Sam Isaacson

Currently I've disabled it until such time as it has been updated with the revised format versions.

support BioNetGen function blocks and more inline function types

8

Currently function blocks are not supported. This would be great to add but note, this requires allowing observables within the functions.

Graphs as input

2

As @ChrisRackauckas requested. Step 1 is figuring out what the graph input should be, then we can convert to an appropriate matrix input.

DiffEqBio rescales ODE/SSA rates by factorials, but these seem to already be included in the BioNetGen rates/expressions. * ~~The fix incorporated for the BCR network needs to be tested more...

package maintenance

14

@kaandocal would you consider putting this under SciML so we could get more people access to maintain it? You could still have full repo permissons, but having it in an...

update docs to use SciML website

4

**Describe the bug 🐞** Docs don't currently appear -- they need to be updated to use the SciML website.

SciMLStyle format for short begin end block

1

@ChrisRackauckas could the rule that sends ```julia rn = @reaction_network begin k/$V, A + B --> C end k ``` to ```julia rn = @reaction_network begin k / $V, A...

EnsembleSummary plots can ignore idxs

5

```julia using Catalyst, DifferentialEquations, Plots rn = @reaction_network begin 1.0, A --> 0 2.0, B --> 0 4.0, C --> 0 end dprob = DiscreteProblem(rn, [:A => 100, :B =>...

make solution indexing work with top level system namespacing

7

If I have a ModelingToolkit ODESystem or such, say `sys`, with a variable `x`, then ```julia @variables t, x(t) ... # solve an ODESystem with x sol[x] ``` works nicely,...

It seems that maybe symbolic initial condition expressions are being substituted for numeric values instead of letting ModelingToolkit handle this downstream, which prevents users from `remake`ing problems easily, see https://discourse.julialang.org/t/performing-global-sensitivity-analysis-on-a-big-reaction-network-imported-as-a-sbml-file/93000/14