Computational Biophysics Workshop - Pittsburgh, May 16-20, 2011
Lectures and Tutorials Evaulation of the Theoretical and Computational Biophysics Workshop held at the Pittsburgh Supercomputing Center
May 16-20, 2011
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 Resource participated in a one-week (May 16-20, 2011) workshop sponsored by the National Resource for Biomedical Supercomputing (NRBSC) at the Pittsburgh Supercomputing Center in 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=18, c=13)
Almost all respondents, 94%, rated the lecture as highly relevant. Sample comments are:
- Professor Schulten’s view of the field is very interesting, he showed several important issues that are not taken into account by beginners but that can be very relevant.
- The lecture has clear introduction of the concept of energy function terms, the different ensembles used in MD and various constraints of calculating short and long-range interactions. Professor was very receptive to questions and clarified questions in detail.
Day 1 Tutorial: Using VMD; NAMD Tutorial (N: r=18, c=14)
A majority of participants, 89%, found the tutorial content highly relevant. Sample comments are:
- I worked on the NAMD tutorial. It was informative and clear in its instructions. It was a good length, and I finished at the end of the session.
- I finished both VMD and NAMD tutorial. I had not have any prior experience with NAMD so they were pretty useful.
Day 2 Lecture: Statistical Mechanics of Proteins (N: r=11, c=7)
A majority, 91%, found the lecture content to be highly relevant. Sample comments are:
- Dr. K. Schulten’s lecture is fabulous. I learned a lot from his example.
- Good illustration of a powerful toolbox for simulations. I am willing to learn further and start applying the different methods.
Day 2 Tutorial: NAMD Tutorial & Stetching Deca-Alanine; or, Expert NAMD Set; or Free Energy Set (N: r=10, c=9)
All of those responding, 100%, rated tutorial relevance as very high. Sample comments are:
- Deca-Alanine. Good! Very useful to study!
- I did the stretching Deca-alanine and shape-based coarse graining tutorials. I also started the user-defined forces in NAMD tutorial. I found all the tutorials useful, but the end of the coarse graining tutorial was a little confusing.
Day 3
Day 3 Lecture: Parameters for Classical Force Fields (N: r=14, c=8)
At 100% participant agreement, ratings indicate the lecture was viewed as highly relevant. Sample comments are:
- Knowing the structure of the PSE, INP & PA files and the meaning for the different options seems trivial until you really know how powerful it is to modify them. Thanks a lot, lots of work to do!
- Excellent – very clear, thorough, and just the right amount of details.
Day 3 Tutorial: Parameterizing a Novel Residue; Topology File Tutorial; Simulation of Water Permeation through Nanotubes (N: r=13, c=8)
With 100% rating relevance as very good to excellent, all respondents found the tutorials relevant. Sample comments are:
- Great tutorials, the allowed me to start working right away in one of my projects. Parameterization; Topology files.
- Nanotubes – lots of fun!
Day 4 Lecture: Simulating Membrane Channels (N: r=13, c=5)
Of those responding, 92% rated the lecture as highly relevant to their interests. Sample comments are:
- Very interesting presentation. Extremely Helpful.
- In general, I learned about more possibilities and applications of MD.
Day 4 Tutorial: Membrane Proteins Tutorial; or, Expert NAMD Set; or, Free Energy Set (N: r=12, c=4)
A majority of participants - 92% - found these tutorials as highly relevant. Sample comments are:
- I am half-way through the membrane simulation tutorial. The tutorial so far is good TAs were polite and helpful during the tutorial session. Overall, this workshop gave a chance to meet many people working closely in the research field of my interest. The lectures, tutorials, and formal, informal discussion were very useful. It’s a very good learning experience over-all.
- Membrane protein, Nanotubes. Apply new knowledge to my data (own project). It is great to be able to start practicing the methods with your own data.
Day 5
Day 5 Lecture 1: Introduction to Bioinformatics (N: r=14, c=7)
A majority of participants, 86%, rated the relevance of the lecture as very high. Sample comments are:
- Excellent. Not my area of specialty, but Zan’s presentation drew me in and I found applicability in my own research.
- Excellent lectures, clear & keeps the attention of the audience. Her explanations are easy to follow. Very good in showing us the utility of the program tied to specific problems.
Day 5 Tutorials: Basic Sequence Analysis; or, Expert Sequence Analysis; or, work on own projects (N: r=13, c=6)
The relevance of the tutorial was high, with 100% of participants rating tutorial relevance as very good to excellent. Sample comments are:
- All good!
- Very good, although I think that it would be nice to have more documentation about the cells or the algorithms to run multiseq by doing script.
The complete set of comments is available by e-mailing brandon@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 | 18 | 0% | 0% | 6% | 28% | 67% |
| Day 1 Tutorial: Using VMD; NAMD Tutorial | 18 | 0% | 0% | 6% | 28% | 61% |
| Day 2 Lecture: Statistical Mechanics of Proteins | 11 | 0% | 0% | 9% | 18% | 73% |
| Day 2 Tutorial: NAMD Tutorial & Stetching Deca-Alanine; or, Expert NAMD Set; or, Free Energy Set |
10 | 0% | 0% | 0% | 20% | 80% |
| Day 3 Lecture: Parameters for Classical Force Fields | 14 | 0% | 0% | 0% | 14% | 86% |
| Day 3 Tutorials: Parameterizing a Novel Residue; Topology Files | 13 | 0% | 0% | 0% | 15% | 85% |
| Day 4 Lecture: Simulating Membrane Channels | 13 | 0% | 8% | 0% | 8% | 85% |
| Day 4 Tutorials: Membrane Proteins & Water Permeation Through Nanotubes; or, Expert NAMD Set; or, Free Energy Set |
12 | 0% | 8% | 0% | 8% | 83% |
| Day 5 Lecture: Introduction to Bioinformatics | 14 | 0% | 0% | 14% | 29% | 57% |
| Day 5 Tutorials: Evolution of Translation Tutorials:
Class I br Aminoacyl-tRNA Synthetase; Elongation Factor Tu; tRNAand the Ribosome; or, Bioinformatics of Aquaporins |
13 | 0% | 0% | 0% | 15% | 85% |
