Computational Biophysics Workshop - Urbana, Nov. 1-5, 2010

'Hands-On' Workshop on Computational Biophysics, Urbana, Illinois
Lectures and Tutorials Eavaluation

November 1-5, 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 1-5, 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 given by K. Schulten (UIUC), Z. Schulten (UIUC), E. Tajkhorshid (UIUC), and C. Chipot (UIUC, CNRS). 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 Lecture Tutorial
Day 1 Introduction to Protein Structure and Dynamics
 Using VMD; NAMD Tutorial
Day 2 Statistical Mechanics of Proteins
 NAMD Tutorial & Stetching Deca-Alanine; or, Expert NAMD Set; or, Free Energy Set
Day 3 Introduction to Bioinformatics
 Basic Sequence Analysis; or, Expert Sequence Analysis; or, work on own projects
Day 4 Parameters for Classical Force Fields Parameterizing a Novel Residue; Topology Files
Day 5 Simulating Membrane Channels Membrane Proteins Tutorial; or, Expert NAMD Set; or, Free Energy Set

Day 1

Day 1 Lecture: Introduction to Protein Structure and Dynamics - K. Schulten(N: r=23, c=22)

All respondents, 100%, rated the lecture as highly relevant. Sample comments are:
  • Really enjoyed the experience. Came here because of a friend’s recommendation. He was a participant last year, will definitely tell everyone how good it was
  • My expertise lies in the area of experimental biology. Though I m familiar with looking at MD simulation date I have never used VMD or set up any simulations before today. I found the VMD & MD lecture very informative. Both talks were very clear and catered to my needs.

Day 1 Tutorial: Using VMD; NAMD Tutorial (N: r=22, c=23)

A majority of participants, 91%, found the tutorial content highly relevant. Sample comments are:
  • Using VMD tutorial, great introduction to creating images, movies, and nice overview of analysis methods.
  • I worked on both. I felt that it was helpful to be able to work o the tutorials in an environment where we could ask questions yet were independently figuring out our own instead of listening to teachers.

Day 2

Day 2 Lecture 1: Analysis of Equilibrium and Non-equilibrium Properties of Proteins with NAMD - K. Schulten (N: r=20, c=13)

All respondents, 100%, rated the lecture as highly relevant. Sample comments are:

  • Very informative at just the right level.
  • The equations were made very simple to understand.
Day 2 Lecture 2: Good Practices in Free-Energy Calculations - C. Chipot (N: r=20, c=13)

A majority of participants, 75%, found the lecture highly relevant. Sample comments are:

  • This was a great overview! – very useful. Thanks!
  • Very useful and insightful.

Day 2 Tutorial:  NAMD Tutorial & Stetching Deca-Alanine; or, Expert NAMD Set; or Free Energy Set (N: r=24, c=22)

Most of those responding, 83%, rated the tutorial relevance as very high.  Sample comments are:

  • Used NAMD tutorial and was satisfied with the scripts and the explanation given for each command.
  • “User-defined forces” and “stretching deca-alanine”. It was great to have experts on hand for questions, and I liked that the tutorials are contained and as useful as references for questions down the road.

Day 3

Day 3 Lecture: Introduction to Bioinformatics - Z. Luthey Schulten (N: r=15, c=13)

A majority of participants, 87%, rated the relevance of the lecture as very high. Sample comments are:

  • Very useful! Never realized VD had all these wonderful features (MultiSeq).
  • Dr. Schulten did a wonderful job explaining her friend and how MD is used. The material was for one of my area of specialization and I learned a lot.

Day 3 Tutorials: Basic Sequence Analysis; or, Expert Sequence Analysis; or, work on own projects (N: r=12, c=12)

The relevance of the tutorial was high, with 83% of participants rating tutorial relevance as very good to excellent. Sample comments are:

  • Implementing MultiSeq to my own protein (own project) and am very pleased with the output.
  • I found the tutorials to be very clear and easy to follow. I was able to work through these tutorials and then use my own data to do similar analysis. This has been very useful.

Day 4

Day 4 Lecture: Molecular Dynamics of Cellular Processes - E. Tajkhorshid (N: r=20, c=16)

Of those responding, 95% rated the lecture as highly relevant to their interests. Sample comments are:

  • Very detailed lecture. It was impossible not to understand. Lecture was very relevant and the whole concept made easy. I learned a lot. Thanks!
  • I especially enjoyed the lecture today. I took us deep down into the nuts and bolts of the files used in running MD.

Day 4 Tutorials: Parameterization; Topology Files (N: r=22, c=23)

All participants - 100% - found these tutorials as highly relevant. Sample comments are:

  • Topology File tutorial Parameterizing a novel residue. I enjoyed the tutorial. It was not overwhelming; it was actually, very enjoyable.
  • I worked on Topology File tutorial and Parameterizing a Novel Residue. The tutorials are very clear and very well organized.

Day 5

Day 5 Lecture: Simulating Membrane Channels - E. Tajkhorshid (N: r=21, c=17)

Nearly all participants, 95% rated the lecture as highly relevant to their interests. Sample comments are:

  • Excellent!! I felt the lecture was relevant, practical, and provided many ideas for future simulations. Dr. Tajkorshid was an excellent lecturer.
  • Dr. Tajkorshid’s talk was excellent. I thought he did a great job covering the practical as well as the theoretical. He talked us through his simulations to the point that I got ideas ho to implement things in my own work. He also fit in well with the work we’ve been doing in the tutorials. I think his talk fit with the tutorials the best. He was also extremely helpful and accessible during the Q and A.
Day 5 Tutorial: Membrane Proteins Tutorial; or, Expert NAMD Set; or, Free Energy Set (N: r=20, c=13)

All participants - 100% - found these tutorials as highly relevant. Sample comments are:

  • Membrane protein tutorial. The structure of this tutorial is easy to follow and enlightening. It mimics the type of work I’ll be doing in the future. It’s practical in that it walks your through the process of downloading from PBD all the way to the final structure.
  • Nanotubes tutorial is a good practical application of the concepts discussed in the lecture.

The complete set of comments is available by e-mailing brandon@ks.uiuc.edu.

 

Table 1: Summary of Relevance Statistics


   Poor Fair Good Very Good Excellent
N % % % % %
Day 1 Lecture: Introduction to Protein Structure and Dynamics 23 0 0 0 35 65
Day 1 Tutorial: Using VMD; NAMD Tutorial 22 0 0 9 41 50
Day 2 Lecture 1: Analysis of Equilibrium and Non-equilibrium Properties of Proteins with NAMD 20 0 0 0 35 64
Day 2 Lecture 2: Good Practices in Free-Energy Calculations 20 0 10 15 30 45
Day 2 Tutorial: NAMD Tutorial & Stetching Deca-Alanine;
or, Expert NAMD Set; or, Free Energy Set		 18 0 0 11 39 50
Day 3 Lecture: Parameters for Classical Force Fields 15 7 0 7 40 47
Day 3 Tutorials:  Parameterizing a Novel Residue; Topology File
Tutorial; Stretching Deca-alanine Tutorial		 12 0 0 8 42 42
Day 4 Lecture: Simulating Membrane Channels 20 0 0 5 25 70
Day 4 Tutorials:  Membrane Proteins Tutorial; Simulation of Waterbr> PPermeation Through Nanotubes 22 0 0 0 23 77
Day 5 Lecture: Introduction to Bioinformatics 21 0 0 5 0 95
Day 5 Tutorials:  Evolution of Translation Tutorials: Class I br> Aminoacyl-tRNA Synthetase; Elongation Factor Tu; tRNA and the
RRibosome; or, Bioinformatics of Aquaporins 		20 0 0 0 15 85