Jonathan Karr
Jonathan Karr
@veitveit could use approve again?
This can be resolved by setting the objective to `R_BIOMASS_mm_1_no_glygln` by replacing ```xml ``` with ```xml ``` With that change, the model appears to simulate correctly.
This could be resolved by deleting this reaction from the model. With that one change, the model will be valid and appears to execute correctly.
Yes, #114 sounds very similar.
We adhere to Xpaths. This is not an XPath to an attribute. The SED-ML examples diverge from true XPaths.
We conceived of SED-ML as agnostic and modular to model language. To enable modularity, we felt its essential for all XML changes to have a clear definition in terms of...
I believe this is correct. Tools, including libRoadRunner, do steady state analysis with other methods.
Simulation is CVODE. Steady state is NLEQ2. These are different methods/algorithms. Biosimulators relies on tellurium/libroadrunner advertising that it can do steady state SED-ML tasks with NLEQ2 (KISAO_0000569). We don't use...
This is sourced from the capabilities of the individual simulation tools which are stored in the BioSimulations MongoDB database. The capabilities are loaded each time a simulation tool is pushed...
The fuzzy/similarity search over KiSAO is implemented in the KiSAO Python package. This relies on information encoded into the ontology.