Patrick AMAR

. Bioinfo group, LRI, Univ. Paris Sud, CNRS UMR 8623
. Synthetic & Systems Biology group, Sys2diag UMR 9005 CNRS, ALCEDIAG

Overview

Pandæsim is an hybrid simulation programme derived from the sub-volumes method used to add coarse-grained spatial localisation capabilities to standard SSA (Stochastic Simulation Algorithm) simulations used for example in the domain of biochemistry. To increase the computing efficiency we also used an original variant of the Gillespie algorithm with tau-leaping, that automatically adapts at each timestep the proportion of randomness vs average-calculation. Our algorithm allows us to easily use either this stochastic variant of SSA, or a deterministic continuous solver, and therefore compare the two methods.

Download Pandæsim

Windows Version (July 16, 2020)

Linux (x86_64) Version (July 16, 2020)

Mac OS X (x86_64) Version (July 14, 2020)

Pandæsim Documentation

To launch PandæSim from the command line type "pandaesim" (without the quotes) or double click its icon if it is present on the desktop. This on-line documentation can be displayed using the User manual item of the Help menu.

2. Anatomy of the main window

The main window shows a map where each "région" has its own colour and each "département" is outlined. The results of a simulation are displayed inside coloured circles for each département. The Paris and surrounding areas are displayed at a bigger scale on the top left corner of the window, while the "Corse" région is shown in the left side of the window, in the Atlantic ocean, because its real location, in the Mediterranean sea would have been far away in the bottom right part of the window...
The size and colour of the circles match the number displayed inside: small and slate grey for a low number to large an red for a high number.

Under the menu bar, there is the Replay slider: when a simulation is done, the sash is automatically placed at the end of the slider. Moving the sash allows the user to go back and forth in time, exploring the trajectory of this simulation. The results displayed on the map and in the curves window are updated accordingly.

A left click on a "département" pops up the corresponding curves window showing the temporal trajectory of the epidemic for this area (the evolution of the epidemic starting from day zero to its end, or to the maximum number of days set in the Parameter dialog box). A left click on any surrounding background area pops up the curves window for the entire country.

The curves show the number of contagious, ill and dead people computed each hour, but displayed each day.

3. Commands

All the commands can be accessed using the menubar or a keyboard shortcut.

• File -> PNG Snapshot
  File -> JPG Snapshot
  Pops up the file selection box to save a snapshot of the current view to a PNG or JPG format image file.
• File -> Options (Ctrl+P)
  Pops up the parameter setting dialog box. The current settings can be validated with a click on the Submit button or with the Enter key.

  

  These parameters are gathered in three main groups:

  • Population data
    The population is split in 4 subpopulations depending on the age. For each subpopulation one can set the lethality rate, the duration of the illness, and the proportion of people that are travelling out of the département but inside the région, and to other régions.
  • Contagion rates
    The contagion rate depends on the location: at home, in public transportation, or at work.
  • Global parameters
    The proportion of ill patients that can propagate the disease, the global proportion of the severe form of the illness, the number of people who are initially contagious (for each département selected in the "From" list, and the maximum length (in days) of the simulation.
  All these parameters can be reset to the factory settings or from a file, and saved to a file using the corresponding buttons.
• File -> Quit (Ctrl+Q)
  Quit the simulator
• Simulation -> Restart (Tab Linux and Windows Ctrl+L on MacOSX)
  Start another simulation with the same parameters. This is valid only with the stochastic solver.
• Simulation -> Mean of 10 (Ctrl+M)
  Start 10 simulations with the current parameters. The averaged values at each timestep are shown on the map and on the curves.
• Simulation -> Stochastic (Ctrl+S)
  Use a discrete stochastic self adaptative solver: when there is a large number of events during a time step, the stochastic part is low and the computations use mainly mean values. When the number of events diminishes the stochastic part grows higher.
• Simulation -> Deterministic (Ctrl+E)
  Use a continuous deterministic solver: all the computations are made using floating point numbers and mean values. This kind of solver is known to lead to wrong results due to the continuous way of counting discrete quantities, mainly when they are low... But sometimes this can gives a fairly good image of what happens on average conditions.
• Methods -> None (Ctrl+N)
  No specific method of action against the epidemic is used, the epidemic eventually stops when enough people are immunised and therefore cannot propagate the disease.
• Methods -> Soft Quarantine (Ctrl+O)
  Methods -> Full Quarantine (Ctrl+F)

  Soft quarantine: no one uses public transportation and neither meeting nor gathering are allowed.
  Full quarantine: everybody stays at home except for one hour per day to go to non highly populated places.

  

  Two more sliders are shown below the Replay slider; The first one indicates when the quarantine begins, and the second how many days it stands. Any change to a slider triggers a new simulation according to these new parameters.

• View -> Reset zoom (Ctrl+0)
  View -> Zoom In (Ctrl++)
  View -> Zoom Out (Ctrl+-)
  Controls the size of the window. The user can zoom in up to 150% or zoom out to 50% of the default window size. The font size is set accordingly.
• View -> Real stats (Ctrl+R)
  Shows the official statistics of deceased people (in hospital) the same way the simulation is shown.
• View -> Deceased (Ctrl+D)
  View -> Contaninated (Ctrl+C)
  View -> Hospitalised (Ctrl+H)
  View -> Ill (Ctrl+I)
  Shows the number of people from the selected category computed by the last simulation.
• Help -> About (Ctrl+A)
  Shows the version and credits for this simulation programme.
• Help -> User manual (Ctrl+U)
  Displays this help window.