SEDML_Tools
The SED-ML website provides a useful overview of software tools and libraries to work with SED-ML [1], including a brief description and information on supported model languages.
Screenshot SED-ML Tools & Libraries 2021-06-21
Based on this overview as well as previous experience, we decided to test several different tools in order to create, edit and export SED-ML files for specific experiments using the selected SBML model.
JWS Online [2]
- simulation of (curated) models from the JWS Online database
- intuitive modification of parameters via the web interface for new, adjusted simulations
- option to export or save new simulations or SED-ML files not available
- generation and simulation of a "default" SED-ML file from an uploaded SBML model
- browser-based editing of a generated or uploaded SED-ML file to modify simulation
- option to download the simulation as SED-ML file alone or integrated into a COMBINE archive
- simulation of SBML models either de novo or based on imported SED-ML files
- modification and extension of the various parameters (species, global quantities, events) and definition of plots via the user interface
- option to export SED-ML files (however, not including adjustments made to the model; the adjusted model has to be exported and saved separately)
- no support for simulations involving more than one model (e.g. for plots containing two different experimental conditions)
- Python-based environment for biological modelling and simulation
- generation and simulation of SED-ML files based on existing SBML models
- possibility to combine several conditions in one plot (e.g. wildtype vs. overexpression)
- modifications of the model (e.g. adjusted parameters for certain experiments) are stored directly in the SED-ML file
Initially, we followed the steps taken by Scharm & Waltemath [4] to generate a default simulation using SED-ML WebTools and modify this for a specific experiment in COPASI. However, given the type of plots to be created, we eventually decided to generate SED-ML files with tellurium in order to reproduce the experiments presented by Bachman et al. [5]. The generation, validation and testing of SED-ML files is described in more detail here.
[1] Waltemath, D. et al. Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language. BMC Syst Biol 5, 198 (2011), https://doi.org/10.1186/1752-0509-5-198
[2] Olivier, B. G. and Snoep, J. L. Web-based kinetic modelling using JWS Online. Bioinformatics 20, 2143-2144 (2004), https://doi.org/10.1093/bioinformatics/bth200
[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
[4] 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
[5] 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