Computational Biophysics Workshop - Lake Tahoe, August 3-7, 2015
Lectures and Tutorials Evaulation of the Theoretical and Computational Biophysics Workshop Atlanta, GA
November 3-7, 2014
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 Zan Luthey-Schulten, Laxmikant Kale, Emad Tajkhorshid, and Aleksei 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 3-7, 2014) workshop at the Georgia Institute of Technology. The Center provided all workshop content, as well as the classroom, catering, and printing costs.
The program of the workshop consisted of lectures and hands-on sessions. Workshop lectures were given by Klaus Schulten (UIUC), Emad Tajkhorshid (UIUC), and James Gumbart (Georgia Tech); 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 composed 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 XXX 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, NAMD Tutorial |
| Day 2 | Statistical Mechanics of Proteins | NAMD Tutorial; Stretching Deca-Alanine; GPU-Accelerated Molecular Dynamics and Visualization Tutorial; User-Defined Forces in NAMD |
| Day 3 | Force Field Parameterization | Parameterizing a Novel Residue; Topology File Tutorial |
| Day 4 | Simulating Membrane Proteins | Membrane Proteins Tutorial |
| Day 5 | Advanced Methods | MDFF Tutorial, Free Energy Tutorial |
Day 1 Lecture: Introduction to Protein Structure and Dynamics (XX% relevance rating)
Sample comments are:
- QUOTE HERE
- QUOTE HERE
Day 1 Tutorials: VMD Tutorial, NAMD Tutorial (XX% relevance rating)
Sample comments are:
- QUOTE HERE
- QUOTE HERE
Day 2 Lecture: Statistical Mechanics of Proteins (XX% relevance rating)
Sample comments are:
- QUOTE HERE
- QUOTE HERE
Day 2 Tutorials: NAMD Tutorial; Stretching Deca-Alanine; GPU-Accelerated Molecular Dynamics and Visualization Tutorial; User-Defined Forces in NAMD (XX% relevance rating)
Sample comments are:
- QUOTE HERE
- QUOTE HERE
Day 3 Lecture: Force Field Parameterization (XX% relevance rating)
Sample comments are:
- QUOTE HERE
- QUOTE HERE
Day 3 Tutorials:Parameterizing a Novel Residue; Topology File Tutorial (XX% relevance rating)
Sample comments are:
- QUOTE HERE
- QUOTE HERE
Day 4 Lecture: Simulating Membrane Proteins (XX% relevance rating)
Sample comments are:
- QUOTE HERE
- QUOTE HERE
Day 4 Tutorials: Membrane Proteins Tutorial (XX% relevance rating)
Sample comments are:
- QUOTE HERE
- QUOTE HERE
Day 5 Lecture: Advanced Methods (XX% relevance rating)
Sample comments are:
- QUOTE HERE
- QUOTE HERE
Day 5 Tutorials: MDFF Tutorial, Free Energy Tutorial (XX% relevance rating)
Sample comments are:
- QUOTE HERE
- QUOTE HERE
The complete set of comments is available by e-mailing workshop+atlanta2014@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 Lectures: Introduction to Protein Structure and Dynamics | NR | XX1% | XX2% | XX3% | XX4% | XX5% | NC | |
| Day 1 Tutorials: VMD Tutorial; NAMD Tutorial | NR | XX1% | XX2% | XX3% | XX4% | XX5% | NC | |
| Day 2 Lectures: Statistical Mechanics of Proteins | NR | XX1% | XX2% | XX3% | XX4% | XX5% | NC | |
| Day 2 Tutorials: NAMD Tutorial; Stretching Deca-Alanine; GPU-Accelerated Molecular Dynamics and Visualization Tutorial; User-Defined Forces in NAMD | NR | XX1% | XX2% | XX3% | XX4% | XX5% | NC | |
| Day 3 Lectures: Force Field Parameterization | NR | XX1% | XX2% | XX3% | XX4% | XX5% | NC | |
| Day 3 Tutorials: Parameterizing a Novel Residue; Topology File Tutorial | NR | XX1% | XX2% | XX3% | XX4% | XX5% | NC | |
| Day 4 Lectures: Simulating Membrane Proteins | NR | XX1% | XX2% | XX3% | XX4% | XX5% | NC | |
| Day 4 Tutorials: Membrane Protein Tutorial | NR | XX1% | XX2% | XX3% | XX4% | XX5% | NC | |
| Day 5 Lectures: Advanced Methods | NR | XX1% | XX2% | XX3% | XX4% | XX5% | NC | |
| Day 5 Tutorials: MDFF Tutorial, Free Energy Tutorial | NR | XX1% | XX2% | XX3% | XX4% | XX5% | NC |
