Computational Biophysics Workshop - Bethesda, Nov. 5-7, 2007
Lectures and Tutorials Evaluation of the Computational Biophysics Workshop at Bethesda, Maryland
November 5-7, 2007
Questionnaire: Klaus Schulten, TCB Group, UIUC, and modified by
David Brandon, TCB Group, UIUC
Analysis and report: David Brandon, TCB Group,
UIUC
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 presented a three-day (November 5-7, 2007) workshop sponsored by Helix Systems, Center for Information Technology at the Bethesda, Maryland campus of the National Institutes of Health. Resource faculty provided morning lectures, and teaching assistants and faculty led afternoon hands-on sessions using Resource software, and tutorials consisting of text and computer files. Helix Systems organized the event on the Bethesda campus, including advertising and registration of participants, ongoing contact with participants, setting up the event room, formatting of laptops, tutorial printing, and overall support of the workshop.
Workshop lectures were provided by K. Schulten (UIUC) and E. Tajkhorshid (UIUC). Three Resource members (M. Sotomayor, J. Gumbart, and J. Hsin) accompanied the lecturers to the workshop and provided instructional support on-site. A special thanks to Dr. Rosemary Braun, a postdoctoral fellow with the NIH's National Cancer Institute (Division of Cancer Prevention) for help in testing the laptops provided for workshop attendees, and for assisting with tutorial sessions during the first two days of the workshop. Tutorials and preparation of the laptops was provided by the graduate students and by other Resource staff, and on-site the tutorial sessions were led by the graduate students. The program of the workshop consisted of lectures and hands-on sessions, with an emphasis on the latter. At the end of each day of the workshop, participants were asked to provide comments and rate the relevance of the lectures and tutorials. A copy of the forms used to collect responses about the lectures and tutorials is available here.
Summaries for the lectures and tutorials are comprised of three 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, and 3) text summarizing the main points of the total body of comments for a lecture or tutorial. 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 Lectures: Structure & Sequence Analysis w/VMD; VMD for Structure Building & Dynamics (N: r=15, c=11)
Most respondents, 87%, rated the lecture as highly relevant. Sample comments are:
- "Excellent introduction. Though I knew VMD before I learned a lot of new things and how to use better tools I already knew."
- "The lecture is excellent, especially for new users."
Other comments indicate that some participants found the lecture too basic, throughout the lectures or just at the beginning.
Day 1 Tutorial: VMD Molecular Graphics Tutorial (N: r=12, c=12)
All respondents, 100%, found the tutorial content highly relevant. Sample comments are:
- "Easy to follow the tutorials. Maybe good to include some advanced tasks and examples."
- "Very good tutorial. Well written and organized. TAs are very helpful."
While a number of other comments are also complimentary of the tutorial, others suggest more detail on some pages, or training on related topics such as using the Unix shell or a tutorial on TCL/TK scripting.
Day 2 Lecture: Molecular Dynamics with NAMD I, II (N: r=13, c=10)
With a 92% relevance rating, most respondents found the lecture content to be highly relevant. Sample comments are:
- "Excellent presentation . . . good balance of theory and applications."
- "I was very impressed at the rigor, yet understandability, of the lecture. Despite all the equations, I never felt lost or overwhelmed. The professor was able to help me see the meaning of all the terms and why they were important. The slides were clean and valuable. I wish we would have had more time at the end of the lecture for the breakdown of steps to do a NAMD simulation."
Further comments again compliment the lecture, with again a suggestion that slides be copied and given to participants for study.
Day 2 Tutorial: NAMD Tutorial (N: r=13, c=6)
Nearly all respondents, 92%, rated the tutorial relevance as very high. Sample comments are:
- "Learned many new things, especially on the analysis part. Tutors very nice and helpful in answering questions."
- "Easy to follow the tutorial manual. May need more time to fully understand."
Other comments include further compliments about the tutorial, along with suggestions such as providing more detail on setting up simulations, less time on analysis, descriptions of mistakes to avoid, and having more time to complete the tutorial.
Day 3 Lecture: Molecular Dynamics of Cellular Processes I, II (N: r=13, c=6)
All respondents, 100%, rated the relevance of the lecture as very high. Sample comments are:
- "I like the wonderful examples. It is very exciting to see them."
- "Very informative about what “can be done”"
Other comments are appreciative of the lectures, with one comment wishing for more time for questions about cryo-EM and SMD.
Day 3 Tutorials: Parameterizing a Novel Residue; Topology Files; Nanotubes; Deca-alanine (N: r=13, c=8)
The rated relevance of the tutorials was high, with a relevance rating from respondents of 100% for the tutorials. Sample comments are:
- "I did Topology Files, the SPARTAN portion of Parameterizing, and the Movies and Graphics with VMD tutorials. All were very detailed, clear, and explained every step. I never got lost, understood everything, and got the results I expected. Very good tutorials!"
- "Very good."
Other comments are appreciative of the tutorials, but also suggest more time was needed for the tutorials, as there was a lot of content to digest within the time frame of the workshop.
The complete set of comments is available by e-mailing workshop+bethesda@ks.uiuc.edu.
Table 1: Summary of Relevance Statistics
| Poor | Fair | Good | Very Good | Excellent | ||
| N | % | % | % | % | % | |
| Day 1 Lecture: Structure & Sequence Analysis w/VMD; VMD for Structure Building & Dynamics | 15 | 13 | 33 | 53 | ||
| Day 1 Tutorial: VMD Molecular Graphics Tutorial | 12 | 33 | 67 | |||
| Day 2 Lecture: Molecular Dynamics with NAMD I, II | 13 | 8 | 15 | 77 | ||
| Day 2 Tutorial: NAMD Tutorial | 13 | 8 | 23 | 69 | ||
| Day 3 Lecture: Molecular Dynamics of Cellular Processes I, II | 13 | 23 | 77 | |||
| Day 3 Tutorials: Parameterizing a Novel Residue; Simulation of Water Permeation through Nanotubes; Stretching Deca-alanine; Topology Files | 13 | 23 | 77 |