From 9f17a89d806c7bb80a65c7819c1bcc5cab193368 Mon Sep 17 00:00:00 2001 From: dilpath Date: Thu, 10 Feb 2022 01:03:14 +0100 Subject: [PATCH 1/6] fix model ids, model names, and references --- .../model_Alkan_SciSignal2018.xml | 2 +- .../Bachmann_MSB2011/model_Bachmann_MSB2011.xml | 2 +- .../model_Beer_MolBioSystems2014.xml | 2 +- .../Bertozzi_PNAS2020/model_Bertozzi_PNAS2020.xml | 2 +- .../model_Borghans_BiophysChem1997.xml | 2 +- .../Brannmark_JBC2010/model_Brannmark_JBC2010.xml | 2 +- .../Chen_MSB2009/model_Chen_MSB2009.xml | 2 +- .../model_Crauste_CellSystems2017.xml | 2 +- .../Elowitz_Nature2000/model_Elowitz_Nature2000.xml | 2 +- .../Fiedler_BMC2016/model_Fiedler_BMC2016.xml | 2 +- .../model_Fujita_SciSignal2010.xml | 13 ++++++++++++- .../Giordano_Nature2020_model.xml | 2 +- .../Isensee_JCB2018/model_Isensee_JCB2018.xml | 2 +- .../model_Lucarelli_CellSystems2018.xml | 2 +- .../Okuonghae_ChaosSolitonsFractals2020_model.xml | 11 ++++++++++- .../Oliveira_NatCommun2021_model.xml | 13 ++++++++++++- .../model_Perelson_Science1996.xml | 2 +- .../Rahman_MBS2016/model_Rahman_MBS2016.xml | 11 +++++++++++ .../Raimundez_PCB2020/model_Raimundez_PCB2020.xml | 11 +++++++++++ .../model_SalazarCavazos_MBoC2020.xml | 11 +++++++++++ .../Schwen_PONE2014/model_Schwen_PONE2014.xml | 2 +- .../Sneyd_PNAS2002/model_Sneyd_PNAS2002.xml | 2 +- .../Weber_BMC2015/model_Weber_BMC2015.xml | 2 +- .../Zhao_QuantBiol2020/SBML_Zhao_QuantBiol2020.xml | 2 +- .../Zheng_PNAS2012/model_Zheng_PNAS2012.xml | 2 +- 25 files changed, 86 insertions(+), 22 deletions(-) diff --git a/Benchmark-Models/Alkan_SciSignal2018/model_Alkan_SciSignal2018.xml b/Benchmark-Models/Alkan_SciSignal2018/model_Alkan_SciSignal2018.xml index 4cd1b5c..a7bf3e7 100644 --- a/Benchmark-Models/Alkan_SciSignal2018/model_Alkan_SciSignal2018.xml +++ b/Benchmark-Models/Alkan_SciSignal2018/model_Alkan_SciSignal2018.xml @@ -1,6 +1,6 @@ - + 
PEtab implementation of the model from Alkan et al. (2018), Science Signaling  24 Jul 2018: Vol. 11, Issue 540, eaat0229
diff --git a/Benchmark-Models/Bachmann_MSB2011/model_Bachmann_MSB2011.xml b/Benchmark-Models/Bachmann_MSB2011/model_Bachmann_MSB2011.xml index 3fb5065..1dd7672 100644 --- a/Benchmark-Models/Bachmann_MSB2011/model_Bachmann_MSB2011.xml +++ b/Benchmark-Models/Bachmann_MSB2011/model_Bachmann_MSB2011.xml @@ -1,6 +1,6 @@ - + 
PEtab implementation of the model from Bachmann et al. (2011), Mol Syst Biol. ; 7: 516.
diff --git a/Benchmark-Models/Beer_MolBioSystems2014/model_Beer_MolBioSystems2014.xml b/Benchmark-Models/Beer_MolBioSystems2014/model_Beer_MolBioSystems2014.xml index 2ecaf21..a9b8df9 100644 --- a/Benchmark-Models/Beer_MolBioSystems2014/model_Beer_MolBioSystems2014.xml +++ b/Benchmark-Models/Beer_MolBioSystems2014/model_Beer_MolBioSystems2014.xml @@ -1,6 +1,6 @@ - + 
PEtab implementation of the model from Beer et al. (2014), Mol Biosyst.;10(7):1709-18
diff --git a/Benchmark-Models/Bertozzi_PNAS2020/model_Bertozzi_PNAS2020.xml b/Benchmark-Models/Bertozzi_PNAS2020/model_Bertozzi_PNAS2020.xml index 805b267..2029f83 100644 --- a/Benchmark-Models/Bertozzi_PNAS2020/model_Bertozzi_PNAS2020.xml +++ b/Benchmark-Models/Bertozzi_PNAS2020/model_Bertozzi_PNAS2020.xml @@ -1,7 +1,7 @@ - + 
Bertozzi2020 - SIR model of scenarios of COVID-19 spread in CA and NY
diff --git a/Benchmark-Models/Borghans_BiophysChem1997/model_Borghans_BiophysChem1997.xml b/Benchmark-Models/Borghans_BiophysChem1997/model_Borghans_BiophysChem1997.xml
index 4057ecb..86105ac 100644
--- a/Benchmark-Models/Borghans_BiophysChem1997/model_Borghans_BiophysChem1997.xml
+++ b/Benchmark-Models/Borghans_BiophysChem1997/model_Borghans_BiophysChem1997.xml
@@ -1,6 +1,6 @@
 
 
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PEtab implementation of the model from Borghans et al. (1997), Biophysical Chemistry 66(1) 25-41

diff --git a/Benchmark-Models/Brannmark_JBC2010/model_Brannmark_JBC2010.xml b/Benchmark-Models/Brannmark_JBC2010/model_Brannmark_JBC2010.xml
index e0fdbb5..aa76abf 100644
--- a/Benchmark-Models/Brannmark_JBC2010/model_Brannmark_JBC2010.xml
+++ b/Benchmark-Models/Brannmark_JBC2010/model_Brannmark_JBC2010.xml
@@ -1,6 +1,6 @@
 
 
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PEtab implementation of the model from Brannmark et al. (2010), THE JOURNAL OF BIOLOGICAL CHEMISTRY VOL. 285, NO. 26, pp. 20171–20179, 

diff --git a/Benchmark-Models/Chen_MSB2009/model_Chen_MSB2009.xml b/Benchmark-Models/Chen_MSB2009/model_Chen_MSB2009.xml
index c979730..c361a82 100644
--- a/Benchmark-Models/Chen_MSB2009/model_Chen_MSB2009.xml
+++ b/Benchmark-Models/Chen_MSB2009/model_Chen_MSB2009.xml
@@ -1,6 +1,6 @@
 
 
-  
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PEtab implementation of the model from Chen et al. (2009), Mol Syst Biol. ;5:239

diff --git a/Benchmark-Models/Crauste_CellSystems2017/model_Crauste_CellSystems2017.xml b/Benchmark-Models/Crauste_CellSystems2017/model_Crauste_CellSystems2017.xml
index b7889a9..a5ebb9a 100644
--- a/Benchmark-Models/Crauste_CellSystems2017/model_Crauste_CellSystems2017.xml
+++ b/Benchmark-Models/Crauste_CellSystems2017/model_Crauste_CellSystems2017.xml
@@ -1,6 +1,6 @@
 
 
-  
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PEtab implementation of the model from Crauste et al. (2017), Cell Syst. 2017 Mar 22;4(3):306-317.e4

diff --git a/Benchmark-Models/Elowitz_Nature2000/model_Elowitz_Nature2000.xml b/Benchmark-Models/Elowitz_Nature2000/model_Elowitz_Nature2000.xml
index 6df4328..3046b4e 100644
--- a/Benchmark-Models/Elowitz_Nature2000/model_Elowitz_Nature2000.xml
+++ b/Benchmark-Models/Elowitz_Nature2000/model_Elowitz_Nature2000.xml
@@ -1,6 +1,6 @@
 
 
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PEtab implementation of the model from Elowitz et al. (2000), Nature. 2000 Jan 20;403(6767):335-8

diff --git a/Benchmark-Models/Fiedler_BMC2016/model_Fiedler_BMC2016.xml b/Benchmark-Models/Fiedler_BMC2016/model_Fiedler_BMC2016.xml
index 70d7071..bef7143 100644
--- a/Benchmark-Models/Fiedler_BMC2016/model_Fiedler_BMC2016.xml
+++ b/Benchmark-Models/Fiedler_BMC2016/model_Fiedler_BMC2016.xml
@@ -1,6 +1,6 @@
 
 
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PEtab implementation of the model from Fiedler et al. (2016), BMC Systems Biology volume 10, Article number: 80

diff --git a/Benchmark-Models/Fujita_SciSignal2010/model_Fujita_SciSignal2010.xml b/Benchmark-Models/Fujita_SciSignal2010/model_Fujita_SciSignal2010.xml
index 008fd6e..d904120 100644
--- a/Benchmark-Models/Fujita_SciSignal2010/model_Fujita_SciSignal2010.xml
+++ b/Benchmark-Models/Fujita_SciSignal2010/model_Fujita_SciSignal2010.xml
@@ -1,6 +1,17 @@
 
 
-  
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diff --git a/Benchmark-Models/Giordano_Nature2020/Giordano_Nature2020_model.xml b/Benchmark-Models/Giordano_Nature2020/Giordano_Nature2020_model.xml
index c597159..0e02441 100644
--- a/Benchmark-Models/Giordano_Nature2020/Giordano_Nature2020_model.xml
+++ b/Benchmark-Models/Giordano_Nature2020/Giordano_Nature2020_model.xml
@@ -1,7 +1,7 @@
 
 
 
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This is a model created on COPASI 4.27 (Build 217) which reproduces the Figures 2b, 2d, 3b, 3d, 4b, 4d in the article - https://www.nature.com/articles/s41591-020-0883-7
diff --git a/Benchmark-Models/Isensee_JCB2018/model_Isensee_JCB2018.xml b/Benchmark-Models/Isensee_JCB2018/model_Isensee_JCB2018.xml
index 5ce0279..c575f94 100644
--- a/Benchmark-Models/Isensee_JCB2018/model_Isensee_JCB2018.xml
+++ b/Benchmark-Models/Isensee_JCB2018/model_Isensee_JCB2018.xml
@@ -1,6 +1,6 @@
 
 
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PEtab implementation of the model from Isensee et al. (2018), The Journal of Cell Biology Jun 2018, 217 (6) 2167-2184

diff --git a/Benchmark-Models/Lucarelli_CellSystems2018/model_Lucarelli_CellSystems2018.xml b/Benchmark-Models/Lucarelli_CellSystems2018/model_Lucarelli_CellSystems2018.xml
index a4153f3..619e513 100644
--- a/Benchmark-Models/Lucarelli_CellSystems2018/model_Lucarelli_CellSystems2018.xml
+++ b/Benchmark-Models/Lucarelli_CellSystems2018/model_Lucarelli_CellSystems2018.xml
@@ -1,6 +1,6 @@
 
 
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PEtab implementation of the model from Lucarelli et al. (2018), Cell Syst. 2018 Jan 24;6(1):75-89.e11

diff --git a/Benchmark-Models/Okuonghae_ChaosSolitonsFractals2020/Okuonghae_ChaosSolitonsFractals2020_model.xml b/Benchmark-Models/Okuonghae_ChaosSolitonsFractals2020/Okuonghae_ChaosSolitonsFractals2020_model.xml
index ce5f9bb..ed0cb01 100644
--- a/Benchmark-Models/Okuonghae_ChaosSolitonsFractals2020/Okuonghae_ChaosSolitonsFractals2020_model.xml
+++ b/Benchmark-Models/Okuonghae_ChaosSolitonsFractals2020/Okuonghae_ChaosSolitonsFractals2020_model.xml
@@ -1,7 +1,7 @@
 
 
 
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diff --git a/Benchmark-Models/Oliveira_NatCommun2021/Oliveira_NatCommun2021_model.xml b/Benchmark-Models/Oliveira_NatCommun2021/Oliveira_NatCommun2021_model.xml
index 94db7ca..b6b6b45 100644
--- a/Benchmark-Models/Oliveira_NatCommun2021/Oliveira_NatCommun2021_model.xml
+++ b/Benchmark-Models/Oliveira_NatCommun2021/Oliveira_NatCommun2021_model.xml
@@ -1,7 +1,7 @@
 
 
 
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Oliveira, Nature 2021.
@@ -14,6 +14,17 @@ To model with a two-step transmission rate, set 'beta_2_multiplier' = 0. To mode
 	

       
     
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diff --git a/Benchmark-Models/Perelson_Science1996/model_Perelson_Science1996.xml b/Benchmark-Models/Perelson_Science1996/model_Perelson_Science1996.xml
index 0987585..39edc76 100644
--- a/Benchmark-Models/Perelson_Science1996/model_Perelson_Science1996.xml
+++ b/Benchmark-Models/Perelson_Science1996/model_Perelson_Science1996.xml
@@ -1,6 +1,6 @@
 
 
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PEtab implementation of the model from Perelson et al. (1996), Science  15 Mar 1996: Vol. 271, Issue 5255, pp. 1582-1586

diff --git a/Benchmark-Models/Rahman_MBS2016/model_Rahman_MBS2016.xml b/Benchmark-Models/Rahman_MBS2016/model_Rahman_MBS2016.xml
index 2eff0bd..98afba0 100644
--- a/Benchmark-Models/Rahman_MBS2016/model_Rahman_MBS2016.xml
+++ b/Benchmark-Models/Rahman_MBS2016/model_Rahman_MBS2016.xml
@@ -1,6 +1,17 @@
 
 
   
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diff --git a/Benchmark-Models/Raimundez_PCB2020/model_Raimundez_PCB2020.xml b/Benchmark-Models/Raimundez_PCB2020/model_Raimundez_PCB2020.xml
index 53556b4..e65bc31 100755
--- a/Benchmark-Models/Raimundez_PCB2020/model_Raimundez_PCB2020.xml
+++ b/Benchmark-Models/Raimundez_PCB2020/model_Raimundez_PCB2020.xml
@@ -1,6 +1,17 @@
 
 
   
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diff --git a/Benchmark-Models/SalazarCavazos_MBoC2020/model_SalazarCavazos_MBoC2020.xml b/Benchmark-Models/SalazarCavazos_MBoC2020/model_SalazarCavazos_MBoC2020.xml
index 15daaee..9c72843 100644
--- a/Benchmark-Models/SalazarCavazos_MBoC2020/model_SalazarCavazos_MBoC2020.xml
+++ b/Benchmark-Models/SalazarCavazos_MBoC2020/model_SalazarCavazos_MBoC2020.xml
@@ -1,6 +1,17 @@
 
 
   
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diff --git a/Benchmark-Models/Schwen_PONE2014/model_Schwen_PONE2014.xml b/Benchmark-Models/Schwen_PONE2014/model_Schwen_PONE2014.xml
index 40e7300..1760145 100644
--- a/Benchmark-Models/Schwen_PONE2014/model_Schwen_PONE2014.xml
+++ b/Benchmark-Models/Schwen_PONE2014/model_Schwen_PONE2014.xml
@@ -1,6 +1,6 @@
 
 
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PEtab implementation of the model from Schwen et al. (2015), PLoS One, 10, e0133653

diff --git a/Benchmark-Models/Sneyd_PNAS2002/model_Sneyd_PNAS2002.xml b/Benchmark-Models/Sneyd_PNAS2002/model_Sneyd_PNAS2002.xml
index d1e8395..6e6c95b 100644
--- a/Benchmark-Models/Sneyd_PNAS2002/model_Sneyd_PNAS2002.xml
+++ b/Benchmark-Models/Sneyd_PNAS2002/model_Sneyd_PNAS2002.xml
@@ -1,6 +1,6 @@
 
 
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PEtab implementation of the model from Sneyd et al. (2002), PNAS February 19, 2002 99 (4) 2398-2403

diff --git a/Benchmark-Models/Weber_BMC2015/model_Weber_BMC2015.xml b/Benchmark-Models/Weber_BMC2015/model_Weber_BMC2015.xml
index 22219cd..58baddd 100644
--- a/Benchmark-Models/Weber_BMC2015/model_Weber_BMC2015.xml
+++ b/Benchmark-Models/Weber_BMC2015/model_Weber_BMC2015.xml
@@ -1,6 +1,6 @@
 
 
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PEtab implementation of the model from Weber et al. (2015), BMC Syst. Biol., 9, 9

diff --git a/Benchmark-Models/Zhao_QuantBiol2020/SBML_Zhao_QuantBiol2020.xml b/Benchmark-Models/Zhao_QuantBiol2020/SBML_Zhao_QuantBiol2020.xml
index 3803da3..d1b80e5 100644
--- a/Benchmark-Models/Zhao_QuantBiol2020/SBML_Zhao_QuantBiol2020.xml
+++ b/Benchmark-Models/Zhao_QuantBiol2020/SBML_Zhao_QuantBiol2020.xml
@@ -1,7 +1,7 @@
 
 
 
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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.

diff --git a/Benchmark-Models/Zheng_PNAS2012/model_Zheng_PNAS2012.xml b/Benchmark-Models/Zheng_PNAS2012/model_Zheng_PNAS2012.xml
index 01c5ab4..a720229 100644
--- a/Benchmark-Models/Zheng_PNAS2012/model_Zheng_PNAS2012.xml
+++ b/Benchmark-Models/Zheng_PNAS2012/model_Zheng_PNAS2012.xml
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PEtab implementation of the model from Zheng et al. (2012), Proc. Natl. Acad. Sci. USA, 109, 13549–13554


From c5449ed217d98b836f22efe673e25aeb7bbd9c5b Mon Sep 17 00:00:00 2001
From: dilpath 
Date: Thu, 10 Feb 2022 01:07:18 +0100
Subject: [PATCH 2/6] typo

---
 .../Oliveira_NatCommun2021/Oliveira_NatCommun2021_model.xml     | 2 --
 1 file changed, 2 deletions(-)

diff --git a/Benchmark-Models/Oliveira_NatCommun2021/Oliveira_NatCommun2021_model.xml b/Benchmark-Models/Oliveira_NatCommun2021/Oliveira_NatCommun2021_model.xml
index b6b6b45..6b3d240 100644
--- a/Benchmark-Models/Oliveira_NatCommun2021/Oliveira_NatCommun2021_model.xml
+++ b/Benchmark-Models/Oliveira_NatCommun2021/Oliveira_NatCommun2021_model.xml
@@ -24,8 +24,6 @@ To model with a two-step transmission rate, set 'beta_2_multiplier' = 0. To mode
           
         
       
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From 47716dbaddc7fc9dfdf6aa843e8849516b7891ac Mon Sep 17 00:00:00 2001
From: dilpath 
Date: Thu, 10 Feb 2022 01:15:35 +0100
Subject: [PATCH 3/6] update overview table

---
 README.md           | 14 +++++++-------
 scripts/_helpers.py |  1 +
 2 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/README.md b/README.md
index bc14522..ab70bf9 100644
--- a/README.md
+++ b/README.md
@@ -5,7 +5,7 @@ Contributions to the collection are very welcome. For this, please create a new
 
 ## Overview
 
-| Model ID                                                                                     |   Conditions |   Estimated Parameters |   Events |   Measurements |   Observables |   Species | References                                                                                                                                                                |
+| PEtab Problem ID                                                                             |   Conditions |   Estimated Parameters |   Events |   Measurements |   Observables |   Species | References                                                                                                                                                                |
 |:---------------------------------------------------------------------------------------------|-------------:|-----------------------:|---------:|---------------:|--------------:|----------:|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
 | [Alkan_SciSignal2018](Benchmark-Models/Alkan_SciSignal2018/)                                 |           73 |                     56 |        0 |           1733 |            12 |        36 | [\[1\]](http://identifiers.org/doi/10.1126/scisignal.aat0229)                                                                                                             |
 | [Bachmann_MSB2011](Benchmark-Models/Bachmann_MSB2011/)                                       |           36 |                    113 |        0 |            541 |            20 |        25 | [\[1\]](http://identifiers.org/doi/10.1038/msb.2011.50)                                                                                                                   |
@@ -20,17 +20,17 @@ Contributions to the collection are very welcome. For this, please create a new
 | [Crauste_CellSystems2017](Benchmark-Models/Crauste_CellSystems2017/)                         |            1 |                     12 |        0 |             21 |             4 |         5 | [\[1\]](http://identifiers.org/doi/10.1016/j.cels.2017.01.014)                                                                                                            |
 | [Elowitz_Nature2000](Benchmark-Models/Elowitz_Nature2000/)                                   |            1 |                     21 |        0 |             58 |             1 |         8 | [\[1\]](http://identifiers.org/doi/10.1038/35002125)                                                                                                                      |
 | [Fiedler_BMC2016](Benchmark-Models/Fiedler_BMC2016/)                                         |            3 |                     22 |        0 |             72 |             2 |         6 | [\[1\]](http://identifiers.org/doi/10.1186/s12918-016-0319-7)                                                                                                             |
-| [Fujita_SciSignal2010](Benchmark-Models/Fujita_SciSignal2010/)                               |            6 |                     19 |        0 |            144 |             3 |         9 |                                                                                                                                                                           |
+| [Fujita_SciSignal2010](Benchmark-Models/Fujita_SciSignal2010/)                               |            6 |                     19 |        0 |            144 |             3 |         9 | [\[1\]](http://identifiers.org/doi/10.1126/scisignal.2000810)                                                                                                             |
 | [Giordano_Nature2020](Benchmark-Models/Giordano_Nature2020/)                                 |            1 |                     50 |        0 |            313 |             7 |        13 | [\[1\]](http://identifiers.org/pubmed/32322102)                                                                                                                           |
 | [Isensee_JCB2018](Benchmark-Models/Isensee_JCB2018/)                                         |          123 |                     46 |        0 |            687 |             3 |        25 | [\[1\]](http://identifiers.org/doi/10.1083/jcb.201708053)                                                                                                                 |
 | [Laske_PLOSComputBiol2019](Benchmark-Models/Laske_PLOSComputBiol2019/)                       |            3 |                     13 |        0 |             42 |            13 |        41 | [\[1\]](http://identifiers.org/biomodels.db/BIOMD0000000463) [\[2\]](http://identifiers.org/biomodels.db/MODEL1307270000) [\[3\]](http://identifiers.org/pubmed/22593159) |
 | [Lucarelli_CellSystems2018](Benchmark-Models/Lucarelli_CellSystems2018/)                     |           16 |                     84 |        0 |           1755 |            65 |        33 | [\[1\]](http://identifiers.org/doi/10.1016/j.cels.2017.11.010)                                                                                                            |
-| [Okuonghae_ChaosSolitonsFractals2020](Benchmark-Models/Okuonghae_ChaosSolitonsFractals2020/) |            1 |                     16 |        0 |             92 |             2 |         9 |                                                                                                                                                                           |
-| [Oliveira_NatCommun2021](Benchmark-Models/Oliveira_NatCommun2021/)                           |            1 |                     12 |        0 |            120 |             2 |         9 |                                                                                                                                                                           |
+| [Okuonghae_ChaosSolitonsFractals2020](Benchmark-Models/Okuonghae_ChaosSolitonsFractals2020/) |            1 |                     16 |        0 |             92 |             2 |         9 | [\[1\]](http://identifiers.org/doi/10.1016/j.chaos.2020.110032)                                                                                                           |
+| [Oliveira_NatCommun2021](Benchmark-Models/Oliveira_NatCommun2021/)                           |            1 |                     12 |        0 |            120 |             2 |         9 | [\[1\]](http://identifiers.org/doi/10.1038/s41467-020-19798-3)                                                                                                            |
 | [Perelson_Science1996](Benchmark-Models/Perelson_Science1996/)                               |            1 |                      3 |        0 |             16 |             1 |         4 | [\[1\]](http://identifiers.org/doi/10.1126/science.271.5255.1582)                                                                                                         |
-| [Rahman_MBS2016](Benchmark-Models/Rahman_MBS2016/)                                           |            1 |                      9 |        0 |             23 |             1 |         7 |                                                                                                                                                                           |
-| [Raimundez_PCB2020](Benchmark-Models/Raimundez_PCB2020/)                                     |          170 |                    136 |        0 |            627 |            79 |        22 |                                                                                                                                                                           |
-| [SalazarCavazos_MBoC2020](Benchmark-Models/SalazarCavazos_MBoC2020/)                         |            4 |                      6 |        0 |             18 |             3 |        75 |                                                                                                                                                                           |
+| [Rahman_MBS2016](Benchmark-Models/Rahman_MBS2016/)                                           |            1 |                      9 |        0 |             23 |             1 |         7 | [\[1\]](http://identifiers.org/doi/10.1016/j.mbs.2016.07.009)                                                                                                             |
+| [Raimundez_PCB2020](Benchmark-Models/Raimundez_PCB2020/)                                     |          170 |                    136 |        0 |            627 |            79 |        22 | [\[1\]](http://identifiers.org/doi/10.1371/journal.pcbi.1007147)                                                                                                          |
+| [SalazarCavazos_MBoC2020](Benchmark-Models/SalazarCavazos_MBoC2020/)                         |            4 |                      6 |        0 |             18 |             3 |        75 | [\[1\]](http://identifiers.org/doi/10.1091/mbc.E19-09-0548)                                                                                                               |
 | [Schwen_PONE2014](Benchmark-Models/Schwen_PONE2014/)                                         |           19 |                     30 |        0 |            286 |             4 |        11 | [\[1\]](http://identifiers.org/doi/10.1371/journal.pone.0133653)                                                                                                          |
 | [Sneyd_PNAS2002](Benchmark-Models/Sneyd_PNAS2002/)                                           |            9 |                     15 |        0 |            135 |             1 |         6 | [\[1\]](http://identifiers.org/doi/10.1073/pnas.032281999)                                                                                                                |
 | [Weber_BMC2015](Benchmark-Models/Weber_BMC2015/)                                             |            2 |                     36 |        0 |            135 |             8 |         7 | [\[1\]](http://identifiers.org/doi/10.1186/s12918-015-0147-1)                                                                                                             |
diff --git a/scripts/_helpers.py b/scripts/_helpers.py
index 68fc022..f58c937 100644
--- a/scripts/_helpers.py
+++ b/scripts/_helpers.py
@@ -6,3 +6,4 @@
     petab_path.name: benchmark_path / petab_path.name / (petab_path.name + '.yaml')
     for petab_path in benchmark_path.glob('*')
 }
+petab_yamls = {k: petab_yamls[k] for k in sorted(petab_yamls)}

From 28936407552660741da3b8c41448d1faea8e3c74 Mon Sep 17 00:00:00 2001
From: dilpath 
Date: Tue, 15 Feb 2022 11:10:50 +0100
Subject: [PATCH 4/6] rename rdf:about

---
 .../Fujita_SciSignal2010/model_Fujita_SciSignal2010.xml         | 2 +-
 .../Okuonghae_ChaosSolitonsFractals2020_model.xml               | 2 +-
 .../Oliveira_NatCommun2021/Oliveira_NatCommun2021_model.xml     | 2 +-
 Benchmark-Models/Rahman_MBS2016/model_Rahman_MBS2016.xml        | 2 +-
 Benchmark-Models/Raimundez_PCB2020/model_Raimundez_PCB2020.xml  | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/Benchmark-Models/Fujita_SciSignal2010/model_Fujita_SciSignal2010.xml b/Benchmark-Models/Fujita_SciSignal2010/model_Fujita_SciSignal2010.xml
index d904120..2f26142 100644
--- a/Benchmark-Models/Fujita_SciSignal2010/model_Fujita_SciSignal2010.xml
+++ b/Benchmark-Models/Fujita_SciSignal2010/model_Fujita_SciSignal2010.xml
@@ -3,7 +3,7 @@
   
     
       
-        
+        
           
             
               
diff --git a/Benchmark-Models/Okuonghae_ChaosSolitonsFractals2020/Okuonghae_ChaosSolitonsFractals2020_model.xml b/Benchmark-Models/Okuonghae_ChaosSolitonsFractals2020/Okuonghae_ChaosSolitonsFractals2020_model.xml
index ed0cb01..23b5ec5 100644
--- a/Benchmark-Models/Okuonghae_ChaosSolitonsFractals2020/Okuonghae_ChaosSolitonsFractals2020_model.xml
+++ b/Benchmark-Models/Okuonghae_ChaosSolitonsFractals2020/Okuonghae_ChaosSolitonsFractals2020_model.xml
@@ -15,7 +15,7 @@
         
       
       
-        
+        
           
             
               
diff --git a/Benchmark-Models/Oliveira_NatCommun2021/Oliveira_NatCommun2021_model.xml b/Benchmark-Models/Oliveira_NatCommun2021/Oliveira_NatCommun2021_model.xml
index 6b3d240..3a7b7ae 100644
--- a/Benchmark-Models/Oliveira_NatCommun2021/Oliveira_NatCommun2021_model.xml
+++ b/Benchmark-Models/Oliveira_NatCommun2021/Oliveira_NatCommun2021_model.xml
@@ -16,7 +16,7 @@ To model with a two-step transmission rate, set 'beta_2_multiplier' = 0. To mode
     
     
       
-        
+        
           
             
               
diff --git a/Benchmark-Models/Rahman_MBS2016/model_Rahman_MBS2016.xml b/Benchmark-Models/Rahman_MBS2016/model_Rahman_MBS2016.xml
index 98afba0..c9d49af 100644
--- a/Benchmark-Models/Rahman_MBS2016/model_Rahman_MBS2016.xml
+++ b/Benchmark-Models/Rahman_MBS2016/model_Rahman_MBS2016.xml
@@ -3,7 +3,7 @@
   
     
       
-        
+        
           
             
               
diff --git a/Benchmark-Models/Raimundez_PCB2020/model_Raimundez_PCB2020.xml b/Benchmark-Models/Raimundez_PCB2020/model_Raimundez_PCB2020.xml
index e65bc31..2f359a2 100755
--- a/Benchmark-Models/Raimundez_PCB2020/model_Raimundez_PCB2020.xml
+++ b/Benchmark-Models/Raimundez_PCB2020/model_Raimundez_PCB2020.xml
@@ -3,7 +3,7 @@
   
     
       
-        
+        
           
             
               

From da634f5d5dffe3ec25759d44af51dca5f2603763 Mon Sep 17 00:00:00 2001
From: dilpath 
Date: Tue, 15 Feb 2022 11:47:56 +0100
Subject: [PATCH 5/6] rename rdf:about

---
 .../SalazarCavazos_MBoC2020/model_SalazarCavazos_MBoC2020.xml   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Benchmark-Models/SalazarCavazos_MBoC2020/model_SalazarCavazos_MBoC2020.xml b/Benchmark-Models/SalazarCavazos_MBoC2020/model_SalazarCavazos_MBoC2020.xml
index 9c72843..f0eada0 100644
--- a/Benchmark-Models/SalazarCavazos_MBoC2020/model_SalazarCavazos_MBoC2020.xml
+++ b/Benchmark-Models/SalazarCavazos_MBoC2020/model_SalazarCavazos_MBoC2020.xml
@@ -3,7 +3,7 @@
   
     
       
-        
+        
           
             
               

From 55de66d0fe5ba4fd9c06cef5626e88f95507bc63 Mon Sep 17 00:00:00 2001
From: dilpath 
Date: Tue, 15 Feb 2022 11:55:30 +0100
Subject: [PATCH 6/6] restore metaid

---
 .../Okuonghae_ChaosSolitonsFractals2020_model.xml             | 4 ++--
 .../Oliveira_NatCommun2021/Oliveira_NatCommun2021_model.xml   | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/Benchmark-Models/Okuonghae_ChaosSolitonsFractals2020/Okuonghae_ChaosSolitonsFractals2020_model.xml b/Benchmark-Models/Okuonghae_ChaosSolitonsFractals2020/Okuonghae_ChaosSolitonsFractals2020_model.xml
index 23b5ec5..f89eeeb 100644
--- a/Benchmark-Models/Okuonghae_ChaosSolitonsFractals2020/Okuonghae_ChaosSolitonsFractals2020_model.xml
+++ b/Benchmark-Models/Okuonghae_ChaosSolitonsFractals2020/Okuonghae_ChaosSolitonsFractals2020_model.xml
@@ -1,7 +1,7 @@
 
 
 
-  
+  
     
       
         
@@ -15,7 +15,7 @@
         
       
       
-        
+        
           
             
               
diff --git a/Benchmark-Models/Oliveira_NatCommun2021/Oliveira_NatCommun2021_model.xml b/Benchmark-Models/Oliveira_NatCommun2021/Oliveira_NatCommun2021_model.xml
index 3a7b7ae..2c6b751 100644
--- a/Benchmark-Models/Oliveira_NatCommun2021/Oliveira_NatCommun2021_model.xml
+++ b/Benchmark-Models/Oliveira_NatCommun2021/Oliveira_NatCommun2021_model.xml
@@ -1,7 +1,7 @@
 
 
 
-  
+  
     
       
         
Oliveira, Nature 2021.
@@ -16,7 +16,7 @@ To model with a two-step transmission rate, set 'beta_2_multiplier' = 0. To mode
     
     
       
-        
+