Computational Biophysics Workshop - Bremen, Oct. 17-21, 2011
'Hands-On' Workshop on Computational Biophysics at Bremen, Germany
Lectures and Tutorials Evaluation
October 17-21, 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 Center co-organized a one-week (October 17-21, 2011) workshop with organizational support and grant funds from thethe Centre Européen de Calcul Atomique et Moléculaire (CECAM) and Jacobs University Bremen.
The program of the workshop consisted of lectures and hands-on sessions. Workshop lectures were provided by K. 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=38, c=30).
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 - K. Schulten (N: r=38, c=30)
A majority of respondents, 84%, rated the lecture as highly relevant. Sample comments are:- Excellent introduction to VMD/NAMD, overview about their capabilities.
- The introduction was very descriptive and gave good idea of the protein dynamics. I am not working in proteins but even then I was able to get the insights of the simulations.
Day 1 Tutorial: Using VMD; NAMD Tutorial (N: r=38, c=36)
Nearly all participants, 89%, found the tutorial content highly relevant. Sample comments are:- Love the tutorials --> learning by doing.
- Very thoroughly described steps. Highly motivated tutors.
Day 2 Lecture: Statistical Mechanics of Proteins - K. Schulten (N: r=36, c=26)
A majority of respondents, 83%, rated the lecture as highly relevant. Sample comments are:
- Excellent! Good to learn the theoretical background behind NAMD.
- K. Schulten can explain difficult/complex physics in a very clear way.
Day 2 Tutorial: NAMD Tutorial & Stetching Deca-Alanine; or, Expert NAMD Set; or Free Energy Set (N: r=33, c=33)
Most of those responding, 79%, rated the tutorial relevance as very high. Sample comments are:
- I worked on the User-Defined Forces in NAMD tutorial. It was very interesting tutorial to design my own job.
- I worked on the NAMD tutorial and on stretching deca-alanine. They are both very detailed and analytical.
Day 3
Nearly all participants, 97%, rated the relevance of the lecture as high. Sample comments are:
- The lectures were both very interesting and lecturers were very good at focusing our attention.
- The bioinformatics introduction was clear and precise. The talk of Dr. Tajkhorshid was very informative and gave me a lot of insights particulary in choosing the Mulliken charges for the molecule.
Day 3 Tutorials: Basic Sequence Analysis; or, Expert Sequence Analysis; or, work on own projects (N: r=29, c=28)
The relevance of the tutorial was very high, with 79% of participants rating tutorial relevance as very good to excellent. Sample comments are:
- Worked on tclForces, ABF and my own project. Learned a lot, thank you for good and detailed answers!
- Basic sequence analysis: very good! Excellent material.
Day 4 Lecture: Molecular Dynamics of Cellular Processes - E. Tajkhorshid (N: r=32, c=19)
Nearly all of those responding, 91% rated the lecture as highly relevant to their interests. Sample comments are:
- Excellent lecture. It makes me understand the charmm forcefield and NAMD input files better.
- Well and clearly structured talk/slides, elaborate discussions of file contents.
Day 4 Tutorials: Parameterization; Topology Files (N: r=26, c=25)
Nearly three-fourths of respondents - 73% - found the tutorials highly relevant. Sample comments are:
- Today I did parameterization, and membrane protein tutorials, and they are explained in a very layman language and they are really nice.
- I read the topology and paramaters tutorials. I found them very good, so I tried to parameterize my residue following the tutorial with good results.
Day 5
Day 5 Lecture: Simulating Membrane Channels - E. Tajkhorshid (N: r=32, c=20)
All participants - 100% - rated the lecture as highly relevant to their interests. Sample comments are:
- The lecture was good. Thanks for the advice to explore new ways, to try extreme conditions for the simulations.
- Clear and precise presentation.
Day 5 Tutorial: Membrane Proteins Tutorial; or, Expert NAMD Set; or, Free Energy Set (N: r=28, c=22)
A high majority of participants - 89% - found these tutorials as highly relevant. Sample comments are:
- I enjoyed the membrane proteins tutorial.
- The tutorials provided me a good idea of the various methods of applying NAMD to membrane proteins.
The complete set of comments is available by e-mailing workshop+bremen@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 | 38 | 16% | 42% | 42% | ||
| Day 1 Tutorial: Using VMD; NAMD Tutorial | 38 | 3% | 8% | 39% | 50% | |
| Day 2 Lecture: Statistical Mechanics of Proteins | 36 | 3% | 14% | 31% | 53% | |
| Day 2 Tutorial: NAMD Tutorial & Stetching Deca-Alanine; or, Expert NAMD Set; or, Free Energy Set | 33 | 3% | 18% | 36% | 42% | |
| Day 3 Lecture: Introduction to Bioinformatics and Forcefields | 35 | 3% | 20% | 77% | ||
| Day 3 Tutorial: Basic Sequence Analysis: Aquaporins with the VMD MultiSeq Tool; or, Expert NAMD Set; or, Free Energy Set | 29 | 3% | 3% | 14% | 34% | 45% |
| Day 4 Lecture: Parameters for Classical Force Fields | 32 | 9% | 31% | 59% | ||
| Day 4 Tutorials: Parameterizing a Novel Residue; Topology Files | 26 | 27% | 27% | 46% | ||
| Day 5 Lecture: Simulating Membrane Channels | 32 | 50% | 50% | |||
| Day 5 Tutorials: Membrane Proteins & Water Permeation Through Nanotubes; or, Expert NAMD Set; or, Free Energy Set | 28 | 4% | 7% | 32% | 57% |
