Lucian Smith
Lucian Smith
For Biomodels 691, one of the requested plots is a species vs. species plot, which I *think* VCell has the right data for, but is not connecting the points in...
[BIOMD0000000019.zip](https://github.com/user-attachments/files/21843559/BIOMD0000000019.zip)
The SBML Stochastic Test Suite has models that should be simulated stochastically many times, then the averages and standard deviations are collected. I've created an OMEX file that *should* handle...
A large number of SBML Test Suite models don't technically fail using VCell, but instead continue 'PROCESSING' for many days. Here's the start of the list; I have them all...
The 'standard' way to package up the SBML Test Suite models is to give them a bunch of SED-ML files (one per SBML level/version) and just flag the latest level/version...
If you go to https://biosimulations.org/runs/685ddc23e6f3a1328ce816af#tab=viz you can select one of the charts from the various SED-ML input files, but it will always show you the chart from the first file...
https://biosimulations.org/runs/685b3031354882ae84cf2eb4 Tellurium's native SED-ML interpreter doesn't get Figure 2 correct, but Figure 1 is supposedly pretty straightforward:  but biosimulations doesn't show either of them.
Implements #448. The auxiliary functions could be put on the FbcAssociation class directly, if desired, but works as-is.
The SBML online validator fails for: ```xml ``` because the value is too small, I guess? It works on my local copy of libsbml, though. [small.xml.txt](https://github.com/user-attachments/files/23055070/small.xml.txt) ``` Error[ Line 6](https://sbml.bioquant.uni-heidelberg.de/validator_servlet/section-print-result.jsp#line-6)...
So, I'm adding some Antimony support for FBC, and I'm realizing that one thing I need is a converter from ASTNodes to and from the and/or logic of GeneProductAssociations. Would...