Synopsis group 4

Synopsis

Our goal was to create SED-ML files that would reproduce selected experiments from Bachmann et al. [1] in combination with the model selected by Group 2.

Following an initial review of available tools for creating SED-ML files we decided on two separate approaches:

• default simulation in SED-ML WebTools as a basis for experiment-specific simulations in COPASI (as described by Scharm & Waltemath [2)]
• experiment-specific simulations in Tellurium, a Python platform for systems biology [3]

The created SED-ML files were validated in SED-ML WebTools and integrated into the COMBINE archive.

Subsequently, output files were created by

• simulating all SED-ML files within the COMBINE archive using Tellurium and
• loading individual SED-ML files in COPASI or SED-ML WebTools, and included in the COMBINE archive.

In summary, we were able to reproduce many, but not all experiments. Several parameters required to reproduce individual plots were not included in the model itself and would have to be added manually based on details provided in the supplementary material. The specific problems encountered while attempting to reproduce the experiments will be addressed in separate GitHub issues for future reference.

References

[1] Bachmann, J. et al. Division of labor by dual feedback regulators controls JAK2/STAT5 signaling over broad ligand range. Molecular Systems Biology 7, 516 (2011). https://doi.org/10.1038/msb.2011.50

[2] Scharm, M. and Waltemath, D. A fully featured COMBINE archive of a simulation study on syncytial mitotic cycles in Drosophila embryos. F1000Research 5, 2421 (2016). https://doi.org/10.12688/f1000research.9379.1

[3] Choi, K. et al. Tellurium: An extensible python-based modeling environment for systems and synthetic biology. Biosystems 171, 74-79 (2018), https://doi.org/10.1101/054601