Computational Biophysics Workshop - Urbana, Oct. 22-26, 2012

Lectures and Tutorials Evaulation of the Theoretical and Computational Biophysics Workshop Urbana

October 22-26, 2012

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 (October 22-26, 2012) 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); 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 Introduction to Bioinformatics Basic Sequence Analysis; Expert Sequence Analysis; Dynamical Network Analysis
Day 3 Statistical Mechanics of Proteins NAMD Tutorial & Stetching Deca-Alanine; Expert NAMD Set; Free Energy Set
Day 4 Parameters for Classical Force Fields Parameterizing a Novel Residue; Topology File Tutorial
Day 5 Simulating Membrane Channels Membrane Proteins Tutorial & Nanotubes Tutorial; Expert NAMD Set; Free Energy Set

 

Day 1

Day 1 Lecture:  Introduction to Protein Structure and Dynamics (100% relevance rating)

Sample comments are:

  • Elegant start - great to see the approach taken by the TCBG in development of tools that enable "thinking".
  • Dr. Schulten highlighted the key feature (algorithms) used in NAMD, which helps me build confidence in NAMD. I feel more confident in MD.

Day 1 Tutorial:  Using VMD; NAMD Tutorial (100% relevance rating)

Sample comments are:

  • NAMD basics - excellent introduction and solid description of theory.
  • The tutorials are really clear. I was able to complete most of the VMD tutorial and start the NAMD tutorial. I wish I had more time to finish the NAMD tutorial during the day sessions.

Day 2

Day 2 Lecture:  Introduction to Bioinformatics (94% relevance rating)

Sample comments are:

  • Super excited about the development of tools to look at the whole cell. Genuine method to approach systems biology from multiple time and spatial scales, from the genome --> phenome.
  • Very impressive. Dr Luthey-Schulten is a very good speaker. I'm a little confused about the question that the "cell" level simulation tries to answer, although itself is very cool.

Day 2 Tutorial:  Basic Sequence Analysis; Expert Sequence Analysis; Dynamical Network Analysis; or, work on own projects (94% relevance rating)

Sample comments are:

  • Basic Sequence Analysis: good introduction, which elucidated the basic concepts for an absolute novice quite well, especially in combination with the lecture.
  • Dynamical Network Analysis --> very nice and useful.

Day 3

Day 3 Lecture:  Statistical Mechanics of Proteins (100% relevance rating)

Sample comments are:

  • Broadened my eyes on the applications that NAMD can do. One really need to understand the system and think before the simulation.
  • I learned a lot! The concepts have become very clearn after Prof. Schulten's explanations. I really enjoyed all the lectures here. The instructors are very knowledgable. They all set up great examples of educators!

Day 3 Tutorial:  NAMD Tutorial & Stetching Deca-Alanine; Expert NAMD Set; Free Energy Set (87% relevance rating)

Sample comments are:

  • Deca-alanine - the tutorial is well-written, very easy to follow.
  • The NAMD tutorial was useful and straighforward.

Day 4

Day 4 Lecture:  Parameters for Classical Force Fields (92% relevance rating)

Sample comments are:

  • Very good lecture (clear/informative). The opportunity to ask questions was great.
  • Fantastic introduction to and explanation of the relevant structures! I don't see much room for improvement.

Day 4 Tutorial: Parameterizing a Novel Residue; Topology File Tutorial (69% relevance rating)

Sample comments are:

  • Topology files: pretty tedious procedure, but I suppose that's just what changing these files is like . . . in that sense, a very relevant introduction.
  • Topology files - very clear. Would like to see the ffTK tool kit tutorial.

Day 5

Day 5 Lecture:  Simulating Membrane Channels (100% relevance rating)

Sample comments are:

  • The best lecture of the workshop!
  • Best lecture of the series!

Day 5 Tutorial:  Membrane Proteins Tutorial & Nanotubes Tutorial; Expert NAMD Set; Free Energy Set (100% relevance rating)

Sample comments are:

  • Membrane proteins: great tutorial that walked through all the steps of preparing the simulation in a thorough, yet understandable way, pointing out possible differences to other systems where necessary. This will come in very handy!
  • Nanotubes - a very cool approach to exploring possible structures for a synthetic pore!

The complete set of comments is available by e-mailing workshop+urbana2012oct@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 20 50% 50% 17
Day 1 Tutorial: Using VMD; NAMD Tutorial 20 35% 65% 19
Day 2 Lecture: Introduction to Bioinformatics and Forcefields 17 6% 47% 47% 13
Day 2 Tutorial: Aquaporins with the VMD MultiSeq Tool; Evol. of tRNA Synthetase/Ribosome/Ef-Tu; Dynamical Network Analysis 16 6% 38% 56% 12
Day 3 Lecture: Statistical Mechanics of Proteins 18 33% 67% 12
Day 3 Tutorial: NAMD Tutorial & Stetching Deca-Alanine; or, Expert NAMD Set; Free Energy Set; or, GPU Tutorial 16 13% 31% 56% 14
Day 4 Lecture: Parameters for Classical Force Fields 13 8% 92% 10
Day 4 Tutorials: Parameterizing a Novel Residue; Topology Files 13 8% 23% 15% 54% 11
Day 5 Lecture: Simulating Membrane Channels 12 17% 83% 7
Day 5 Tutorials: Membrane Proteins & Water Permeation Through Nanotubes; or, Expert NAMD Set; or, Free Energy Set 12 25% 75% 10