ACowan0105

@jcschaff we have discussed this several times over the years. At one point Dan found a newer version of the java help we had used, but it never progressed beyond...

Create a way to use the current documentation structure to automatically output an HTML file of the current Help version and deposit within the web site.

This may be related to the bug I reported as well, that I related to the "at all times" scale selection. See Issue #898.

Also affects Geometry Editor directly: From a simulation with a 3D geometry, select edit image to open the geometry editor and the same problem appears.

Tested 2.6.2024 and simulations now are complete. Results seem correct for membrane species in spherical membrane (see sim results for BioModel Test Gaussian Projection Application Spherical Membrane.

@jcschaff we actually have a "user materials" project that I initiated for the moving boundaries tutorial. However, it is in limbo at the moment. I think it would be good...

@jcschaff this relates to a number of things, and needs myself and Michael (and perhaps you) to sit down and decide. Probably requires some software or at least some scripts....

I think this relates to website of published models having the option to either open the model directly in VCell or open directly in RunBiosim. I am not sure this...

@jcschaff @danv61 To reproduce this bug: Start with new model (I used one with multiple compartments and one species). Add new deterministic application. Select Geometry Definition>CreateNew>Analytic 3D. Pick any thing...

Discussion at software meeting: Pedro suggested may relate to annotations, since this model has flybase annotations and our annotations do not have that yet. Issue #843 requests addition of annotations...