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I suspect the initial setup will be similar to `HydeNet`.
We will need an object on which to act, so let's call that `dbn`. It will need the following attributes
- [x] network formula (the call…
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In my models, running Gillespie stochastic simulations has been producing negative values (!) for species.
I have traced the issue back to reactions of the form X + X -> Y and produced a simple SBML…
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- [ ] Update Figure 1, left panel, to the mean of all 454 instead of 454-5. Adjust the position.
- [ ] One a big picture standpoint, the tools presented in this manuscript are useful only if there ar…
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Hi Chris
Gitter is down atm (and github very slow) so I use an issue to write down stuff, hope thats ok.
1) The idea of multiscalemodels is brilliant. Your approach made it so much more general too.…
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The WFP function gives the timesteps x species matrix as its second output:
set.seed(2)
wfp
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I have just tried to construct an Indo-European analysis using the IE tree from glottolog.
This did not work as easily as expected.
_Excourse: Context_
This was to see whether an issue running an `xm…
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When you plot a simulation with timeseries.plot(),
the time axis is not scaled correctly.
if you run a simulation like this:
``` python
sim = nsim.RepeatedSim(Model, T=100, repeat=2)
sim.timeseries…
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We need to decide which summary statistics should be calculated for a simulation run at a given spatial and temporal resolution and detection probability.
Here's a start.. please modify/add:
_(statis…
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I tried running 25 ns md with the script from the attached zip ([opennm_nan.zip](https://github.com/pandegroup/openmm/files/583926/opennm_nan.zip)) on several frames from a gromacs md run (which have …
sroet updated
7 years ago