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Here's links to all the biomodels that currently fail when running PySCeS:
[pysces_failures.csv](https://github.com/biosimulators/Biosimulators_PySCeS/files/13193249/pysces_failures.csv)
(Many o…
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= Description =
- Provide the API for adding or removing compartments in SBML models through the Change mechanism in SED-ML.
= Context =
- Compartments are an important element of the SBML language, …
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in the SBML model (e_coli_core), if I set the extracellular species as a boundary species (e.g. for kinetic simulation), and then load the model to cobra, even though the exchange reactions (and bound…
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= Description =
- Provide the API for adding or removing parameters in SBML models through the Change mechanism in SED-ML.
= Context =
- Parameters are used in reaction nodes in the SBML language; it…
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= Description =
- Provide the API for adding or removing reactions in SBML models through the Change mechanism in SED-ML.
= Context =
- Biochemical reactions are central to the SBML language; it shou…
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= Description =
- Provide the API for adding or removing species in SBML models through the Change mechanism in SED-ML.
= Context =
- Biochemical species are central to the SBML language; it should b…
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MoBi-Import of [BIOMD0000000528](http://www.ebi.ac.uk/biomodels-main/BIOMD0000000528) and [BIOMD0000000489](http://www.ebi.ac.uk/biomodels-main/BIOMD0000000489) Biomodels fails due to wrong import of …
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It turns out that people do simulations where 'time' doesn't start at zero: they might have an SBML model saved where time=2, and want to simulate from time=2 to time=10 or the like.
In this case,…
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If the model has to be flattened, the resulting SBML file creates a valid prism model which does not yield the same result as iBioSim simulation. That issue does not occur when building a flat model a…
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Moved from sourceforge, from @draeger:
The page http://sbml.org/Facilities/Database/Simulator has two entries about SBSCL (the Systems Biology Simulation Core Library):
* Simulation Core Library 1…