Computational Biophysics Workshop - Beijing, China, Oct. 14-17, 2013

 

Evaluation of the Computational Biophysics Workshop Using VMD and NAMD at Beijing, China
Computer Network Information Center
Chinese Academy of Sciences
Beijing, China
October 14-17, 2013

A "collaborative workshop" involves significant contributions by the Theoretical and Computational Biophysics Group (TCBG), e.g. lectures, learning materials, and funding, to a training event organized by an external group. From October 14-17, 2013, a collaborative workshop titled "Computational Biophysics Workshop Using VMD and NAMD" was held at the Computer Network Information Center of the Chinese Academy of Sciences in Beijing, China. At the event, TCBG postdoctoral associate Yanxin Liu provided lectures, and workshop participants worked through TCBG tutorials whilst utilizing TCBG's VMD and NAMD software programs. The event was co-sponsored by TCBG and the Supercomputing Center and the Institute of Biophysics of the Chinese Academy of Sciences. The program of the workshop consisted of lectures and hands-on sessions, with an emphasis on the latter. On the last day of the workshop, participants were asked to complete a general evaluation form consisting of questions about outcomes, lectures, hands-on tutorial sessions, evening lecture sessions, environment and technical resources, communication and dissemination, and overall satisfaction. Summary tables of results and compilations of comments from that evaluation are below.

I. Outcomes:

  N Strongly Disagree Disagree Unsure Agree Strongly Agree
1. The Workshop broadened my understanding of concepts and principles in the field of Computational and Theoretical Biophysics. 25     8% 40% 52%
2. The Workshop improved my ability to carry out original research in the field of Theoretical and Computational Biophysics. 25   4% 16% 52% 28%
3. The Workshop improved significantly my computational skills. 25   4% 32% 48% 16%
4. The Workshop taught me techniques directly applicable to my career. 25   4% 24% 40% 32%
5. The material presented in the Workshop was relevant to my research. 25     20% 44% 36%

 

II. Lectures:

  N Strongly Disagree Disagree Unsure Agree Strongly Agree
1. The instructors' knowledge of the subjects was good. 25     4% 32% 64%
2. The instructors explained the material well. 25       48% 52%
3. The instructors provided real-world examples. 25       32% 68%
4. The lectures were coordinated between instructors. 23     9% 57% 35%
5. Lectures incorporated recent developments in the field. 25       44% 56%
6. The range of lectures captured the overall essentials of the field. 25   4% 12% 52% 32%
7. The level of the lectures was appropriate. 25     16% 60% 24%
8. The underlying rationale of the techniques presented was clear. 25     8% 60% 32%
9. The instructors stimulated my intellectual curiosity. 25     8% 56% 36%
10. The daily Q&A period was beneficial. 25     12% 48% 40%
11. Day 1 Lecture on "Structure and Sequence Analysis with VMD" is excellent. 25     12% 48% 40%
12. Day 2 Lecture on "Introduction to Molecular Dynamics Simuation with NAMD" is excellent. 25       48% 52%
13. Day 3 Lecture on "Applications of VMD / NAMD in Modern Research" is excellent. 25     8% 52% 40%
14. Day 4 Lecture on "Molecular Dynamics Flexible Fitting" is excellent. 25     12% 40% 48%

 

III. Hands-on Sessions:

  N Strongly Disagree Disagree Unsure Agree Strongly Agree
1. The hands-on sessions were important for the learning process in the Workshop. 25 4%   8% 32% 56%
2. The concrete examples in the hands-on tutorials increased my understanding of the lectures. 25 4%     60% 36%
3. The hands-on sessions were long enough. 25     20% 44% 36%
4. The hands-on sessions were coordinated with the lectures. 25 4%     68% 28%
5. TAs were well-prepared to answer questions. 25 4%   8% 56% 32%
6. There were sufficient instructions to proceed with the hands-on assignments. 25 4%   8% 52% 36%
7. There were enough TAs / instructional staff to help the participants. 25     16% 60% 24%
8. The tutorial options accommodated the differing interests of participants. 25     20% 48% 32%
9. The tutorial options accommodated the differing expertise levels of participants. 25   4% 24% 40% 32%

 

IV. Environment and Technical Resources:

  N Strongly Disagree Disagree Unsure Agree Strongly Agree
1. The software used in the Workshop ran well on my (circle one: Windows/Mac/Linux) laptop. 24       38% 63%
2. The lecture room was conducive to learning. 25       36% 64%
3. The projection system was sufficient for the lectures. 25   4%   44% 52%
4. The hotel provided sufficient accommodations (answer if applicable to you). 8     25% 63% 13%

 

V. Communication and Dissemination:

  N Strongly Disagree Disagree Unsure Agree Strongly Agree
1. Instructors were readily available for Q&A outside the lecture periods. 25     4% 56% 40%
2. The Workshop web site was informative about the event. 25     8% 52% 40%
3. The organizational emails about setting up laptops for the Workshop were helpful. 24   4% 4% 50% 42%

 

VI. Overall Satisfaction:

  N Strongly Disagree Disagree Unsure Agree Strongly Agree
1. The Workshop was well organized. 25     8% 36% 56%
2. The balance between lectures and hands-on sessions was optimal. 25 4%   12% 60% 24%
3. The Workshop addressed my research needs. 25   4% 12% 56% 28%
4. Overall, the Workshop met my expectations. 25   4% 16% 60% 20%
5. I would recommend this Workshop to others. 25     8% 52% 40%

VII. Comments

Participants were solicited for comments in four areas, 1) suggestions for improving the workshop, 2) suggestions for similar workshops, 3) most valuable/least valuable/future workshop topics, and 4) other comments. An inexhaustive list of comments in each area is provided below; a compilation of raw statements can be obtained by e-mailing workshop+beijing@ks.uiuc.edu. If a comment was made in one area of the open questions, it is not repeated again in another area below.

  • Suggestions for improving the workshop:
    • "Advanced topics should be covered and some simple assignments should be supplied, the hands-on session should be longer."
    • "More case studies if possible, especially on analysis part."
    • "For some important and vital steps, the instructors could show us the detailed information and how to do them so we can follow and understand better."
  • Suggestions for similar workshops:
    • "More advanced tutorials, more detailed skills (tricks)."
    • "Discussion of previous research work in more details."
    • "If the lecture room could provide PC, things will be better."
  • Most/least valuable topics and suggestions for future workshop topics
    • "For now, the simulation about membrane protein and DNA/RIVA is what I am interested in most, and new technology about using NAMD is very helpful as well."
    • "Membrane protein simulations most valuable, PMF calculation should be covered."
    • "Molecular flexible fitting based on cryo-EM map was most valuable to me. I hope to learn more details about the applications of NAMD, especially in hands-on sections."
  • Other comments:
    • "It's very good and very helpful, I hope this lecture can be done more."
    • "Overall, it is a nice workshop!"
    • "Maybe more tutorials on coarse graining."