Computational Biophysics Workshop - Urbana, Nov. 29 - Dec. 3, 2010
'Hands-On' Workshop on Computational Biophysics, Urbana, Illinois
Lectures and Tutorials Eavaluation
November 29 - December 3, 2010
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 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 organized a one-week (November 29 - December 3, 2010) workshop using grant funds from the National Center for Research Resources.
The program of the workshop consisted of lectures and hands-on sessions. Workshop lectures were provided by K. Schulten (UIUC), Z. Schulten (UIUC), and E. Tajkhorshid (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 for the lectures and tutorials are comprised of two 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. 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.
- 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, lecture, and tutorial, and can be located using the navigation table below or by scrolling down the page.
Day 1 Lecture: Introduction to Protein Structure and Dynamics - K. Schulten(N: r=18, c=14)
A majority of respondents, 89%, rated the lecture as highly relevant. Sample comments are:- I think that the lecture format was fairly informal which was nice. It allowed for some necessary discussion without worrying about time constraints. Discussion about the mathematics behind NAMD was welcome and sufficiently general for someone with my background (experimental organic chemistry).
- This lecture gave a good background on both VMD and NAMD.
Day 1 Tutorial: Using VMD; NAMD Tutorial (N: r=17, c=18)
Nearly all participants, 94%, found the tutorial content highly relevant. Sample comments are:- The VMD tutorial was very easy to follow, and the TA’s did a great job.
- Tutorial was excellent. Opportunity to get advice from developers was a great opportunity.
Day 2 Lecture: Statistical Mechanics of Proteins (N: r=21, c=17)
A majority of respondents, 76%, rated the lecture as highly relevant. Sample comments are:
- Lecture and Q/A was great. TA’s were extremely helpful. Very organized, and it shows. Dr. Schulten was extremely helpful as well.
- Very illuminating. The way the tough looking com0licated things are explained in a very fluent, engaging and revealing way is a kind experience in itself. The passion and desire to answer any question in deep and dual engaging way is very encouraging. The answers as given, are more than a mere to the point answers. Answers are more like a detailed description of the topic of such
Day 2 Tutorial: NAMD Tutorial & Stetching Deca-Alanine; or, Expert NAMD Set; or Free Energy Set (N: r=19, c=17)
Most of those responding, 84%, rated the tutorial relevance as very high. Sample comments are:
- Worked on NAMD tutorial: Chapter 2 (analysis) and 3 (steered MD). TAs was very helpful and they patiently explained different things. Thanks!
- Expert NAMD set: User defined forces. Really interesting. I’m currently trying to run this kind of simulations on my own system. Difficult! But that’s typically what I want to do with NAMD so very good tutorial.
Day 3
Day 3 Lecture: Introduction to Bioinformatics - Z. Luthey Schulten (N: r=13, c=8)
A majority of participants, 62%, rated the relevance of the lecture as high. Sample comments are:
- Good to get introduction about the sequencing vis a vis to structure.
- Offered good scope to discuss individual project topics. Encouraged use of bioinformatics as a support tool for molecular dynamics.
Day 3 Tutorials: Basic Sequence Analysis; or, Expert Sequence Analysis; or, work on own projects (N: r=10, c=11)
The relevance of the tutorial was very high, with 100% of participants rating tutorial relevance as very good to excellent. Sample comments are:
- Ramya the TA was very kind and spent about 2 hours with me to work on my personal project. Having no experience in NAMD, I managed to follow the written tutorials quite well but when I come to work on my personal project it wasn’t easy at all and she just set with me all this time and instructed me until we solve the problem. I learned a lot just from seeing how she works. There are so may technical details that the tutorial didn’t cover and it’s really important to have someone with a wider point of view to sit with you.
- I worked on parts of aquaporins and class-I. The MultiSeq program seems to be very useful although, I’m not sure that I will be using it in my research.
Day 4 Lecture: Molecular Dynamics of Cellular Processes - E. Tajkhorshid (N: r=17, c=14)
All of those responding, 100% rated the lecture as highly relevant to their interests. Sample comments are:
- This lecture was extremely relevant and help0fuyl. I learned a lot about parameterization.
- Emad's lecture was excellent!!! Very effective,. Dealt exactly with the things that usually aren’t dealt with. I learned a lot from him.
Day 4 Tutorials: Parameterization; Topology Files (N: r=14, c=16)
Nearly all participants - 86% - found the tutorials highly relevant. Sample comments are:
- The tutorials today were my favorite. My interest in this workshop was centered on learning to use VMD and NAMD to simulate synthetic molecules and these tutorials provide the procedures needed to parameterize new molecules. It would be nice if there were examples of parameter zing more unconventional molecules (i.e. non-biophysics workshop.
- I worked on the parameterization tutorial. This was extremely helpful and will make a great reference in the future.
Day 5
Day 5 Lecture: Simulating Membrane Channels - E. Tajkhorshid (N: r=16, c=14)
Nearly all participants, 94% rated the lecture as highly relevant to their interests. Sample comments are:
- Excellent lecture, excellent answers to questions, excellent examples. Great interaction, thanks for being so accessible.
- I really enjoyed today’s lectures, and thought they were good examples of the method one should use when using VMD/NAMD to find our properties of their system. Very interesting example.
Day 5 Tutorial: Membrane Proteins Tutorial; or, Expert NAMD Set; or, Free Energy Set (N: r=13, c=13)
A high majority of participants - 92% - found these tutorials as highly relevant. Sample comments are:
- I learned a lot in these tutorials. Definitely the best day of the workshop. I worked on my own project and being able to complete a simulation on my system is a great achievement.
- In silica alchemy: This was very helpful. Building up from small molecules kept things simple.
The complete set of comments is available by e-mailing workshop+urbana2010b.
Table 1: Summary of Relevance Statistics
