From 44ef0839f75691c851ccc9c25813b8689874e991 Mon Sep 17 00:00:00 2001 From: stephanmg Date: Tue, 8 Jul 2025 12:50:05 +0200 Subject: [PATCH 1/4] Rename Okuonghae_ChaosSolitonsFractals2020_model.xml -> model_Okuonghae_ChaosSolitonsFractals2020.xml --- .../Okuonghae_ChaosSolitonsFractals2020.yaml | 2 +- ...onghae_ChaosSolitonsFractals2020_model.xml | 934 ------------------ 2 files changed, 1 insertion(+), 935 deletions(-) delete mode 100644 Benchmark-Models/Okuonghae_ChaosSolitonsFractals2020/Okuonghae_ChaosSolitonsFractals2020_model.xml diff --git a/Benchmark-Models/Okuonghae_ChaosSolitonsFractals2020/Okuonghae_ChaosSolitonsFractals2020.yaml b/Benchmark-Models/Okuonghae_ChaosSolitonsFractals2020/Okuonghae_ChaosSolitonsFractals2020.yaml index c66474e8..a1b617f5 100644 --- a/Benchmark-Models/Okuonghae_ChaosSolitonsFractals2020/Okuonghae_ChaosSolitonsFractals2020.yaml +++ b/Benchmark-Models/Okuonghae_ChaosSolitonsFractals2020/Okuonghae_ChaosSolitonsFractals2020.yaml @@ -8,6 +8,6 @@ problems: observable_files: - observables_Okuonghae_ChaosSolitonsFractals2020.tsv sbml_files: - - Okuonghae_ChaosSolitonsFractals2020_model.xml + - model_Okuonghae_ChaosSolitonsFractals2020.xml visualization_files: - visualizationSpecification_Okuonghae_ChaosSolitonsFractals2020.tsv diff --git a/Benchmark-Models/Okuonghae_ChaosSolitonsFractals2020/Okuonghae_ChaosSolitonsFractals2020_model.xml b/Benchmark-Models/Okuonghae_ChaosSolitonsFractals2020/Okuonghae_ChaosSolitonsFractals2020_model.xml deleted file mode 100644 index 3256f99a..00000000 --- a/Benchmark-Models/Okuonghae_ChaosSolitonsFractals2020/Okuonghae_ChaosSolitonsFractals2020_model.xml +++ /dev/null @@ -1,934 +0,0 @@ - - - - - - - - - - - 2020-11-13T14:20:23Z - - - - - - - - - - - - - - - - - - - - - - - - 2020-11-16T11:16:14Z - - - - - - - - - - k1 - - - k2 - - - substrate - - - - k1 - k2 - substrate - - - - - - - - - - - - 2020-11-16T11:17:52Z - - - - - - - - - - k1 - - - k2 - - - substrate - - - - k1 - - - 1 - k2 - - substrate - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2020-11-13T14:22:21Z - - - - - - - - - - - - - - - - - 2020-11-13T14:22:33Z - - - - - - - - - - - - - - - 2020-11-13T14:23:01Z - - - - - - - - - - - - - - - 2020-11-13T14:23:15Z - - - - - - - - - - - - - - - 2020-11-13T14:23:27Z - - - - - - - - - - - - - - - 2020-11-13T14:23:41Z - - - - - - - - - - - - - - - 2020-11-13T14:24:07Z - - - - - - - - - - - - - - - 2020-11-16T08:59:04Z - - - - - - - - - - - - - - - 2020-11-16T09:21:09Z - - - - - - - - - - - - - - - 2020-11-23T10:24:46Z - - - - - - - - - - - - - - - - - 2020-11-16T08:59:36Z - - - - - - - - - - - - - - - 2020-11-16T09:01:17Z - - - - - - - - - - - - - - - 2020-11-16T09:01:21Z - - - - - - - - - - - - - - - 2020-11-16T09:01:27Z - - - - - - - - - - - - - - - 2020-11-16T09:01:33Z - - - - - - - - - - - - - - - 2020-11-16T09:01:36Z - - - - - - - - - - - - - - - 2020-11-16T09:01:39Z - - - - - - - - - - - - - - - 2020-11-16T09:01:51Z - - - - - - - - - - - - - - - 2020-11-16T09:04:14Z - - - - - - - - - - - - - - - 2020-11-16T09:04:28Z - - - - - - - - - - - - - - - 2020-11-16T09:04:35Z - - - - - - - - - - - - - - - 2020-11-16T09:15:09Z - - - - - - - - - - - - - - - 2020-11-16T09:15:11Z - - - - - - - - - - - - - - - 2020-11-16T09:16:05Z - - - - - - - - - - - - - - - 2020-11-23T10:09:40Z - - - - - - - - - - - - - - - 2020-11-23T10:09:51Z - - - - - - - - - - - - - - - 2020-11-23T10:10:09Z - - - - - - - - - - - - exposed_start - - - - - asymptomatic_start - - - - - symptomatic_start - - - - - - - - - asymptomatic - detected - exposed - recovered - susceptible - symptomatic - - - - - - - - - - transmission_rate_effective - - - 1 - eps - - - - 1 - delta - - - - - - alpha - asymptomatic - - symptomatic - - - - - total_pop - detected - - - - - - - - - - - - - - 2020-11-16T09:03:29Z - - - - - - - - - - - - - - - - - Lagos - lam - susceptible - - - - - - - - - - - - 2020-11-16T09:03:50Z - - - - - - - - - - - - - - - - - Lagos - - Rate_Law_for_exposed_to_symptomatic - sigma - nu - exposed - - - - - - - - - - - - - 2020-11-16T09:03:58Z - - - - - - - - - - - - - - - - - Lagos - - Rate_Law_for_exposed_to_asymptopmatic - sigma - nu - exposed - - - - - - - - - - - - - 2020-11-16T09:05:10Z - - - - - - - - - - - - - - - - - - Lagos - psi - symptomatic - - - - - - - - - - - - 2020-11-16T09:05:12Z - - - - - - - - - - - - - - - - - - Lagos - theta - asymptomatic - - - - - - - - - - - - 2020-11-16T09:05:53Z - - - - - - - - - - - - - - - - - Lagos - gamma_0 - symptomatic - - - - - - - - - - - - 2020-11-16T09:05:56Z - - - - - - - - - - - - - - - - - Lagos - gamma_a - asymptomatic - - - - - - - - - - - - 2020-11-16T09:06:02Z - - - - - - - - - - - - - - - - - Lagos - gamma_i - detected - - - - - - - - - - - - 2020-11-16T09:06:34Z - - - - - - - - - - - - - - - - - Lagos - d_0 - symptomatic - - - - - - - - - - - - 2020-11-16T09:06:41Z - - - - - - - - - - - - - - - - - Lagos - d_D - detected - - - - - - - From 63a4d2f2a0ae3865002934b5d95a6453bd58e8d6 Mon Sep 17 00:00:00 2001 From: stephanmg Date: Tue, 8 Jul 2025 12:51:17 +0200 Subject: [PATCH 2/4] Renaming Zhao. --- .../SBML_Zhao_QuantBiol2020.xml | 1585 ----------------- .../Zhao_QuantBiol2020.yaml | 2 +- 2 files changed, 1 insertion(+), 1586 deletions(-) delete mode 100644 Benchmark-Models/Zhao_QuantBiol2020/SBML_Zhao_QuantBiol2020.xml diff --git a/Benchmark-Models/Zhao_QuantBiol2020/SBML_Zhao_QuantBiol2020.xml b/Benchmark-Models/Zhao_QuantBiol2020/SBML_Zhao_QuantBiol2020.xml deleted file mode 100644 index d1b80e55..00000000 --- a/Benchmark-Models/Zhao_QuantBiol2020/SBML_Zhao_QuantBiol2020.xml +++ /dev/null @@ -1,1585 +0,0 @@ - - - - - - - 
Background - The coronavirus disease 2019 (COVID-19) is rapidly spreading in China and more than 30 countries over last two months. COVID-19 has multiple characteristics distinct from other infectious diseases, including high infectivity during incubation, time delay between real dynamics and daily observed number of confirmed cases, and the intervention effects of implemented quarantine and control measures. Methods - We develop a Susceptible, Un-quanrantined infected, Quarantined infected, Confirmed infected (SUQC) model to characterize the dynamics of COVID-19 and explicitly parameterize the intervention effects of control measures, which is more suitable for analysis than other existing epidemic models. Results - The SUQC model is applied to the daily released data of the confirmed infections to analyze the outbreak of COVID-19 in Wuhan, Hubei (excluding Wuhan), China (excluding Hubei) and four first-tier cities of China. We found that, before January 30, 2020, all these regions except Beijing had a reproductive number R > 1, and after January 30, all regions had a reproductive number R lesser than 1, indicating that the quarantine and control measures are effective in preventing the spread of COVID-19. The confirmation rate of Wuhan estimated by our model is 0.0643, substantially lower than that of Hubei excluding Wuhan (0.1914), and that of China excluding Hubei (0.2189), but it jumps to 0.3229 after February 12 when clinical evidence was adopted in new diagnosis guidelines. The number of unquarantined infected cases in Wuhan on February 12, 2020 is estimated to be 3,509 and declines to 334 on February 21, 2020. After fitting the model with data as of February 21, 2020, we predict that the end time of COVID-19 in Wuhan and Hubei is around late March, around mid March for China excluding Hubei, and before early March 2020 for the four tier-one cities. A total of 80,511 individuals are estimated to be infected in China, among which 49,510 are from Wuhan, 17,679 from Hubei (excluding Wuhan), and the rest 13,322 from other regions of China (excluding Hubei). Note that the estimates are from a deterministic ODE model and should be interpreted with some uncertainty. Conclusions - We suggest that rigorous quarantine and control measures should be kept before early March in Beijing, Shanghai, Guangzhou and Shenzhen, and before late March in Hubei. The model can also be useful to predict the trend of epidemic and provide quantitative guide for other countries at high risk of outbreak, such as South Korea, Japan, Italy and Iran.
- - - - - - - - - - Ramachandran - Kausthubh - - kramachandran@ebi.ac.uk - - EMBL-EBI - - - - - - 2020-08-26T10:14:39Z - - - 2020-08-26T10:14:39Z - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2020-08-26T10:14:39Z - - - - - kramachandran@ebi.ac.uk - - - Ramachandran - Kausthubh - - - - - EMBL-EBI - - - - - - - - - - - - - - - - - - 2020-08-26T09:17:34Z - - - - - - - - - - alpha - - - S - - - U - - - N - - - - - - alpha - S - U - - N - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2020-08-26T10:14:57Z - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2020-08-26T10:15:02Z - - - - - - - - - - - - - 
Wuhan - initial values
-Stage I - 258
-Stage II - 15270
-Stage III - 4000
-
-Hubei - initial values
-Stage I - 270
-Stage II - 5700
-
-China - initial values
-Stage I - 291 (Set model initial time to -30. Keep it at 0 for everything else)
-Stage II - 2800
- - - - - - - - - - - - - - - - - - - - - - - 2020-08-26T10:15:04Z - - - - - - - - - - - - - 
Wuhan - initial values
-Stage I - 0
-Stage II - 0
-Stage III - 5000
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-Hubei - initial values
-Stage I - 0
-Stage II - 1500
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-China - initial values
-Stage I - 0 (Set model initial time to -30 for Stage I alone. Keep it at 0 for everything else)
-Stage II - 2000
- - - - - - - - - - - - - - - - - - - - - - - - - - - - 2020-08-26T10:15:06Z - - - - - - - - - - - - - - 
Wuhan - initial values
-Stage I - 258
-Stage II - 2000
-Stage III - 36000
-
-Hubei - initial values
-Stage I - 0
-Stage II - 1600
-
-China - initial values
-Stage I - 0 (Set model initial time to -30. Keep it at 0 for everything else)
-Stage II - 4000
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2020-08-26T12:42:49Z - - - - - - - - - - - - - - - 2020-08-26T12:42:54Z - - - - - - - - - - - - Total_Pop - - - - - - - - - Trigger_Wuhan - - - - - Trigger_Stage_I - 258 - - - - Trigger_Stage_II - 15270 - - - - Trigger_Stage_III - 4000 - - - - - - Trigger_Hubei - - - - - Trigger_Stage_I - 270 - - - - Trigger_Stage_II - 5700 - - - - - - Trigger_China - - - - - Trigger_Stage_I - 291 - - - - Trigger_Stage_II - 2800 - - - - - - - - - - - - - Trigger_Wuhan - - - - - Trigger_Stage_I - 0 - - - - Trigger_Stage_II - 0 - - - - Trigger_Stage_III - 5000 - - - - - - Trigger_Hubei - - - - - Trigger_Stage_I - 0 - - - - Trigger_Stage_II - 1500 - - - - - - Trigger_China - - - - - Trigger_Stage_I - 0 - - - - Trigger_Stage_II - 2000 - - - - - - - - - - - - - Trigger_Wuhan - - - - - Trigger_Stage_I - 258 - - - - Trigger_Stage_II - 2000 - - - - Trigger_Stage_III - 36000 - - - - - - Trigger_Hubei - - - - - Trigger_Stage_I - 0 - - - - Trigger_Stage_II - 1600 - - - - - - Trigger_China - - - - - Trigger_Stage_I - 0 - - - - Trigger_Stage_II - 4000 - - - - - - - - - - - - - Confirmed_Infected - Quarantined_Infected - Unquarantined_Infected - - - - - - - - - - Trigger_Wuhan - - - - - Trigger_Stage_I - gamma_1_Stage_I_Wuhan - - - - Trigger_Stage_II - gamma_1_Stage_II_Wuhan - - - - Trigger_Stage_III - gamma_1_Stage_III_Wuhan - - - - - - Trigger_Hubei - - - - - Trigger_Stage_I - gamma_1_Stage_I_Hubei - - - - Trigger_Stage_II - gamma_1_Stage_II_Hubei - - - - - - Trigger_China - - - - - Trigger_Stage_I - gamma_1_Stage_I_China - - - - Trigger_Stage_II - gamma_1_Stage_II_China - - - - - - - - - - - - - Trigger_Wuhan - Total_Pop_Wuhan - - - - Trigger_Hubei - Total_Pop_Hubei - - - - Trigger_China - Total_Pop_China - - - - - - - - - - - Trigger_Wuhan - - - - - Trigger_Stage_I - gamma_2_Stage_I_Wuhan - - - - Trigger_Stage_II - gamma_2_Stage_II_Wuhan - - - - Trigger_Stage_III - gamma_2_Stage_III_Wuhan - - - - - - Trigger_Hubei - - - - - Trigger_Stage_I - gamma_2_Stage_I_Hubei - - - - Trigger_Stage_II - gamma_2_Stage_II_Hubei - - - - - - Trigger_China - - - - - Trigger_Stage_I - gamma_2_Stage_I_China - - - - Trigger_Stage_II - gamma_2_Stage_II_China - - - - - - - - - - - gamma_2 - - - - - 1 - gamma_2 - - sigma - - - - - - - - - - - Trigger_Wuhan - - - - - Trigger_Stage_I - R_Stage_I_Wuhan - - - - Trigger_Stage_II - R_Stage_II_Wuhan - - - - Trigger_Stage_III - R_Stage_III_Wuhan - - - - - - Trigger_Hubei - - - - - Trigger_Stage_I - R_Stage_I_Hubei - - - - Trigger_Stage_II - R_Stage_II_Hubei - - - - - - Trigger_China - - - - - Trigger_Stage_I - R_Stage_I_China - - - - Trigger_Stage_II - R_Stage_II_China - - - - - - - - - - - R - gamma_1 - - - - - - - - - - - - - - - - - - - - - - - - - - - 2020-08-26T10:15:35Z - - - - - - - - - - - - - - - - - - - China - - Rate_Law_for_R1 - alpha - Susceptible - Unquarantined_Infected - Total_Pop - - - - - - - - - - - - - - - - - - - - - - - - - - - 2020-08-26T10:15:37Z - - - - - - - - - - - - - - - - - - - China - gamma_1 - Unquarantined_Infected - - - - - - - - - - - - - - - - - - - - - - - - - - 2020-08-26T10:15:38Z - - - - - - - - - - - - - - - - - - - China - beta - Quarantined_Infected - - - - - - - diff --git a/Benchmark-Models/Zhao_QuantBiol2020/Zhao_QuantBiol2020.yaml b/Benchmark-Models/Zhao_QuantBiol2020/Zhao_QuantBiol2020.yaml index 13c66049..dfa84884 100644 --- a/Benchmark-Models/Zhao_QuantBiol2020/Zhao_QuantBiol2020.yaml +++ b/Benchmark-Models/Zhao_QuantBiol2020/Zhao_QuantBiol2020.yaml @@ -8,7 +8,7 @@ problems: observable_files: - observable_Zhao_QuantBiol2020.tsv sbml_files: - - SBML_Zhao_QuantBiol2020.xml + - model_Zhao_QuantBiol2020.xml visualization_files: - visualizationSpecification_Zhao_QuantBiol2020.tsv From 199f30af0cd0697e0abf51c93ff4681849daa638 Mon Sep 17 00:00:00 2001 From: Stephan Grein Date: Tue, 8 Jul 2025 12:51:32 +0200 Subject: [PATCH 3/4] Adding renamed XML files. --- ...el_Okuonghae_ChaosSolitonsFractals2020.xml | 934 ++++++++++ .../model_Zhao_QuantBiol2020.xml | 1585 +++++++++++++++++ 2 files changed, 2519 insertions(+) create mode 100644 Benchmark-Models/Okuonghae_ChaosSolitonsFractals2020/model_Okuonghae_ChaosSolitonsFractals2020.xml create mode 100644 Benchmark-Models/Zhao_QuantBiol2020/model_Zhao_QuantBiol2020.xml diff --git a/Benchmark-Models/Okuonghae_ChaosSolitonsFractals2020/model_Okuonghae_ChaosSolitonsFractals2020.xml b/Benchmark-Models/Okuonghae_ChaosSolitonsFractals2020/model_Okuonghae_ChaosSolitonsFractals2020.xml new file mode 100644 index 00000000..3256f99a --- /dev/null +++ b/Benchmark-Models/Okuonghae_ChaosSolitonsFractals2020/model_Okuonghae_ChaosSolitonsFractals2020.xml @@ -0,0 +1,934 @@ + + + + + + + + + + + 2020-11-13T14:20:23Z + + + + + + + + + + + + + + + + + + + + + + + + 2020-11-16T11:16:14Z + + + + + + + + + + k1 + + + k2 + + + substrate + + + + k1 + k2 + substrate + + + + + + + + + + + + 2020-11-16T11:17:52Z + + + + + + + + + + k1 + + + k2 + + + substrate + + + + k1 + + + 1 + k2 + + substrate + + + + + + + + + + + + + + + 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a/Benchmark-Models/Zhao_QuantBiol2020/model_Zhao_QuantBiol2020.xml b/Benchmark-Models/Zhao_QuantBiol2020/model_Zhao_QuantBiol2020.xml new file mode 100644 index 00000000..d1b80e55 --- /dev/null +++ b/Benchmark-Models/Zhao_QuantBiol2020/model_Zhao_QuantBiol2020.xml @@ -0,0 +1,1585 @@ + + + + + + + 
Background - The coronavirus disease 2019 (COVID-19) is rapidly spreading in China and more than 30 countries over last two months. COVID-19 has multiple characteristics distinct from other infectious diseases, including high infectivity during incubation, time delay between real dynamics and daily observed number of confirmed cases, and the intervention effects of implemented quarantine and control measures. Methods - We develop a Susceptible, Un-quanrantined infected, Quarantined infected, Confirmed infected (SUQC) model to characterize the dynamics of COVID-19 and explicitly parameterize the intervention effects of control measures, which is more suitable for analysis than other existing epidemic models. Results - The SUQC model is applied to the daily released data of the confirmed infections to analyze the outbreak of COVID-19 in Wuhan, Hubei (excluding Wuhan), China (excluding Hubei) and four first-tier cities of China. We found that, before January 30, 2020, all these regions except Beijing had a reproductive number R > 1, and after January 30, all regions had a reproductive number R lesser than 1, indicating that the quarantine and control measures are effective in preventing the spread of COVID-19. The confirmation rate of Wuhan estimated by our model is 0.0643, substantially lower than that of Hubei excluding Wuhan (0.1914), and that of China excluding Hubei (0.2189), but it jumps to 0.3229 after February 12 when clinical evidence was adopted in new diagnosis guidelines. The number of unquarantined infected cases in Wuhan on February 12, 2020 is estimated to be 3,509 and declines to 334 on February 21, 2020. After fitting the model with data as of February 21, 2020, we predict that the end time of COVID-19 in Wuhan and Hubei is around late March, around mid March for China excluding Hubei, and before early March 2020 for the four tier-one cities. A total of 80,511 individuals are estimated to be infected in China, among which 49,510 are from Wuhan, 17,679 from Hubei (excluding Wuhan), and the rest 13,322 from other regions of China (excluding Hubei). Note that the estimates are from a deterministic ODE model and should be interpreted with some uncertainty. Conclusions - We suggest that rigorous quarantine and control measures should be kept before early March in Beijing, Shanghai, Guangzhou and Shenzhen, and before late March in Hubei. The model can also be useful to predict the trend of epidemic and provide quantitative guide for other countries at high risk of outbreak, such as South Korea, Japan, Italy and Iran.
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Wuhan - initial values
+Stage I - 258
+Stage II - 15270
+Stage III - 4000
+
+Hubei - initial values
+Stage I - 270
+Stage II - 5700
+
+China - initial values
+Stage I - 291 (Set model initial time to -30. Keep it at 0 for everything else)
+Stage II - 2800
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Wuhan - initial values
+Stage I - 0
+Stage II - 0
+Stage III - 5000
+
+Hubei - initial values
+Stage I - 0
+Stage II - 1500
+
+China - initial values
+Stage I - 0 (Set model initial time to -30 for Stage I alone. Keep it at 0 for everything else)
+Stage II - 2000
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + 2020-08-26T10:15:06Z + + + + + + + + + + + + + + 
Wuhan - initial values
+Stage I - 258
+Stage II - 2000
+Stage III - 36000
+
+Hubei - initial values
+Stage I - 0
+Stage II - 1600
+
+China - initial values
+Stage I - 0 (Set model initial time to -30. Keep it at 0 for everything else)
+Stage II - 4000
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Unquarantined_Infected + + + + + + + + + + + + + + + + + + + + + + + + + + 2020-08-26T10:15:38Z + + + + + + + + + + + + + + + + + + + China + beta + Quarantined_Infected + + + + + + + From b7af7a091e4d3879d4fb4e271230c7aeb3d0428f Mon Sep 17 00:00:00 2001 From: Stephan Grein Date: Tue, 8 Jul 2025 12:53:09 +0200 Subject: [PATCH 4/4] Renaming Giordano. --- Benchmark-Models/Giordano_Nature2020/Giordano_Nature2020.yaml | 2 +- ...rdano_Nature2020_model.xml => model_Giordano_Nature2020.xml} | 0 2 files changed, 1 insertion(+), 1 deletion(-) rename Benchmark-Models/Giordano_Nature2020/{Giordano_Nature2020_model.xml => model_Giordano_Nature2020.xml} (100%) diff --git a/Benchmark-Models/Giordano_Nature2020/Giordano_Nature2020.yaml b/Benchmark-Models/Giordano_Nature2020/Giordano_Nature2020.yaml index f8c46e13..0680268c 100644 --- a/Benchmark-Models/Giordano_Nature2020/Giordano_Nature2020.yaml +++ b/Benchmark-Models/Giordano_Nature2020/Giordano_Nature2020.yaml @@ -8,6 +8,6 @@ problems: observable_files: - observables_Giordano_Nature2020.tsv sbml_files: - - Giordano_Nature2020_model.xml + - model_Giordano_Nature2020.xml visualization_files: - visualizationSpecification_Giordano_Nature2020.tsv diff --git a/Benchmark-Models/Giordano_Nature2020/Giordano_Nature2020_model.xml b/Benchmark-Models/Giordano_Nature2020/model_Giordano_Nature2020.xml similarity index 100% rename from Benchmark-Models/Giordano_Nature2020/Giordano_Nature2020_model.xml rename to Benchmark-Models/Giordano_Nature2020/model_Giordano_Nature2020.xml