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Interactive plot of BNGL model output is not plotting entire trajectories with respect to time. #22

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LarkinIt opened this issue Mar 14, 2024 · 0 comments

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@LarkinIt
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Hello,

I am working with a BNGL model in VSCode with the extension on a WSL (Ubuntu 20.04 on Windows).

The issue occurs when I run a model with automatic built-in plotting. Specifically, the entire trajectories for all model species are cut off at a specific, seemingly random time point. It is important to note that the model simulation is run for the entire time specified in the BNGL file when I check the corresponding .gdat file generated. For the example shown below, the model simulate is called as follows in BNG:

simulate({method=>"ode",suffix=>"ode",t_end=>24, n_steps=>4800, print_functions=>1})

Screenshot:
image

Here is a zoomed-in screenshot:
image

Things that I have tried but have NOT worked:

  • I have tried this on other BNG files/models of varying complexity
  • Autoscaling interactive plot/manually shifting axes with mouse
  • Re-running the model with less time points
  • Changing the extension settings to plot less species' times series

Current workaround. If I click the .gdat file and click the Built-In Plotting button, the entire plot x-axis is scaled and plotted correctly:
image

clicking the button on the right of this screenshot results in the correct interactive plot:
image

I also want to note that this seems to happen with any BioNetGen model I have tested.

Here is the relevant environment information:

The following are related to BioNetGen and its execution: 
BNG version: 2.9.0
BNG2.pl path: /home/larkinit/anaconda3/lib/python3.9/site-packages/bionetgen/bng-linux (the main executable for BNG)
Perl version: 5.30.0 (used to run BNG2.pl)
CLI version: 0 8 2 alpha 0
pyBNG path: /home/larkinit/anaconda3/lib/python3.9/site-packages/bionetgen (the PyBNG installation)

The following libraries are required by PyBioNetGen: 
numpy version: 1.23.5
pandas version: 1.4.4
libRoadRunner version: 2.2.2
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