up

Author: vyudu

.DS_Store

@@ -7,8 +7,9 @@ author:
 using JumpProcesses, Plots, StableRNGs, Random, BenchmarkTools, ReactionNetworkImporters, StatsPlots, Catalyst
 ```
 
-# Model Benchmark
+We will benchmark the aggregators of JumpProcesses on a B-cell receptor network (1122 species, 24388 reactions).[^1]
 
+# Model Benchmark
 We define a function to benchmark the model and then plot the results in a benchmark. 
 ```julia
 function benchmark_and_bar_plot(model, end_time, algs)
@@ -42,3 +43,12 @@ BCR_net = loadrxnetwork(BNGNetwork(), joinpath(@__DIR__, "Data/BCR.net"));
 benchmark_and_bar_plot(BCR_net, tf, algs)
 ```
 
+### References
+[^1]:  Barua D, Hlavacek WS, Lipniacki T. A Computational Model for Early Events in B Cell Antigen Receptor Signaling: Analysis of the Roles of Lyn and Fyn.
+[^2]: Loman TE, Ma Y, Ilin V, et al. Catalyst: Fast and flexible modeling of reaction networks.
+
+
+```julia, echo = false
+using SciMLBenchmarks
+SciMLBenchmarks.bench_footer(WEAVE_ARGS[:folder], WEAVE_ARGS[:file])
+```

benchmarks/Jumps/BCR_Benchmark.jmd

@@ -7,8 +7,9 @@ author:
 using JumpProcesses, Plots, StableRNGs, Random, BenchmarkTools, ReactionNetworkImporters, StatsPlots, Catalyst
 ```
 
-# Model Benchmark
+We will benchmark the aggregators of JumpProcesses on a epidermal growth factor receptor signaling network (356 species, 3749 reactions).[^1]
 
+# Model Benchmark
 We define a function to benchmark the model and then plot the results in a benchmark. 
 ```julia
 function benchmark_and_bar_plot(model, end_time, algs)
@@ -42,3 +43,12 @@ EGFR_net = loadrxnetwork(BNGNetwork(), joinpath(@__DIR__, "Data/egfr_net.net"));
 benchmark_and_bar_plot(EGFR_net, tf, algs)
 ```
 
+### References
+[^1]: Blinov ML, Faeder JR, Goldstein B, Hlavacek WS. A network model of early events in epidermal growth factor receptor signaling that accounts for combinatorial complexity.
+[^2]: Loman TE, Ma Y, Ilin V, et al. Catalyst: Fast and flexible modeling of reaction networks.
+
+
+```julia, echo = false
+using SciMLBenchmarks
+SciMLBenchmarks.bench_footer(WEAVE_ARGS[:folder], WEAVE_ARGS[:file])
+```

benchmarks/Jumps/EGFR_Benchmark.jmd

@@ -7,8 +7,9 @@ author:
 using JumpProcesses, Plots, StableRNGs, Random, BenchmarkTools, ReactionNetworkImporters, StatsPlots, Catalyst
 ```
 
-# Model Benchmark
+We will benchmark the aggregators of JumpProcesses on a human IgE receptor signaling network (3744 species, 58276 reactions).[^1, ^2]
 
+# Model Benchmark
 We define a function to benchmark the model and then plot the results in a benchmark. 
 ```julia
 function benchmark_and_bar_plot(model, end_time, algs)
@@ -42,3 +43,12 @@ fceri_gamma2_net = loadrxnetwork(BNGNetwork(), joinpath(@__DIR__, "Data/fceri_ga
 benchmark_and_bar_plot(fceri_gamma2_net, tf, algs)
 ```
 
+### References
+[^1]: Faeder JR, Hlavacek WS, Reischl I, Blinov ML, Metzger H, Redondo A, et al. Investigation of Early Events in FcεRI-Mediated Signaling Using a Detailed Mathematical Model.
+[^2]: Loman TE, Ma Y, Ilin V, et al. Catalyst: Fast and flexible modeling of reaction networks.
+
+
+```julia, echo = false
+using SciMLBenchmarks
+SciMLBenchmarks.bench_footer(WEAVE_ARGS[:folder], WEAVE_ARGS[:file])
+```