Logan Drescher

According to the SED-ML L1V4 standard, the `anyURI` type isn't strictly a URI, but rather either a URL or a relative path name. Jlibsedml is designed to parse with java's...

Call to `__build_result_from_ts` (et all?) causes ValueError when imported SBML model names species "Time"

2

Specifically, the call: df.set_index('Time') Causes an exception in Pandas, as it will find two Columns named "Time". The example SBML model attached has a model with id="s23" and name="Time". [ExampleSBML.zip](https://github.com/user-attachments/files/17295669/ExampleSBML.zip)...

We need to post an updates, even if minimal, documentation of VCML (plus update our namespace URI)

CLI has a number of bugs we need to fix to get things to an acceptable state 1) Python reliance removed, and plotting / logging done java side [COMPLETE] 2)...

VCell Export needs a face-lift

1

There's a few tasks regarding this issue: - [ ] VCell CLI has a 50% slowdown in export compared to GUI - [ ] The code surrounding export almost 2...

Jlibsedml and SedmlImporter should be upgraded to be able to read and appropriately handle v1.5

1

Currently, we do a custom version which can process up to SedML level 1 version 3 (we only support L1V2 features). We do not need to support the features at...

SedML describes a way to apply a "generic parameter scan" (RepeatedTask) to any other task, but also to potentially multiple tasks. VCell doesn't natively support this feature, but it can...

Renaming Applications in the tree view does not implement correct "onLoseFocus" behavior

1

If the user does not confirm the rename with `enter`, the changes are lost on focus change

This should allow us to publish a new, much faster container on biosimulations.

While VCell CLI is separate from VCell Client, they share an underlying component of VCell Core. This means that some code that was originally designed with a GUI in mind...