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## Issue
We need to make it possible to exchange SED-ML files between simulation tools while allowing modelers to specify particular algorithms (e.g., that they actually used) and their parameters th…
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From KiSAO surveymonkey:
Q3: Algorithm name (e.g. tau-leaping method):
Maximal Timestep Method
Q4: Short description:
Hybrid simulation algorithm integrating Gillespie exact simulation and…
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In the following method, the rates for the Gillespie algorithm are computed by multiplying the number of compartments by the probability. Why we are doing that?
Check if this is working for all Ken…
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In the iteration loop for the Gillespie algorithm, there is a reference to compartments. The algorithm should be more generic (not only used for epidemiological models).
```Smalltalk
doGillespieIt…
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Currently, COPASI appears to only support KISAO terms for three algorithms. COPASI also appears to have no KISAO support for algorithm parameters.
- Timecourse
- Continuous
- KISAO:0000019: C…
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Question for tellurium/libRoadRunner developers:
Algorithms
- euler
- NLEQ1: KISAO_0000568
Algorithm parameters (`tellurium name: default`)
- CVODE
- stiff: true
- multiple_steps: false…
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When using rewiring with the ADBM model, the whole web is rewired following extinction events, independently of the identity of the extinct species.
We could add a parameter (`adbm_directlinks = t…
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I am trying to code up an SEIR model in pomp and am seeing a rather large discrepancy in the distribution of sample paths that I generate when simulating with the Euler-multinomial stepper compared wi…
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Hi,
I tried to run a Jump DDE and, given the supreme coolness of DifferentialEquations.jl, I rather expected this to just work. However, it did not.
M(not)WE:
```julia
using DifferentialEqua…
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Hello @shahriariravanian, I'm working with @paulflang on SbmlInterface and he sent me the following to open here below:
Similar to the CellML to MTK conversion done by CellMLToolkit.jl, we have bee…