Computational Biophysics Workshop - San Diego, Jul. 12-16, 2010
Lectures and Tutorials Evaulation of the Theoretical and Computational Biophysics Workshop at San Diego
July 12-16, 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 (July 12-16, 2010) workshop sponsored by the National Biomedical Computation Resource (NBCR) and the National Resource for Automated Molecular Microscopy (NRAMM) and held at the The Scripps Rsearch Institute in San Diego, California. The NBCR provided some lectures and administrative support, while NRAMM provided the classroom space, technical support, and some lectures for the workshop. Using funds provided by a grant from the National Center for Research Resources, TCBG covered hotel, catering and printing costs for participants, as well as travel, hotel, honoraria, and catering costs for teaching staff.
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.
- 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=15)
A majority of respondents, 83%, rated the lecture as highly relevant. Sample comments are:
- Very nice presentation, practical, vivid and informative. Profess Schulten showed his wide and deep knowledge in answering questions.
- I will say that the most relevant part of this lecture is the overview one get about things you can do with VMD/NAMD. I really like the idea of thinking of VMD as “a tool to think”.
Day 1 Tutorial: Using VMD; NAMD Tutorial (N: r=17, c=19)
A majority of participants, 88%, found the tutorial content highly relevant. Sample comments are:
- Worked on VMD tutorial. Learnt the calculation of electrostatic potential using ABS tool. The TA’s were helpful. Worked on the ‘volmap’ command. Overall a productive and informative day.
- I worked on both VMD and NAMD tutorial. They were very well written and easy to follow. Described not only VMD/NAMD commands but also biological / physical properties that are relevant.
Day 2 Lecture: Statistical Mechanics of Proteins (N: r=20, c=18)
Nearly all participants, 95%, found the lecture content to be highly relevant. Sample comments are:
- Really good lecture. It helps understand what the scope and leaning of MD-sims is. Specially in terms of understanding it as a “microscope” onto the biological world.
- Dr. Schulten conducted his lecture even better today with very careful and detailed explanation. I really enjoyed his lecture.
Day 2 Tutorial: NAMD Tutorial & Stetching Deca-Alanine; or, Expert NAMD Set; or Free Energy Set (N: r=17, c=21)
Most of those responding, 88%, rated the tutorial relevance as very high. Sample comments are:
- NAMD Tutorial – the tutorial handbook was very clear and useful in guiding me through the preparation, MD simulation, and analysis steps.
- SMD, Free Energy Calculations and my own projects. TA’s are very kind and helped a lot during the tutorial sessions. Brainstorming was really good. Even I ask very simple questions, they gave answers!
Day 3
Day 3 Lecture 1: Introduction to Bioinformatics (N: r=15, c=11)
All participants, 100%, rated the relevance of the lecture as very high. Sample comments are:
- I must recognize that I have not previously seen the power and versatility of MultiSeq and the way it can be applied to evolutionary studies.
- The focus on science of Ribosome in the second lecture of the day was very interesting. Learning through example, in this case as very effective in showing the power VMD in data analysis.
Day 3 Tutorials: Basic Sequence Analysis; or, Expert Sequence Analysis; or, work on own projects (N: r=15, c=14)
The relevance of the tutorial was high, with 93% of participants rating tutorial relevance as very good to excellent. Sample comments are:
- Evolution of Translation – The Ribosome. The accompanying information explanation the function of Ribosome was very insightful. Excellent.
- I worked on the Aquaporin tutorial. I thought it was very well written – very informative but still understandable from a beginners view.
Day 4
Day 4 Lecture: Parameters for Classical Force Fields (N: r=12, c=14)
At 83% participant agreement, ratings indicate the lecture was viewed as highly relevant by a majority of participants. Sample comments are:
- Dr. Tajkorshid explains things carefully and patiently. It might be trivial for experienced MD simulation but is the exact way I want to learn about MD and its file system.
- Very clear explanation of the meaning of FF parameters and how they can be defined for new molecules.
Day 4 Tutorial: Parameterizing a Novel Residue; Topology File Tutorial; Simulation of Water Permeation through Nanotubes (N: r=12, c=14)
With 83% rating relevance as very good to excellent, a majority of respondents found the tutorials relevant. Sample comments are:
- The examples well designed and TAs are helpful as usual.
- Worked on both tutorials very clearly written, to follow. They were very helpful.
Day 5 Lecture: Simulating Membrane Channels (N: r=16, c=14)
Of those responding, 100% rated the lecture as highly relevant to their interests. Sample comments are:
- Fascinating, well paced and clearly conveyed.
- Excellent lecture. Clear, interesting. It really gives you an idea of what kind of questions can be confronted with MD SMS.
Day 5 Tutorial: Membrane Proteins Tutorial; or, Expert NAMD Set; or, Free Energy Set (N: r=13, c=12)
All participants - 100% - found these tutorials as highly relevant. Sample comments are:
- Worked on Membrane Proteins Tutorial. Very well written and useful tutorial.
- Membrane Tutorial -) very good tutorial and relevant to morning discussion.
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 | 18 | 0 | 0 | 17 | 39 | 44 |
| Day 1 Tutorial: Using VMD; NAMD Tutorial | 17 | 0 | 0 | 12 | 41 | 47 |
| Day 2 Lecture: Statistical Mechanics of Proteins | 20 | 0 | 0 | 5 | 40 | 55 |
| Day 2 Tutorial: NAMD Tutorial & Stetching Deca-Alanine; or, Expert NAMD Set; or, Free Energy Set |
17 | 0 | 12 | 12 | 29 | 59 |
| Day 3 Lecture: Introduction to Bioinformatics | 15 | 0 | 0 | 0 | 33 | 67 |
| Day 3 Tutorials: Evolution of Translation Tutorials:
Class I br>
Aminoacyl-tRNA Synthetase; Elongation Factor Tu; tRNA
and the RRibosome; or, Bioinformatics of Aquaporins |
15 | 0 | 0 | 7 | 27 | 67 |
| Day 4 Lecture: Parameters for Classical Force Fields | 12 | 0 | 0 | 17 | 17 | 67 |
| Day 4 Tutorials: Parameterizing a Novel Residue;
Topology File Tutorial; Stretching Deca-alanine Tutorial |
12 | 0 | 0 | 17 | 25 | 58 |
| Day 5 Lecture: Simulating Membrane Channels | 16 | 0 | 0 | 0 | 6 | 94 |
| Day 5 Tutorials: Membrane Proteins Tutorial; Simulation of Waterbr> PPermeation Through Nanotubes | 13 | 0 | 0 | 0 | 46 | 54 |
