Petri net modeling and simulation of post-transcriptional regulatory networks of human embryonic stem cell (hESC) differentiation to cardiomyocytes

Petri net modeling and simulation of post-transcriptional regulatory networks of human embryonic stem cell (hESC) differentiation to cardiomyocytes Supplementary publication data including: Day 4, 9, and 15 GRNs in SBML format Day 4, 9, and 15 Petri nets in SBML format Day 4, 9, and 15 Petri net simulation results in CSV format Day 15 small Petri net and miRNA knockout variant in SBML format Day 15 small and miRNA knockout variant simulation results in CSV format Rules file in YAML format for transforming GRNs to Petri nets in VANESA Short manual of VANESA Download: VANESA is hostet on GitHub:https://github.com/cbrinkrolf/VANESAThe latest pre release (v.0.5_pre_2) is required. Opening of networks: Networks, biological networks and Petri nets, can be opened by "File" -> "Open File" (using the SBML file extension filter) Opening transformation rules: "Transformation" -> "Rule Management" -> "Load rules from file"Already available rules in VANESA should be removed first by clicking "Remove all rules". Rules can be set to active/inactive, viewed/edited, deleted, and their order can be manipulated. Transforming a biological network to a Petri net: If a biological network is loaded and transformation rules are also present, the biological network can be transformed to a Petri net by clicking: "Transformation" -> "Transform to Petri net".After successful transformation, the underlying Petri net can be shown by: "Transformation" -> "Show Petri net". This Petri net can be saved independently of the biological network it was generated from. Run a Petri net simulation: For the Petri net simulation, the installation of OpenModelica is required. Please install a compatible version of OpenModelica, such as OpenModelica 1.24.4.If a Petri net is loaded or generated, click "Petri Net" -> "Simulate" to show the simulation window. Set the stop time and, especially for larger networks, enable the developer options and select "use short model name" and "Eq. per file". Set the equations per file to 2000 before starting the simulation. Saving and loading simulation results: Computed simulation results shown in the simulation window can be set to active, renamed, exported as a CSV file, and deleted. Only active simulation results are shown in the "Petri Net Simulation" panel on the left side of the main window. If a Petri net is present, an already generated simulation result file can be loaded by clicking "Petri Net" -> "Load Simulation Result". The simulation result(s) can be investigated by selecting one or multiple nodes or arcs.