Computational Biophysics Workshop - Atlanta, Mar. 21-25, 2011
Lectures and Tutorials Evaulation of the Computational Biophysics Workshop held at the Georgia Institute of Technology in Atlanta, Georgia
March 21-25, 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 (CMMB) 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 participated in a one-week (March 21-25, 2011) workshop sponsored by the NIH National Center for Research Resources (NCRR), the NIH Center for Macromolecular Modeling and Bioinformatics (NIH P41-RR005969), the Integrative BioSystems Institute at Georgia Tech, the Institute for Data and High Performance Computing at Georgia Tech, and the Parker H. Petit Institute for Bioengineering and Bioscience at Georgia Tech. While the NCRR and the CMMB provided instruction, learning materials, housing, and some other expenses, co-sponsors at Georgia Tech provided the workshop classroom site, catering, and additional administrative support. About half the participants were local participants from Georgia Tech, while others were selected by the CMMB from off-campus organzations.
The program of the workshop consisted of lectures and hands-on sessions. Workshop lectures were given by K. Schulten (UIUC), Z. Schulten (UIUC), E. Tajkhorshid (UIUC), and one guest speaker, Jeff Skolnick of the CSSB. Teaching assistants from the CMMB 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=37, c=32)
A majority of respondents, 76%, rated the lecture as highly relevant. Sample comments are:
- Dr. Schulten gave an excellent overview. Dr. Skolnick gave a great lecture on his lab’s FINDSITE and a-dock program which has great relevance to my work.
- Enjoyed both lectures by Klaus and Jeff. During the introduction to VMD and NAMD. I learned things about both programs that I did not know from experts in my lab who have taught me the basics of both. Likewise I learned a lot from the second lecture by Jeff.
Day 1 Tutorial: Using VMD; NAMD Tutorial (N: r=36, c=39)
A majority of respondents, 83%, found the tutorial content highly relevant. Sample comments are:
- A very useful session indeed. The TA’s are real helpful. To have Prof. Schulten personally chat w/all the participants was the best.
- VMD and NAMD tutorials are very easy to understand and the exercises are very good examples.
Day 2 Lecture: Statistical Mechanics of Proteins (N: r=34, c=25)
Nearly all respondents, 97%, found the lecture content to be highly relevant. Sample comments are:
- Interesting talk about the necessity to correctly capture the physics of the systems.
- Excellent representation of modern biophysics problems that can be investigated using computers. Very motivating!
Day 2 Tutorial: NAMD Tutorial & Stetching Deca-Alanine; or, Expert NAMD Set; or Free Energy Set (N: r=32, c=32)
All of those responding, 78%, rated tutorial relevance as very high. Sample comments are:
- NAMD tutorial I finished today. I feel like I learned alot. I feel like I don’t have a good sense of practical aspects of setting up my own calculations, but that will come. I also started the membrane tutorial and so far so good.
- Worked through the Deca-Alanine tutorial and when I need help I received great help.
Day 3
Day 3 Lecture 1: Introduction to Bioinformatics (N: r=25, c=21)
A majority of respondents, 88%, rated the relevance of the lecture as very high. Sample comments are:
- Lectures were really good. I was not familiar with VMD for bioinformatics, it seems really powerful. It should benefit my research directly.
- A very nice overview of sequence and structured analysis for generation signatures and visualizing them.
Day 3 Tutorials: Basic Sequence Analysis; or, Expert Sequence Analysis; or, work on own projects (N: r=27, c=18)
The relevance of the tutorial was high, with 89% of respondents rating tutorial relevance as very good to excellent. Sample comments are:
- Basis sequence analysis is something I’ve always been interested in but never had the skills to pursue. Very relevant and interesting.
- Evolution of translation (class-I Aminoacyl-tRNA synthetases complexes). I found the tutorial easy to follow and make sense of it in light of the lecture.
Day 4
Day 4 Lecture: Parameters for Classical Force Fields (N: r=22, c=16)
At 86% respondent agreement, ratings indicate the lecture was viewed as highly relevant. Sample comments are:
- A very nice overview of force field parameters in CHARMM and methods used to derive the parameters for novel residues.
- The lecture made clear what approximations were made to derive a force field from ab inito or physical data, and where the limitations of force fields are.
Day 4 Tutorial: Parameterizing a Novel Residue; Topology File Tutorial; Simulation of Water Permeation through Nanotubes (N: r=21, c=17)
With 100% rating relevance as very good to excellent, all respondents found the tutorials relevant. Sample comments are:
- A clear and concise documentation for generating a novel residue and parameterize it. I loved all the tutorials so far.
- Parameterization and Topology – good explanation.
Day 5 Lecture: Simulating Membrane Channels (N: r=26, c=14)
Of those responding, 92% rated the lecture as highly relevant to their interests. Sample comments are:
- This lecture was fascinating, from a scientific point of view. This really excites my scientific sense and makes me think on my own system.
- Very good examples with some VMD scripting provided. Educational and attractive. Emad also took us through a history of his research to show how NAMD and VMD have been useful for him.
Day 5 Tutorial: Membrane Proteins Tutorial; or, Expert NAMD Set; or, Free Energy Set (N: r=22, c=16)
Nearly all respondents - 95% - found these tutorials as highly relevant. Sample comments are:
- I have worked on the membrane proteins tutorial. It is helpful for us to learn how to set up.
- Exactly what I need.
The complete set of comments is available by e-mailing workshop+atlanta@ks.uiuc.edu.
| N | Poor | Fair | Good | Very Good | Excellent | |
| Day 1 Lecture: Introduction to Protein Structure and Dynamics | 37 | 3% | 22% | 51% | 24% | |
| Day 1 Tutorial: Using VMD; NAMD Tutorial | 36 | 3% | 14% | 39% | 44% | |
| Day 2 Lecture: Statistical Mechanics of Proteins | 34 | 3% | 47% | 50% | ||
| Day 2 Tutorial: NAMD Tutorial & Stetching Deca-Alanine; or, Expert NAMD Set; or, Free Energy Set |
32 | 3% | 19% | 25% | 53% | |
| Day 3 Lecture: Introduction to Bioinformatics | 25 | 4% | 8% | 48% | 40% | |
| Day 3 Tutorials: Evolution of Translation Tutorials: Class I br Aminoacyl-tRNA Synthetase; Elongation Factor Tu; tRNA and the Ribosome; or, Bioinformatics of Aquaporins |
27 | 11% | 44% | 44% | ||
| Day 4 Lecture: Parameters for Classical Force Fields | 22 | 14% | 27% | 59% | ||
| Day 4 Tutorials: Parameterizing a Novel Residue; Topology Files | 21 | 24% | 76% | |||
| Day 5 Lecture: Simulating Membrane Channels | 26 | 4% | 4% | 46% | 46% | |
| Day 5 Tutorials: Membrane Proteins & Water Permeation Through Nanotubes; or, Expert NAMD Set; or, Free Energy Set |
22 | 5% | 41% | 55% |
