From 7677949697204934f1ca8619691627ca0b0413aa Mon Sep 17 00:00:00 2001 From: abhro <5664668+abhro@users.noreply.github.com> Date: Sat, 6 Dec 2025 08:15:37 -0500 Subject: [PATCH 1/3] Fix spelling and typos --- lib/BVProblemLibrary/src/BVProblemLibrary.jl | 2 +- .../src/DDEProblemLibrary.jl | 2 +- .../src/JumpProblemLibrary.jl | 4 ++-- .../src/SDEProblemLibrary.jl | 22 +++++++++---------- 4 files changed, 15 insertions(+), 15 deletions(-) diff --git a/lib/BVProblemLibrary/src/BVProblemLibrary.jl b/lib/BVProblemLibrary/src/BVProblemLibrary.jl index 2b98b36..b56e54a 100644 --- a/lib/BVProblemLibrary/src/BVProblemLibrary.jl +++ b/lib/BVProblemLibrary/src/BVProblemLibrary.jl @@ -216,7 +216,7 @@ flat_earth_drag_tspan = (0, 100) @doc raw""" flat_earth_drag -Launch into circular orbit from a flat Earth including athmosferic drag. +Launch into circular orbit from a flat Earth including atmospheric drag. Given by diff --git a/lib/DDEProblemLibrary/src/DDEProblemLibrary.jl b/lib/DDEProblemLibrary/src/DDEProblemLibrary.jl index 0ee4e26..c733b2c 100644 --- a/lib/DDEProblemLibrary/src/DDEProblemLibrary.jl +++ b/lib/DDEProblemLibrary/src/DDEProblemLibrary.jl @@ -39,7 +39,7 @@ export # RADAR5 problems export prob_dde_RADAR5_oregonator, prob_dde_RADAR5_robertson, prob_dde_RADAR5_waltman -# QS exaple +# QS example export prob_dde_qs include("constant_delays.jl") diff --git a/lib/JumpProblemLibrary/src/JumpProblemLibrary.jl b/lib/JumpProblemLibrary/src/JumpProblemLibrary.jl index f3ae84c..4f6fe55 100644 --- a/lib/JumpProblemLibrary/src/JumpProblemLibrary.jl +++ b/lib/JumpProblemLibrary/src/JumpProblemLibrary.jl @@ -9,7 +9,7 @@ RuntimeGeneratedFunctions.init(@__MODULE__) export prob_jump_dnarepressor, prob_jump_constproduct, prob_jump_nonlinrxs, # examples mixing mass action and constant rate jumps prob_jump_osc_mixed_jumptypes, -# examples used in published benchmarks / comparisions +# examples used in published benchmarks / comparisons prob_jump_multistate, prob_jump_twentygenes, prob_jump_dnadimer_repressor, # examples approximating diffusion by continuous time random walks prob_jump_diffnetwork @@ -231,7 +231,7 @@ prob = DiscreteProblem(rn, u0, (0.0, tf), rnpar, eval_module = @__MODULE__) """ Negative feedback autoregulatory gene expression model. Dimer is the repressor. Taken from Marchetti, Priami and Thanh, -"Simulation Algorithms for Comptuational Systems Biology", +"Simulation Algorithms for Computational Systems Biology", Springer (2017). """ prob_jump_dnadimer_repressor = JumpProblemNetwork(rn, rnpar, tf, u0, prob, diff --git a/lib/SDEProblemLibrary/src/SDEProblemLibrary.jl b/lib/SDEProblemLibrary/src/SDEProblemLibrary.jl index cb9c450..0392544 100644 --- a/lib/SDEProblemLibrary/src/SDEProblemLibrary.jl +++ b/lib/SDEProblemLibrary/src/SDEProblemLibrary.jl @@ -241,13 +241,13 @@ function oval2ModelExample(; largeFluctuations = false, useBigs = false, noiseLe kd_tgfR = 1.0 kd_zeb = 0.1 kd_Op = 10.0 - lamda1 = 0.5 - lamda2 = 0.5 - lamda3 = 0.5 - lamda4 = 0.5 - lamda5 = 0.5 - lamdas = 0.5 - lamdatgfR = 0.8 + lambda1 = 0.5 + lambda2 = 0.5 + lambda3 = 0.5 + lambda4 = 0.5 + lambda5 = 0.5 + lambdas = 0.5 + lambdatgfR = 0.8 nO = 6.0 nSO = 2.0 nzo = 2.0 @@ -279,7 +279,7 @@ function oval2ModelExample(; largeFluctuations = false, useBigs = false, noiseLe (1 + y[2] / J_snail1) - kd_snail * (y[1] - y[4]) - kd_SR1 * y[4] dy[2] = k_SNAIL * (y[1] - y[4]) - kd_SNAIL * y[2] dy[3] = k0_34 + k_34 / (1 + ((y[2] / J1_34))^2 + ((y[6] / J2_34))^2) - - kd_34 * (y[3] - y[4]) - kd_SR1 * y[4] + lamdas * kd_SR1 * y[4] + kd_34 * (y[3] - y[4]) - kd_SR1 * y[4] + lambdas * kd_SR1 * y[4] dy[4] = Timescale * (Ks * (y[1] - y[4]) * (y[3] - y[4]) - y[4]) dy[5] = k0_zeb + k_zeb * ((y[2] / J_zeb))^2 / @@ -294,9 +294,9 @@ function oval2ModelExample(; largeFluctuations = false, useBigs = false, noiseLe (5 * y[8] + 2 * 10 * y[9] + 3 * 10 * y[10] + 4 * 5 * y[11] + 5 * y[12]) - y[15]) - dk_ZR1 * 5 * y[8] - dk_ZR2 * 2 * 10 * y[9] - dk_ZR3 * 3 * 10 * y[10] - dk_ZR4 * 4 * 5 * y[11] - dk_ZR5 * 5 * y[12] + - lamda1 * dk_ZR1 * 5 * y[8] + lamda2 * dk_ZR2 * 2 * 10 * y[9] + - lamda3 * dk_ZR3 * 3 * 10 * y[10] + lamda4 * dk_ZR4 * 4 * 5 * y[11] + - lamda5 * dk_ZR5 * 5 * y[12] - kd_tgfR * y[15] + lamdatgfR * kd_tgfR * y[15] + lambda1 * dk_ZR1 * 5 * y[8] + lambda2 * dk_ZR2 * 2 * 10 * y[9] + + lambda3 * dk_ZR3 * 3 * 10 * y[10] + lambda4 * dk_ZR4 * 4 * 5 * y[11] + + lambda5 * dk_ZR5 * 5 * y[12] - kd_tgfR * y[15] + lambdatgfR * kd_tgfR * y[15] dy[8] = Timescale * (K1 * (y[7] - (5 * y[8] + 2 * 10 * y[9] + 3 * 10 * y[10] + 4 * 5 * y[11] + 5 * y[12]) - From f02ee2a8588c7af0b807b22b193088d5ac153455 Mon Sep 17 00:00:00 2001 From: abhro <5664668+abhro@users.noreply.github.com> Date: Sat, 6 Dec 2025 11:58:28 -0500 Subject: [PATCH 2/3] Add "strat" to .typos.toml --- .typos.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/.typos.toml b/.typos.toml index 2f35caf..fdd9aee 100644 --- a/.typos.toml +++ b/.typos.toml @@ -38,6 +38,7 @@ sde = "sde" dde = "dde" bvp = "bvp" ivp = "ivp" +strat = "strat" # Common abbreviations tol = "tol" From f43edd17331120fa30fc9f0bf695b8d4e983d277 Mon Sep 17 00:00:00 2001 From: Christopher Rackauckas Date: Sat, 6 Dec 2025 13:34:07 -0500 Subject: [PATCH 3/3] Update .typos.toml --- .typos.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/.typos.toml b/.typos.toml index fdd9aee..1568a2d 100644 --- a/.typos.toml +++ b/.typos.toml @@ -39,6 +39,7 @@ dde = "dde" bvp = "bvp" ivp = "ivp" strat = "strat" +OT = "OT" # Common abbreviations tol = "tol"