NIH Resource for Macromolecular Modeling & Visualization University of Illinois at Urbana-Champaign

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Computational Biophysics Workshop - Pittsburgh, Nov. 28 - Dec. 1, 2005

 

General Evaluation of the Theoretical and Computational Biophysics Workshop in at the Pittsburgh Supercomputing Center

November 28 - December 1, 2005

Questionnaire: Gila Budescu, 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 (TCB), an NIH Resource for Macromolecular Modeling and Bioinformatics is headed by Klaus Schulten, and Co-PIs Z. Luthey-Schulten and L. Kale. As part of its outreach, the Resource offers workshops to introduce and transfer its programs and technological solutions to the biomedical community. The Biomedical Initiative of the Pittsburgh Supercomputing Center (PSC) at Carnegie Mellon University and the University of Pittsburgh sponsored a four-day TCB workshop in Pittsburgh, Pennsylvania from November 28 to December 1, 2005.  The TCB provided lectures and tutorials, while PSC provided the classroom site and computer, as well as all other arrangements including printing the tutorials.

Workshop lectures were given by K. Schulten (UIUC) and E. Tajkhorshid (UIUC).  Two graduate students accompanied the lecturers to the workshop and provided instructional support on-site.  Tutorials and preparation of the laptops was provided by the graduate students and by other Resource staff, and on-site the tutorial sessions were led by the graduate students.  The program of the workshop consisted of lectures and hands-on sessions, with an emphasis on the latter.

At the end of the week, PSC asked participants to complete a general evaluation questionnaire. The general evaluation form asks about topics and instructors, personal value to the participant, facilities and food services, and asks a number of other general questions; click here to see the form used.  Participation in the evaluation was voluntary.  A total of 23 general evaluation forms were returned, providing an overall response rate of 96%.  Demographically, education levels of participants were high, with a majority of participants indicating having obtained a PhD.

All responses in the following tables are reported in percentages, rows adding up to 100%. Not all respondents answered to all items; the number of responses per item is presented next to each question. Those who chose an 'NA' response are also not counted. References to 'agreement' among respondents is calculated by adding together the percentages for the 'agree' and 'strongly agree' responses. Please note that the scale included five rating points from a high of 5 to a low of 1; however, since no scores of 1 or 2 were indicated by any participant, they are excluded in the tables below. For the sake of summary, percentage results for the two highest point values, 5 and 4, are added together when discussing results.  Also, after each set of numbered scale items, there was space for comments; some of the comments are provided below.  Lastly, participants were asked to answer a number of open questions about the workshop.  Three selected responses are provided below, the entire body of comments can be obtained by writing brandon@ks.uiuc.edu.

I.  Topics and Instruction

	N	Scale High End	5	4	3	Scale Low End
The choice of subjects was…	23	well chosen	78%	22%		poorly chosen
The instructors were…	23	excellent	91%	9%		unsatisfactory
The methods of instruction were…	23	most appropriate	65%	35%		unsatisfactory
The prerequisite of readings were…	22	very useful	45%	41%	14%	of no benefit
The lecture notes were…	22	very useful	41%	36%	23%	of no benefit
The hands-on examples were…	22	very useful	68%	27%	5%	of no benefit

All participants found that the choice of subjects was well chosen for the course, that the instructors were excellent, and that the methods of instruction were appropriate.  A majority found that the prerequisite readings were useful (86%), that the lecture notes were useful (77%), and that the hands-on examples were useful (95%). A sample participant comment for this area is "I couldn't find the Schulten notes.  Lectures were fabulous".

II.  Personal Value

	N	Scale High End	5	4	3	Scale Low End
Informal conversations with other participants were…	20	very beneficial	40%	50%	10%	of no benefit
I gained new knowledge and insights…	23	definitely	87%	13%		not at all
As a result of this program, I feel my research will improve…	23	greatly	48%	52%		not at all
I would recommend this program to others…	22	highly	82%	18%		not at all

While a majority (90%) found that informal conversations with other participants were beneficial, all participants indicated that they gained new knowledge and insights, that the workshop would improve their research, and indicated they would recommend the course to others. A sample participant comment for this area is "Excellent instruction to the material/simulation world".

III.  Facilities and Food Services

	N	Scale High End	5	4	3	Scale Low End
The hotel facility was…	19	excellent	37%	42%	21%	unsatisfactory
The meeting rooms were…	21	excellent	52%	33%	14%	unsatisfactory
The computer room was…	22	excellent	68%	27%	5%	unsatisfactory
The food service and breaks were…	23	excellent	52%	39%	9%	unsatisfactory

A majority of participants felt the hotel facility was excellent (79%), and that the food service and breaks were excellent (91%). Of factors impacting day-to-day instruction, a majority felt the meeting rooms were excellent (85%) and that the computer room was excellent (95%). A sample participant comment for this area is "Computer room was hot one day".

IV. Overall Comments and Suggestions

How did this workshop address your current training needs?

• I used VMD but didn't know it's full potential.  Also learning NAMD was very beneficial.  Now I have a more powerful tool in my hand.

• I am a beginner and it has taken in months trying to get started.  This workshop has taught me what I suspect would have taken me a year to learn if I wouldn't have given up.  Now I have a fundamental background language etc. to really get started on some.

• I was desperately seeking free MD simulation engine and analysis tools for studying a membrane-associated liquid-gated ion channel.  This workshop covered almost everything I needed trained me to use new and powerful software and analysis strategies forms.

The topic that was most valuable to me was……why?

• Use of NAMD and VMD, particularly the latter.- using VMD to represent models and molecules in 3-D makes a superb tool.  Membrane models are a very important developing topic.

• Detail of file content- these were a black box to me.  Now I understand they are under my control and I just need to learn how to control them.

• MD theory and FF parametrical, and MD analysis- I constantly use (need) in research.

The topic that was least valuable to me was……why?

• Lecture walking through file formats- feel this is best learned by PTFM.

• Protein membrane channels- this was not related to what I do- but the lecture was done very well.

• Introduction to MD simulations- I knew this topic.

In a future workshop of this type, I would like to have the following areas covered:

• More on fundamentals of membrane channels, maybe more numerical techniques for programming.

• I think if we need two workshops, the second just for application.

• Free energy perturbation type concepts and tutorials.

How and where do you think we can most effectively advertise this type of workshop?

• At the biophysical society meetings.

• The NAMD, CHARMM mailing lists.  Maybe send some posters/info to institutions.

• CCL (still ok), send out emails to chem depts of various schools- this is not as difficult as it sounds.

Please recommend topics for future workshops or for a follow-up to this workshop.

• Would really like to learn more about simulating non-protein systems, and the special issues that arise.

• QM-MM methods in more detail.

• More cluster building workshops, numerical techniques behind HPC.

Other suggestions that I feel would improve future workshops are?

• Very good at present.

• More analysis of results by VMD and NAMD.

• Perhaps open the CTC at night for optional time to complete the tutorials?

How was your overall experience with the hotel?

• Very good.  Service was excellent.  Breakfast service was excellent.

• Shuttle was never on time on our way back.  Checking in was quick.  Hotel service was professional.

• Fine, no problems.  I forgot what the shuttle schedules were in the morning.