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The global parameter must be applied in the repeated tasks. The seed exception can be removed.
Currently it states:
>Then, for each SubTask child of the RepeatedTask, in the order specified by it…
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---
id: netpyne
version: 1.0.0.2
specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_pyNeuroML/65687288d4c2cc3aa48f3814a6c5503f32701c32/biosimulators-netpyne.json
specific…
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There doesn't seem to be a KiSAO id for "step size", which would be useful to have for one-step methods such as the [Euler forward method](http://bioportal.bioontology.org/ontologies/KISAO/?p=classes&…
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We suggest to replace the term "Logical Model Simulation Model", because “Discrete Event Simulation algorithm” is more generic, and it refers to the actual type of simulation rather than to the charac…
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- [ ] Get the closest algorithm(s) among the algorithms supported by a simulation tool to a specific algorithm
- [ ] Get all of relatives of the specific algorithm
- 1: parents and siblings (o…
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# Issue
it must be possible to easily calculate summary functions over the runs of the stochastic simulation or over repeatedTasks in general. Things like mean, variance, std, min, max, ...
Currentl…
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name: initial step size
definition: initial time step size
subClassOf: KISAO_0000242
algorithm: KISAO_0000019, KISAO_0000087, KISAO_0000088, KISAO_0000089, KISAO_0000436, VODE, ZVODE
isImp…
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Some recently added terms are not visibile in OLS. Examples:
- https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http://www.biomodels.net/kisao/KISAO#KISAO_0000526
- https://www.ebi.ac.uk/ols/o…
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---
id: smoldyn
version: "2.65"
specificationsUrl: https://raw.githubusercontent.com/ssandrews/Smoldyn/541673cc7a93d8ea0752db0959bc51fc1790518a/biosimulators.json
specificationsPatch:
version: …
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Hello,
in order to be able to express parameter estimation tasks in SED-ML we need the capability of defining some optimization methods. Under:
KISAO_0000472:
Simulated Annealing
Random Sea…