture as highly relevant to their interests. Sample comments are:
- Very interesting lectures on a topic of general relevance. I think you really got your point across – there’s a lot of information in these simulations, if you can see it.
- The lecture was to the point, very well organized, clear and to the point on the membrane protein simulation and it helped me a lot during the tutorial.
Day 4 Tutorial: Membrane Proteins Tutorial; or, Expert NAMD Set; or, Free Energy Set (N: r=17, c=18)
All participants - 100% - found these tutorials as highly relevant. Sample comments are:
- As usual the tutorials are detailed and provide a good starting point for analyzing membrane proteins. Also for people who have not worked with membrane proteins before, this is great tutorial to learn to place protein in the membrane.
- Nanotubes. Very well-designed tutorial. Good workflow, illustrates relevant details.
Day 5
Day 5 Lecture 1: Introduction to Bioinformatics (N: r=14, c=12)
A majority of participants, 79%, rated the relevance of the lecture as very high. Sample comments are:
- Excellent lecture on how to combine sequence and structure information for probing certain research problems. Liked the second half (examples) on how insights can be gained using the tools/software. Also on some of the potential pitfalls.
- Great case sample with the ribosome, however very outside my research. Very detailed and informative, however, to someone involved in this kind of work.
Day 5 Tutorials: Basic Sequence Analysis; or, Expert Sequence Analysis; or, work on own projects (N: r=14, c=13)
The relevance of the tutorial was high, with 93% of participants rating tutorial relevance as very good to excellent. Sample comments are:
- Expert Sequence Analysis Evolution . Good tutorial with many details and explanations the appendices are also very helpful to complement the tutorial.
- Aquaporin, good tutorial. Served as general intro to these systems and reinforced previously introduced VMD skills.
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: Introduction to Protein Structure and Dynamics | 26 | 0 | 0 | 8 | 42 | 50 |
| Day 1 Tutorial: Using VMD; NAMD Tutorial | 25 | 0 | 0 | 16 | 36 | 48 |
| Day 2 Lecture: Statistical Mechanics of Proteins | 26 | 0 | 0 | 15 | 27 | 58 |
| Day 2 Tutorial: NAMD Tutorial & Stetching Deca-Alanine; or, Expert NAMD Set; or, Free Energy Set |
24 | 0 | 0 | 17 | 33 | 50 |
| Day 3 Lecture: Parameters for Classical Force Fields | 16 | 0 | 0 | 6 | 38 | 56 |
| Day 3 Tutorials: Parameterizing a Novel Residue;
Topology File Tutorial; Stretching Deca-alanine Tutorial |
15 | 0 | 0 | 7 | 47 | 47 |
| Day 4 Lecture: Simulating Membrane Channels | 18 | 0 | 0 | 0 | 39 | 61 |
| Day 4 Tutorials: Membrane Proteins Tutorial; Simulation of Waterbr> PPermeation Through Nanotubes | 17 | 0 | 0 | 0 | 41 | 59 |
| Day 5 Lecture: Introduction to Bioinformatics | 14 | 0 | 0 | 21 | 29 | 50 |
| Day 5 Tutorials: Evolution of Translation Tutorials:
Class I br>
Aminoacyl-tRNA Synthetase; Elongation Factor Tu; tRNA
and the RRibosome; or, Bioinformatics of Aquaporins |
14 | 0 | 0 | 7 | 29 | 64 |
