Modeling of Multicellular Development and Cancer European CompuCell3DSBW Hands-on Workshop


October 8-13, 2012


Scientific Summary


The workshop brought together 30 scientists interested in biomedical modeling of tissue development, homeostasis and disease. The research interest spectrum was quite broad from few cell systems to organ and organism level modeling. Although the workshop was focused on modeling about 30% of participants identified themselves as core experimentalists. This was very encouraging given that one of the goals of the workshop was to facilitate discussion and collaboration between experimental and modeling research groups. There was also a good mix between senior and junior scientists.


The workshop had several focus areas:

1) Expose participants to cell-based quantitative tissue modeling.

2) Encourage discussions between scientists to start new research collaboration.

    To facilitate that, each participant gave 15 minute talk on his/her research

3) Collaboratively work on select modeling projects.


Unlike traditional workshops where people spend most of their time listening to talks, this workshop assumed that participants would try to complete modeling project within 6 days. This was quite ambitious and challenging given that some of the participants were relatively inexperienced modelers and that number of possible modeling projects that could be of interest to participants could easily be greater than the number of attendees. Despite these initial challenges organizers decided to stick to the project-based format. As it turned out all most participants were happy with such workshop style and managed to accomplish more work than they initially anticipated. The key to workshop’s success was to ensure that there were enough modeling experts who would help participants with their projects. After each participant gave a talk, the organizers divided attendees into workgroups. Each workgroups consisted of 1-5 people sharing similar modeling interests.


The participants were allowed to change working groups during the workshop or participate in more than one working group. This created great research opportunity for junior participants who wanted to get exposure to multiple research topics. Because the level of participants sophistication varied the organizers ensured that people who needed additional introduction to modeling concepts had an opportunity to get it. The lack of formal lectures was slightly inconvenient from organizers’ stand point because they were forced to repeat similar material few times. However, given limited duration of the workshop squeezing formal lectures into workshop agenda would be quite challenging.


The organizers closely monitored progress of the working groups (on a daily basis) and made sure that all groups advance their models.


Overall the level of participant involvement was excellent. Although the workshop officially ended at 6 pm many participants worked longer hours trying to complete as much work as possible.


Assessment of the results


The Workshop was highly successful, judging by the feedback from the participants. The organization was flawless with no logistic glitches of any kind. The Lorentz Center Staff organized excellent social program which allowed participants to engage in discussions in a less formal atmosphere. This had tremendous impact on formal part of the workshop. Once people got to know each other better they were able to communicate and work more effectively. The hotel and facilities at the Lorentz Center were excellent. Everybody seemed to appreciate the efforts that Lorentz Center put into organizing this event.


We hoped that this Workshop would significantly raise the profile of QuantTissue Consortium and Lorentz Center in the area of biomedical modeling, computational tissue biology. Given the level of interest from scientists around the world we feel confident that we were able to convey the message that there exist significant involvement of European organizations (QuantTissue, ESF) in quantitative modeling of development and disease of tissues.


We were very pleased with the talk by invited speaker Carl-Philip Heisenberg. It was very stimulating talk especially that the topics he discussed (force-based approach to tissue dynamics during zebrafish gastrulation) were directly relevant to workshop main themes. In particular he has presented an approach based on Cellular Potts Model (a model that CompuCell3D implements) to study impact of tensile forces on germ layer organization during gastrulation. One of the working groups was modeling gastrulation in chick embryos so Carl-Philip’s talk was directly relevant to this group.


This workshop was quite experimental and the organizers were somewhat skeptical whether project-based workshop format would work out. The big concern was that level of familiarity with cell-based modeling would vary among different participants and it would lead to some attendees feeling left out. Since we could not accommodate lectures in the workshop schedule we had to ensure that people who needed to be brought up-tospeed in modeling topics had an opportunity to learn the material as quickly as possible.


For this reason we invited modeling experts who served as instructors for workshop participants. Each time a workshop participant would struggle with completion of particular tasks or needed one-on-one coaching, instructors were available to help. At the conclusion of the workshop all working groups had made significant advancement in their projects. It was somewhat surprising to organizers to see so much progress being done at the workshop given relatively short duration of the workshop and the fact that several groups started coding the simulations from scratch. The gastrulation working group was able to finish the project completely and they are ready to submit the paper based on their model. This group, however, started working on the project earlier so it would be unreasonable to expect other groups show same level of accomplishment during just few days.


Besides working in groups participants had ample opportunities to talk to each other and discuss possible new collaborations. Many participants who were graduate students, were able to talk senior researchers and get advice, suggestions or feedback on their research. Such informal conversations have often significant impact on student’s careers. Having access to experienced researchers other than student’s own advisor allows students to get different perspective on their research , get advice for future research and consequently help students make more informed decisions when they transfer to post-doctoral positions.


Finally, during the workshop we had several short brainstorming sessions on how to improve modeling software. Although most of the suggestions applied mainly to CompuCell3D and SBW many of ideas solicited from participants applied to other biomedical packages. Several bugs reported during the workshop were fixed by CompuCell3D and SBW developers and new features which seemed to be important were also added to the packages.


Overall, by avoiding rigid workshop structure we were able to engage all participants in scientific projects and open discussions. All participants were enthusiastic and it was obvious that the level of interest in quantitative tissue modeling is significant. Given that the registration for the workshop was open for only few weeks we were surprised to see that all the slots were filled and we had to reject several applications. This clearly shows the importance of cell-based modeling of tissues. Consequently, it is critical that adequate training programs exist for young scientist to embrace state-of-the art tools which will impact how future research is done. QuantTissue Consortium has already made significant investments in outreach and training and the we hope that this workshop fulfilled part of the QuantTissue mission.


We have asked all participants to acknowledge QuantTissue and European Science Foundation in any publication that will originate from the research done during the workshop. Overall we were very happy with the workshop outcomes and we hope that ESF and QuantTissue share our enthusiasm.


James Glazier (Bloomington, United States)
Roeland Merks (Amsterdam, Netherlands)
Herbert Sauro (Seattle, United States)
Maciej Swat (Bloomington, United States)