March '25 presentations (#21)

* Synthesis on Pluto

* Add start of why QNs notebook

* Update notebooks

Author: ReubenJ

experiments/Synth/.gitignore

@@ -413,3 +413,5 @@ $RECYCLE.BIN/
 
 ## Acknowledgements
 # Many thanks to `https://gitignore.io/`, written and maintained by Joe Blau, which contributed much material to this gitignore file.
+
+.direnv

experiments/Synth/Manifest.toml

@@ -2,8 +2,10 @@ name = "Synth"
 
 [deps]
 AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"
+Attractors = "f3fd9213-ca85-4dba-9dfd-7fc91308fec7"
 BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
+Clingo_jll = "e1d4ad0e-dc8b-5d2d-8155-e9a55b531f08"
 CondaPkg = "992eb4ea-22a4-4c89-a5bb-47a3300528ab"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"
@@ -14,6 +16,7 @@ Git = "d7ba0133-e1db-5d97-8f8c-041e4b3a1eb2"
 GraphDynamicalSystems = "13529e2e-ed53-56b1-bd6f-420b01fca819"
 GraphRecipes = "bd48cda9-67a9-57be-86fa-5b3c104eda73"
 Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
+Herb = "c09c6b7f-4f63-49de-90d9-97a3563c0f4a"
 HerbConstraints = "1fa96474-3206-4513-b4fa-23913f296dfc"
 HerbCore = "2b23ba43-8213-43cb-b5ea-38c12b45bd45"
 HerbGrammar = "4ef9e186-2fe5-4b24-8de7-9f7291f24af7"
@@ -34,7 +37,6 @@ ProgressBars = "49802e3a-d2f1-5c88-81d8-b72133a6f568"
 ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
 PythonCall = "6099a3de-0909-46bc-b1f4-468b9a2dfc0d"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
-SBML = "e5567a89-2604-4b09-9718-f5f78e97c3bb"
 SlurmClusterManager = "c82cd089-7bf7-41d7-976b-6b5d413cbe0a"
 SoleLogics = "b002da8f-3cb3-4d91-bbe3-2953433912b5"
 StatsPlots = "f3b207a7-027a-5e70-b257-86293d7955fd"