ReactionNetworkImporters.jl

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Internal conversion of integer Float values (e.g. `1.0`) to Int (e.g. 1)

1

I have a BCR model stored in a .net file. If I try this: ```julia using Catalyst, JumpProcesses using ReactionNetworkImporters BCR = loadrxnetwork(BNGNetwork(), "BCR.net") d_prob = remake(d_prob; u0=Int64.(d_prob.u0)) j_prob =...

TorkelE

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

isaacsas

ODE, SDE, and Discrete Problem dispatches for `ParsedReactionNetwork`

2

Since these contain initial conditions and parameter values, would it make sense to create dispatches to e.g. do ``` using ReactionNetworkImporters BCR = loadrxnetwork(BNGNetwork(), "BCR.net") tspan = (0.0,1000.0) oprob =...

TorkelE

`functions` is not recognized

6

Hi, thanks for developing and maintaining the amazing tool! ## Reproduce: I am testing [a simple Michaelis-Menten model](https://github.com/RuleWorld/bionetgen/blob/5529f396e9a8ac30c50f942435f197a2240b3676/bng2/Validate/DAT_validate/michment.net) provided in BioNetGen. I installed this file locally and renamed it "mm.net"....

himoto

Error with importing functions from .NET files

3

Hi all, I am using BioNetGen to generate my reaction network and define some rate laws, different from the standard ones, as functions in the BioNetGen file. However, while the...

NikosMemmos

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.

isaacsas

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.

isaacsas

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...

isaacsas