Computational Biophysics Workshop - Atlanta, Nov. 3-7, 2014
General Evaluation of the Computational Biophysics Workshop at Atlanta, GA
November 3-7, 2014
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 Zan Luthey-Schulten, Laxmikant Kale, Emad Tajkhorshid, and Aleksei 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 organized a one-week (November 3-7, 2014) workshop at the Georgia Institute of Technology. The Center provided all workshop content, as well as the classroom, catering, and printing costs.
The program of the workshop consisted of lectures and hands-on sessions. Workshop lectures were given by Klaus Schulten (UIUC), Emad Tajkhorshid (UIUC), and James Gumbart (Georgia Tech). Teaching assistants from the research group of each faculty member helped participants during the hands-on tutorial sessions. Tutorials and software used in the workshop were developed by Center members. 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, after-lunch lectures, environment and technical resources, communication and dissemination, overall satisfaction, and questions soliciting open comments. A copy of the form is available here; summary tables of results are below.
Highlights of the results include 95% of participants indicating an increased understanding of computational and theoretical biophysics, 89% of participants indicating they would recommend the workshop addressed their research needs, and 100% of participants indicating they would recommend the workshop to others.
| 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. | 19 | 0% | 0% | 5.2% | 26.3% | 68.4% |
| 2. The Workshop improved my ability to carry out original research in the field of Theoretical and Computational Biophysics. | 19 | 0% | 0% | 10.5% | 42.1% | 47.4% |
| 3. The Workshop improved significantly my computational skills. | 19 | 5.3% | 5.3% | 26.3% | 31.6% | 31.6% |
| 4. The Workshop taught me techniques directly applicable to my career. | 19 | 0% | 0% | 5.3% | 31.6% | 63.2% |
| 5. The material presented in the Workshop was relevant to my research. | 19 | 0% | 5.3% | 5.3% | 36.8% | 52.6% |
| N | Strongly Disagree | Disagree | Unsure | Agree | Strongly Agree | |
| 1. The instructors' knowledge of the subjects was good. | 19 | 0% | 0% | 0% | 26.3% | 73.7% |
| 2. The instructors explained the material well. | 19 | 0% | 0% | 5.3% | 36.8% | 57.9% |
| 3. The instructors provided real-world examples. | 19 | 0% | 0% | 5.3% | 26.3% | 68.4% |
| 4. The lectures were coordinated between instructors. | 19 | 0% | 0% | 5.3% | 31.6% | 63.2% |
| 5. Lectures incorporated recent developments in the field. | 19 | 0% | 0% | 0% | 31.6% | 68.4% |
| 6. The range of lectures captured the overall essentials of the field. | 19 | 0% | 0% | 0% | 36.8% | 63.2% |
| 7. The level of the lectures was appropriate. | 19 | 0% | 0% | 15.8% | 42.1% | 42.1% |
| 8. The underlying rationale of the techniques presented was clear. | 19 | 0% | 5.3% | 0% | 31.6% | 63.2% |
| 9. The instructors stimulated my intellectual curiosity. | 19 | 0% | 0% | 5.3% | 36.8% | 57.9% |
| 10. The daily Q&A period was beneficial. | 19 | 0% | 0% | 5.3% | 42.1% | 52.6% |
| N | Strongly Disagree | Disagree | Unsure | Agree | Strongly Agree | |
| 1. The hands-on sessions were important for the learning process in the Workshop. | 18 | 0% | 0% | 16.7% | 11.1% | 72.2% |
| 2. The concrete examples in the hands-on tutorials increased my understanding of the lectures. | 18 | 0% | 0% | 27.8% | 22.2% | 50.0% |
| 3. The hands-on sessions were long enough. | 19 | 0% | 0% | 0% | 26.3% | 73.7% |
| 4. The hands-on sessions were coordinated with the lectures. | 19 | 0% | 0% | 5.3% | 47.4% | 47.4% |
| 5. TAs were well-prepared to answer questions. | 19 | 0% | 0% | 15.8% | 31.6% | 52.6% |
| 6. There were sufficient instructions to proceed with the hands-on assignments. | 19 | 0% | 0% | 5.3% | 42.1% | 52.6% |
| 7. There were enough TAs / instructional staff to help the participants. | 19 | 0% | 0% | 10.5% | 26.3% | 63.2% |
| 8. The tutorial options accommodated the differing interests of participants. | 19 | 0% | 5.3% | 15.8% | 36.8% | 42.1% |
| 9. The tutorial options accommodated the differing expertise levels of participants. | 19 | 0% | 5.3% | 10.5% | 52.6% | 31.6% |
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. | 17 | 0% | 5.9% | 0% | 35.3% | 58.9% |
| 2. The lecture room was conducive to learning. | 17 | 0% | 0% | 0% | 29.4% | 70.6% |
| 3. The projection system was sufficient for the lectures. | 17 | 0% | 0% | 0% | 17.6% | 82.4% |
V. Communication and Dissemination
| N | Strongly Disagree | Disagree | Unsure | Agree | Strongly Agree | |
| 1. Instructors were readily available for Q&A outside the lecture periods. | 18 | 0% | 0% | 0% | 33.3% | 66.7% |
| 2. The Workshop web site was informative about the event. | 18 | 0% | 0% | 11.1% | 27.8% | 61.1% |
| 3. The emails about setting up laptops for the Workshop were helpful. | 18 | 0% | 0% | 22.2% | 16.7% | 61.1% |
| 4. The organizational emails before the Workshop were helpful. | 18 | 0% | 0% | 0% | 33.3% | 66.7% |
| N | Strongly Disagree | Disagree | Unsure | Agree | Strongly Agree | |
| 1. The Workshop was well organized. | 18 | 0% | 0% | 0% | 27.8% | 72.2% |
| 2. The balance between lectures and hands-on sessions was optimal. | 18 | 0% | 0% | 0% | 50.0% | 50.0% |
| 3. The Workshop addressed my research needs. | 18 | 0% | 5.6% | 11.1% | 22.2% | 61.1% |
| 4. Overall, the Workshop met my expectations. | 18 | 0% | 0% | 11.1% | 22.2% | 66.7% |
| 5. I would recommend this Workshop to others. | 18 | 0% | 0% | 0% | 27.8% | 72.2% |
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+atlanta2014@ks.uiuc.edu. If a comment was made in one area of the open questions, it is generally not repeated again in another area below.
- Suggestions for improving the workshop:
- "I think it might be best to offer workshops for different levels of familiarity with the software. i.e. Beginner, Intermediate, etc...."
- "Provide lecture slides in advance. I would thinks a day of unstructured hands on work would help. Maybe a section dealing with the different packages and how to work with its files in VMD/NAMD."
- Suggestions for similar workshops:
- "Maybe more focus on basic workshops? These are so helpful, especially for being able to answer questions about current projects. I would definitely attend more. I also appreciate the chance to connect with people who have a lot of NAMD/VMD experience. It's really valuable for me since I don’t work with any other NAMD/VMD users."
- "A workshop with more of a slant on visualization of simulation results using VMD BEYOND the most basic manipulation. What tools are available? Can VMD be used as a tool engine for analysis? If so how do you start to unearth them?"
- Most/least valuable topics and suggestions for future workshop topics
- "Free energy calculation was the most valuable topic for me. Parameterizing novel residues and membrane simulation was also very helpful. I would definitely want to know more about the various advanced sampling methods like Replica Exchange."
- "Pros and cons of different coupling algorithms - typical pitfalls. Most useful topic to me was the one on parameterizations of force fields. Even if I'm not doing my own parameterization, hearing about how it's done was very useful and enlightening."
- Other comments:
- "I appreciate the wide range of topics and I hope instructors and TAs would be open to questions via email. Also, a couple of the TAs were excellent! They were really patient and helpful in solving some of my big issues."
- "Excellent planning and support by organizers, lectures, TAs, staff, etc. Thank you for great advice and assisting. This was definitely a highlight in my view. A+ for the TAs."
