Morpheus 2 is a major release that improves modeling flexibility, usability, and allowing extensibility.
Reporters, plugins that generate statistics and mappings, have been revised and generalized.
NeighborhoodReporterprovides statistics (e.g.sum, mean) on properties of the cell's directly adjacent microenvironment
CellReporterprovides statistics on properties of the cellular environment such as including the concentration of
AddCell: add CPM cells during simulation based on a condition and a location specified by a probability density function.
ChangeCelltype: change the cell type of a cell based on a condition.
Protrusion: actin-inspired feedback model that control shape and motility of CPM cells, as proposed by Niculescu et al., 2015.
Loggerplugin provides generic tool for data export.
avconv(download from here)
ParamSweepresults including images or movies (viewable in HTML5-enabled web browsers)
The changes in this version focus on improving modeling flexibility, but also include several improvements in automatic scheduling as well as a new preview panel in the user interface. Download version 1.2 here.
Proliferation. This supports the representation of asymmetric cell divisions by providing a symbolic handle to treat daughter cells differently after cell division.
ChangeCellTypeplugin to conditionally change the cell type of a cell. By default, cell properties are copied, but may be overridden using
PropertyVector, either in x,y,z or phi,theta,radius (spherical coordinates). This facilitates vector computations to e.g. control directed cell motility.
FlipCellsplugin to represent cell motility in CA-like models. This plugin enables the conditional switching of positions with a random neighboring site.
PopulationReporterto collect population-level statistics on cell
Properties. This allows individual cell behavior to depend on population-level properties, or to collect population statistics to log and plot.
StopConditionto terminate a simulation upon a
StopTime. This can significantly improve efficiency in e.g. parameter explorations or sensitivity analysis.
Event. This provides a choice to trigger events (1) whenever the condition changes from false to true (as in SBML) or (2) whenever the condition is true.
InitCAplugin to populate CA-like models.
HistogramLoggernow supports logarithmic binning and plotting
Many of these new features are the result of requests from users. In particular, we thank Maria Herberg (Medical Faculty, TU Dresden), Angelo Torelli (Mannheim University of Applied Sciences) and Ovidiu Pârvu (Brunel University) for useful suggestions.
DelayPropertythat returns assigned values after a specified time lag which enables the simulation of delay differential equations. An example model is added.
Rules whereby the latter are equations within a
Rules may have recurrency and be part algebraic loops.
Events are now triggered whenever the condition change from false to true, for SBML compatibility.