Computational Biophysics Workshop - Pittsburgh, May 19-23, 2014
Lectures and Tutorials Evaulation of the Theoretical and Computational Biophysics Workshop Urbana
May 19-23, 2014
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), 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 participated in a one-week (May 19-23, 2014) workshop co-sponsored by the National Center for Multiscale Modeling of Biological Systems (MMBioS) at the University of Pittsburgh, and held at the Pittsburgh Supercomputing Center (PSC) at Pittsburgh, Pennsylvania. The PSC provided the classroom and administrative support, while instructional duties were split up amongst TCBG and CMMBS faculty and group members.
The program of the workshop consisted of lectures and hands-on sessions. Workshop lectures were given by K. Schulten (UIUC), A. Aksimentiev (UIUC), I. Bahar (MMBioS), T. Lezon (MMBioS), and C. Chennubhotla (MMBioS); teaching assistants from both groups 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. Note that the information presented below only represents those dates when TCBG faculty were lecturing; the lecture and tutorial results for the workshop dates covered by the MMBioS faculty were left with that group to use as they see fit.
Summaries below for the lectures and tutorials are comprised of two elements: 1) a relevance rating (sum of the 'very good' + 'excellent' ratings for relevance - see Table 1: Summary of Relevance Statistics), and 2) participant comments considered illustrative of respondent opinion.
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 and can be located using the navigation table below or by scrolling down the page.
| Day | Lecture | Tutorial |
|---|---|---|
| Day 1 | Introduction to Protein Structure and Dynamics | VMD Tutorial - Using VMD; NAMD Tutorial |
| Day 2 | Statistical Mechanics of Proteins | NAMD Tutorial & Stretching Deca-alanine; GPU Accelerated Molecular Dynamics and Visualization Tutorial; Shape-Based Coarse Graining; User-Defined Forces in NAMD |
| Day 3 | Computational Nano-Bio | Modeling Nanopores for Sequencing DNA; Introduction to MD Simulation of DNA-protein Systems |
Day 1 Lecture: Introduction to Protein Structure and Dynamics (96% relevance rating)
Sample comments are:
- Dr. Schulten is always a great speaker. I had no idea VMD had all the capabilities that it does until this talk - will be quite useful to my work efforts. Q & A was also invaluable.
- The examples were very cool, and the idea of "tools that help thinking" was very helpful.
Day 1 Tutorial: Using VMD; NAMD Tutorial (96% relevance rating)
Sample comments are:
- The VMD tutorial is very detailed and clear.
- Worked on NAMD tutorial. The tutorials are thorough and contain a lot of explanations. The TAs did great too.
Day 2 Lecture: Statistical Mechanics of Proteins (91% relevance rating)
Sample comments are:
- I enjoyed the current state-of-the-art applications of MD and the introduction to the necessary theory was also very helpful.
- Excellent. Dr. Schulten shows his passion for MD and for science in general.
Day 2 Tutorial: NAMD Tutorial & Stretching Deca-alanine; GPU Accelerated Molecular Dynamics and Visualization Tutorial; Shape-Based Coarse Graining; User-Defined Forces in NAMD (86% relevance rating)
Sample comments are:
- Tutorials are great. If we can include our own molecules, that would be great.
- I did the stretching deca-alanine and coarse grain tutorials, and they were really helpful. I especially liked the stretching tutorial because I didn't know that I could interact with MD simulations in VMD.
Day 3 Lecture: Computational Nano-Bio (88% relevance rating)
Sample comments are:
- Lecture was very interesting and did a great job discussing new and relevant research. This was the best portion of the workshop for me.
- I enjoyed Alek's lecture. He does a good job getting across main/important points.
Day 3 Tutorial: Modeling Nanopores for Sequencing DNA; Introduction to MD Simulation of DNA-protein Systems (75% relevance rating)
Sample comments are:
- The most practical workshop I have participated in; I can use the knowledge immediately.
- The nanopores tutorial was a great tutorial. I enjoyed working on it. It is definitely an advanced tutorial.
The complete set of comments is available by e-mailing workshop+pitts2014@ks.uiuc.edu.
Table 1: Summary of Relevance Statistics and Number of Participant Comments
| N | Poor | Fair | Good | Very Good | Excellent | No. of Comments | ||
| Day 1 Lecture: Introduction to Protein Structure and Dynamics | 24 | 4% | 50% | 46% | 24 | |||
| Day 1 Tutorial: Using VMD; NAMD Tutorial | 23 | 4% | 35% | 61% | 23 | |||
| Day 2 Lecture: Statistical Mechanics of Proteins | 22 | 9% | 36% | 55% | 21 | |||
| Day 2 Tutorial: NAMD Tutorial & Stretching Deca-alanine; GPU Accelerated Molecular Dynamics and Visualization Tutorial; Shape-Based Coarse Graining; User-Defined Forces in NAMD | 21 | 5% | 10% | 29% | 57% | 22 | ||
| Day 3 Lecture: Computational Nano-Bio | 16 | 13% | 50% | 38% | ||||
| Day 3 Tutorial: Modeling Nanopores for Sequencing DNA; Introduction to MD Simulation of DNA-protein Systems | 12 | 8% | 17% | 33% | 42% |
