Evaluations for the Computational Methods for Spatially Realistic Microphysiological Simulations Workshop

April 2014

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Participants were asked to evaulate the workshop in the following areas. Numeric scales ranged from 1 -5, with one being the lowest satisfaction and 5 being the highest.

The Cell Modeling workshop was very valuable for my current/future research

1 2 3 4 5 Average score
- - - 2 7 4.8

I would recommend the Cell Modeling Workshop to my colleagues

1 2 3 4 5 Average score
- - 1 2 6 4.6

The instructors and teaching assistants were well prepared.

1 2 3 4 5 Average score
- - - 2 7 4.8

The instructors and teaching assistants were helpful and assisted me with my problems and questions.

1 2 3 4 5 Average score
- - - 2 7 4.8

The online tutorials were useful (www.mcell.org/tutorials).

1 2 3 4 5 Average score
- - 3 4 3 4.1

Which aspect of the workshop was most useful to you?

  • The fact there many instructors were around to help. All of them knew how to trouble shoot. Everyone was cheerful, positive and willing to help. 
  • The application of blender into Mcell offered a really simple and intuitive way to create a topology for the system.
  • CellOrganizer and Cellblender
  • It is great to have learned how to navigate in CellBlender.
  • Knowing that something like CellOrganizer exists has inspired various project ideas.
  • The mCell lab class with Justin, and the extra help from the instructors especially Tom.
  • hands on tutorial and  discussions with classmates  and instructors.
  • 1. Hands-on tutorial of Blender and Mcell. Blender is very cool, and fun to play with!
    2. Modeling workflow and the relationships between these different spatial modeling tools. It's nice and very helpful to have a big picture in mind, and getting to know how people in computational field think about biology.

 

What workshop topics would you like to see emphasized more in the future?

  • It would be really interesting if each day we worked on a third of a project that would be complete by the end of the workshop. The pdf tutorial hinted somewhat at this but I don't think we ended up going through with it. Creating a project that incorporates all that we learned with results would give a nice take home piece to look back and refer to, as well as show how each of these tools come together.
  • Direction of promising research
  • Hands-on MDL scripting tutorial session.
  • How to actually make useful models in mCell. It was cool to get an overview, but without extra help 1 day on each software package is not enough to actually go home and use it independently.
  • It would be nice to have more social events.
  • Maybe we can have simpler examples in hand-on tutorial session, especially for cell blender and cell organizer. It's nice to see super cool examples during the lecture, but as beginners it can be frustrated handling a very complex model.  It would also be a good idea to we can have a complete experience in combining the three tools together and really think about spatially effect during the process. For example, maybe start from day1, we can get familiar with Blender, and start thinking about a spatial toy model (involving just 2 or 3 reactions and some simple geometry), then on day2 we can set up the model in cBNGL and run it in Blender, and in day3 play with the parameters and different geometries trained in CellOrganizer.

Other comments

  • It would help to have - Notepads - Pens
  • I really learned a lot and I don't think I would have been introduced to these tools otherwise. Whether or not they I will use them depends on what I pursue in the future, but it is an exciting field to say the least
  • I really admire the effort your group is making to not only produce great tools, but to make them smooth and accessible and easy to use. Lots of researchers write clever software, but to make it easy to use is much harder and it's wonderful that you prioritize it.
  • This workshop is very helpful for solving problems in my research. Moreover, it gives me an opportunity to know the latest tools developed for biology research. Everyone is extremely helpful. I wish the computational tools can be more broadly used as more knowledge is gained from experiments. I will follow up MCell, maybe through the forum.
  • 1. I think people would like to have printer around in the future. 2. Many thanks to all instructors and assistants! I had a great time in this workshop:)

The presentation was clear and well structured.

1 2 3 4 5 Average score
- - - 1 8 4.9

The lecture taught me the basics of building MCell Models

1 2 3 4 5 Average score
- - - 1 8 4.9

I expect that MCell modeling will be important to my current or planned research projects.

1 2 3 4 5 Average score
- - 1 1 7 4.7

Comments or Suggestions

  • I hope more can be showed for how to combine MCell codes and Cell blender.

The presentation was clear and well structured.

1 2 3 4 5 Average score
- - - 1 8 4.9

The lecture taught me the basics of MCell methods for diffusion and reaction.

1 2 3 4 5 Average score
- - - 2 7 4.8

Comments

  • The videos are very impressive.

Ease of use of CellBlender

1 2 3 4 5 Average score
- 1 2 2 4 4.0

I expect that CellBlender will be important to my current or planned research projects.

1 2 3 4 5 Average score
- - - 4 4 4.5

In your opinion, what aspect of CellBlender needs the most improvement (e.g. model design, running simulations, analysis)?

  • It is not always clear what CellBlender is doing
  • it needs an easy button for cancelling mcell simulation when it is stuck
  • Running multiple simulations while making incremental changes would be cool design and analysis
  • analysis
  • Making the physics built into MCell more manipulable would be helpful.

Are any features missing from CellBlender or MCell which are crucial for your workflow? Please elaborate.

  • It would be nice for Cell Blender to follow some "steps". It is there but would help if it were just clearer in the tutorials with additional pictures. You could also have a small video uploaded that shows each screen shot and how each step goes into play. Additional it would help in the video to talk about hotkeys, and common linux issues encountered by folks still trying to get familar with the linux environment.
  • It is hard to say as I am just starting

Comments or suggestions

  • I think it was a great first day, but a shame we didn't get to do more modelling. Another day on mCell would have suited my goals.
  • Very cool to see the data gets animated. it can be good for science education too

Clarity of Presentation

1 2 3 4 5 Average score
- - 2 3 4 4.2

How much you learned

1 2 3 4 5 Average score
- - 1 4 4 4.3

Usefulness of rule-based modeling to your current or planned research projects.

1 2 3 4 5 Average score
- 2 4 1 2 3.3

Comments

  • I have no immediate plans to model large networks, but I do work with protein networks, so I might use it in the future. The lecture was challenging but I understood the advantages of rule-based modelling by the end, and it was very interesting.
  • I can see this tool is very useful for my biochemistry and development friend.

Clarity of presentation

1 2 3 4 5 Average score
- - 2 3 4 4.2

How much you learned

1 2 3 4 5 Average score
- - 1 5 3 4.2

Pace of the tutorial

Too fast About right
4 5

Ease of use of RuleBender

1 2 3 4 5 Average score
- - 4 4 1 3.7

Usefulness of RuleBender to your current or planned research projects.

1 2 3 4 5 Average score
- 2 4 1 2 3.3

Comments

  • RuleBender is a powerful tool but the amount of material covered in a day is very dense. It would be nice to study the same exact problem in MCell on day1 and cover it using RuleBender on day2. This, before you progress to more specific problems.

    Also, it will help to come up with alternate examples (other scales?) that dont study just intracellular pathways and protein dynamics.

  • Jose was too quick on the file openings, but he was very responsive when asked to slow down. I was impressed with his patience. The actual coding part of the lab was quite clear and I had no problem following. I quite liked the lab structure, starting by building a small model then playing with a larger one. The only thing missing was that I don't entirely follow what one would do with the out-putted data (i.e. what kind of hypothesis would you address and how).
  • It certainly made modeling reactions easy.

Are there any additional features that you would like to have in RuleBender or in the interface with CellBlender/MCell? Please elaborate.

  • I am still not sure how to write reactions in Cellblender by using RuleBender
  • I just wonder how the diffusion coefficient is defined when cBNGL is translated in to SBML? Can we specify them manually?

Please add any other suggestions you have for improving Day 2 of the workshop.

  • A lot of time was spent on the slides covering RuleBender but it was a very specific problem used to convey concepts on RuleBender. It would be useful to have a generic model that explains the audience about RuleBender and then go over a specific problem.
  • After we import the complex cell , we didn't get a chance to build reactions and visualize them in CellBlender