Computational Biophysics Workshop - Urbana, Nov. 18-22, 2013
Lectures and Tutorials Evaulation of the Theoretical and Computational Biophysics Workshop Urbana
November 18-22, 2013
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 organized a one-week (November 18-22, 2013) workshop at the Center's home offices in the Beckman Institute, on the University of Illinois at Urbana-Champaign campus, in Urbana, Illinois. The Center provided all workshop cotent, as well as the classroom, housing, catering, and printing costs.
The program of the workshop consisted of lectures and hands-on sessions. Workshop lectures were given by K. Schulten (UIUC), Z. Schulten (UIUC), and E. Tajkhorshid (UIUC), and A. Aksimentiev (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 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 | Force Field Parameterization | Parameterizing a Novel Residue; Topology File Tutorial |
| Day 3 | Computational Nano-Bio | Modeling Nanopores for Sequencing DNA; Visualizing MD Results: Stretching dsDNA Mini Tutorial; Introduction to MD Simulation of DNA-protein Systems; User-Defined Forces in NAMD |
| Day 4 | Introduction to Bioinformatics | Basic Sequence Analysis; Expert Sequence Analysis; Dynamical Network Analysis |
| Day 5 | Simulating Membrane Proteins | Membrane Proteins Tutorial; Open tutorial time |
Day 1 Lecture: Introduction to Protein Structure and Dynamics (89% relevance rating)
Sample comments are:
- As a physicist, the only thing I would have liked to see was further discussion of the force field formulism.
- The lecture introduced an an excellent way the most important characteristics of VMD and NAMD, which although I was using, did not have the entire or holistic appreciation I got today. Namely what are the limits, what can be expected and, most importantly, the fact that one has to use one’s brains to make the best use and get close to real results with VMD-NAMD. It was just a great lecture.
Day 1 Tutorial: Using VMD; NAMD Tutorial (83% relevance rating)
Sample comments are:
- Very nice manual. Did not get lost or even struggle till the steps I completed today. One suggestion is to introduce the various folders in the tutorial and give an overview of the contents so that we have some idea up front and not learn as we go.
- The tutorial helps me to clear up different issues on the visualization of trajectories. For the fist time I successfully implement a movie from MD trajectories in VMD.
Day 2 Lecture: Force Field Parameterization (100% relevance rating)
Sample comments are:
- Lecture was good. It was nice to go through each file type and discuss what everything specifically meant.
- Very informative lecture. Especially for a novice NAMD user it was very important to get introduced to the principle of force field and parameter.
Day 2 Tutorial: Parameterizing a Novel Residue; Topology File Tutorial (78% relevance rating)
Sample comments are:
- The contents were a lot to cover in the time. But aided as a good reference source for future.
- I worked on both tutorials plus the stretching deca-alanine tutorial. The 2 listed above did a very good job of explaining topology files and how to alter them. The stretching tutorial seemed to be not very interactive.
Day 3 Lecture: Computational Nano-Bio (89% relevance rating)
Sample comments are:
- The lecture was very interesting and informative. The promise of nano-bio sequencing sounds enormous.
- This was a very intensive studying day in which real world simulations were introduced. Modeling biological and other types of materials requires the settings of the systems and thus one has to imagine out several aspects of the systems to be immolated.
Day 3 Tutorial: Modeling Nanopores for Sequencing DNA; Visualizing MD Results: Stretching dsDNA Mini Tutorial; Introduction to MD Simulation of DNA-protein Systems; User-Defined Forces in NAMD (67% relevance rating)
Sample comments are:
- Visualizing MD results, Introduction to MD simulation of DNA-protein systems. I really liked the Intro to MD simulation of DNA-protein systems. It provided a good intro to tcl scripting in VMD.
- Too many choices for tutorials, they were all tempting.
Day 4 Lecture: Introduction to Bioinformatics (100% relevance rating)
Sample comments are:
- This was a magnificent talk on all the functionality of VMD to study evolution, from sequence analysis and structural similarity. Furthermore the network analysis to study allosteric processes made me figure out many biological processes that can be studied from this point of view. So I feel that my entire concept of the system has changed with this presentation.
- The lecture was great. It was exciting experience to see that whole cell can be simulated. Dynamic network analysis is also of great importance, so are all the other topics covered much as Multiseq & STAM. I thoroughly enjoyed the lecture.
Day 4 Tutorial: Basic Sequence Analysis; Expert Sequence Analysis; Dynamical Network Analysis (100% relevance rating)
Sample comments are:
- I did the Dynamic Network Analysis tutorial and then worked on my project. The tutorial could have clarified which type of file to load in the main window and which into the Network tool.
- Dynamical Network Analysis. It was difficult to get it to work but it was interesting once it worked.
Day 5 Lecture: Simulating Membrane Proteins (100% relevance rating)
Sample comments are:
- It was a very interesting lecture on membrane-protein simulations. 5% of the encoded genes in Huma genome are about transport proteins so, the tools to make these type of complex simulations are there. The example and the subsequent analysis of the aquaporin channel was excellent.
- Today’s lecture was very pertinent to my research! The lectures were well-taught and easy to follow!
Day 5 Tutorial: Membrane Proteins Tutorial; open tutorial time (100% relevance rating)
Sample comments are:
- One of the topics I wanted to really learn was those concerning the execution of NAMD and VMD on GPU’s. The lecture and the subsequent tutorial were what I was looking for, this added enormously to the knowledge I could grasp during this excellent tutorial. Thank you.
- Good tutorial. Very useful because my research focuses on membrane proteins. Rather than using the provided protein in the tutorial, I followed the steps using my own protein PDB and it worked well.
The complete set of comments is available by e-mailing workshop+urbana2013nov@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 | 18 | 11% | 50% | 39% | 18 | |||
| Day 1 Tutorial: Using VMD; NAMD Tutorial | 18 | 6% | 11% | 17% | 67% | 18 | ||
| Day 2 Lecture: Force Field Parameterization | 18 | 17% | 83% | 12 | ||||
| Day 2 Tutorial: Parameterizing a Novel Residue; Topology Files | 18 | 22% | 39% | 39% | 14 | |||
| Day 3 Lecture: Computational Nano-Bio | 19 | 11% | 42% | 47% | 17 | |||
| Day 3 Tutorial: Modeling Nanopores for Sequencing DNA; Visualizing MD Results: Stretching dsDNA Mini Tutorial; Introduction to MD Simulation of DNA-protein Systems; User-Defined Forces in NAMD | 18 | 33% | 33% | 33% | 18 | |||
| Day 4 Lecture: Introduction to Bioinformatics | 9 | 56% | 44% | 7 | ||||
| Day 4 Tutorials: Basic Sequence Analysis; Expert Sequence Analysis; Dynamical Network Analysis | 9 | 56% | 44% | 8 | ||||
| Day 5 Lecture: Simulating Membrane Proteins | 16 | 13% | 88% | 11 | ||||
| Day 5 Tutorials: Membrane Proteins | 16 | 25% | 75% | 11 |
