How applicable are current standards
for modeling and simulation in Systems Biology
to the needs of today’s research tasks?
using the example of the Whole-Cell model (Karr et al. 2012)
Karr et al. have recently published the first whole-cell computational model which studies the cell cycle on different levels of detail, using a plethora of state-of-the-art modeling techniques, ranging from ODEs to Boolean network and constraint-based modeling. Since publication in 2012, the Karr model has been referenced above 250 times and parts of it have been reused in other works. However, the model is currently encoded in MATLAB.
The goal of the whole-cell summer school is to encode the popular model into standard formats. We aim to
- Provide a reusable version of the whole-cell model to the community,
- Demonstrate the power and the limits of standard formats, and
- Establish a roadmap for standard development in systems biology.
We organise the fully-funded summer school with a total of 50 researchers (late Master to early postdoc level) from March, 9th 2015 to March, 13th 2015 in Rostock, Germany. Apply to our summer school on the provided project homepage. Together with these tutors you could share and extend your knowledge to get an opportunity for new insights to the capabilities of standards.
Official homepage of summer school for people wishing to join the summer school
Google group for people interested in joining the summer school.
Google code for people interested in contributing code.
Slideshare presentation about the model itself and the project in detail.