-
With the clarification of SBML namespaces in https://sourceforge.net/p/sbml/sbml-specifications/358/, it might be possible to relax a restriction currently in L3v2. This is the current text:
"Any …
-
A lot of time is spent searching the sbml tree for elements.
![image](https://user-images.githubusercontent.com/19502680/145400428-03f0a35e-2147-4bfc-989d-1094197b8ee9.png)
Sbml does a linear s…
-
I picked up an issue when species are in conc, and output is in conc as well, with a model that has compartments (even only a single compartment) with a volume other than 1.
Illustrated with a simp…
-
This is an issue I think is due to updates in `cobra`. With `cobra` version 0.21.0 `create_smoment_model_reaction_wise_with_sbml()` runs in a reasonable amount of time. However, once I use an environm…
-
#### Problem description
Reading a SBML model with ASCII codes in the IDs may generate invalid cobrapy IDs during parsing (for instance names including spaces).
#### Code Sample
That one aros…
-
Following the discussion today at HARMONY I was trying a few examples to see where I had issues with models with negative start times.
One example are events which are triggered based on `time>=0`. B…
-
Over the last year, we got rid of most of the symbolic model stuff in favor of doing direct SBML/SimBio -> kroneckerbio model conversions. However, there's still a bunch of symbolic model code in the …
-
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,…
-
### Background
The file format [SBML](http://sbml.org) constitutes the *de facto* standard exchange format for computational models in computational systems biology. It has been established nearly …
-
**Describe the bug**
sybil-SBML will raise compilation errors during install with libSBML version 5.19 or above.
**Steps to reproduce**
Install a recent libSBML, then run
```R
remotes::in…