Clarify provenance of models in benchmarks.jl

.gitignore

@@ -31,4 +31,6 @@ Manifest.toml
 # VSCode settings
 .vscode/
 
+benchmarking/local
+
 # End of https://www.toptal.com/developers/gitignore/api/julia

benchmarking/benchmarks.jl

@@ -44,6 +44,7 @@ benchmarks = Dict(
             y1(t) = x0(t)
         ),
         :skip => false,
+        :cite => "bib/Pharm.bib"
     ),
     :SEAIJRC => Dict(
         :name => "SEAIJRC Covid model",
@@ -458,6 +459,7 @@ benchmarks = Dict(
             y2(t) = a2 * (pAkt(t) + pAkt_S6(t)),
             y3(t) = a3 * pS6(t)
         ),
+        :cite => "bib/Fujita.bib"
     ),
     :LLW => Dict(
         # https://github.com/Xabo-RB/Local-Global-Models/blob/main/Models/General/LLW1987_io.jl
@@ -484,6 +486,7 @@ benchmarks = Dict(
             x4'(t) = k41 * x1(t) - k14 * x4(t),
             y1(t) = x1(t)
         ),
+        :cite => "bib/Bilirubin2_io.bib"
     ),
     :HIV2 => Dict(
         # https://github.com/Xabo-RB/Local-Global-Models/blob/main/Models/Virology/HIV2_io.jl
@@ -509,6 +512,7 @@ benchmarks = Dict(
             y1(t) = x4(t),
             y2(t) = x5(t)
         ),
+        :cite => "bib/Biohydrogenation_io.bib"
     ),
     :Treatment => Dict(
         # https://github.com/Xabo-RB/Local-Global-Models/blob/main/Models/Epidemiology/Treatment_io.jl
@@ -534,6 +538,7 @@ benchmarks = Dict(
             Q'(t) = -gamma * Q(t) + psi * I(t),
             y1(t) = Q(t)
         ),
+        :cite => "bib/SEIR_1_io.bib"
     ),
     :JAK_STAT => Dict(
         # https://arxiv.org/pdf/2207.09745.pdf
@@ -562,6 +567,7 @@ benchmarks = Dict(
             y7(t) = x10(t),
             y8(t) = -x7(t) + 165
         ),
+        :cite => "bib/JAK_STAT_1.bib"
     ),
     :SIR24 => Dict(
         # https://arxiv.org/pdf/2006.14295.pdf
@@ -873,6 +879,7 @@ benchmarks = Dict(
             q7'(t) = k7 * q1(t),
             y1(t) = q7(t)
         ),
+        :cite => "bib/CGV1990.bib",
     ),
     :LeukaemiaLeon2021 => Dict(
         # https://github.com/Xabo-RB/Local-Global-Models/blob/main/Models/Immunology/LeukaemiaLeon2021.jl
@@ -987,6 +994,7 @@ benchmarks = Dict(
             x2'(t) = r2 * x2(t) + beta21 * x1(t) * x2(t) + beta22 * x2(t)^2,
             y1(t) = x1(t)
         ),
+        :cite => "bib/genLV.bib"
     ),
     :Pivastatin => Dict(
         # https://github.com/Xabo-RB/Local-Global-Models/blob/main/Models/Pharmacokinetics/Pivastatin.jl

benchmarking/bib/Akt_pathway.bib

@@ -0,0 +1,11 @@
+@article{Fujita2010Akt,
+	title   = {Decoupling of Receptor and Downstream Signals in the Akt Pathway by Its Low-Pass Filter Characteristics},
+	author  = {Fujita, K. A. and Toyoshima, Y. and Uda, S. and Ozaki, Y. I. and Kubota, H. and Kuroda, S.},
+	journal = {Science Signaling},
+	year    = {2010},
+	volume  = {3},
+	number  = {141},
+	pages   = {ra56},
+	doi     = {10.1126/scisignal.2000810},
+	url     = {https://doi.org/10.1126/scisignal.2000810}
+}

benchmarking/bib/Bilirubin2_io.bib

@@ -0,0 +1,11 @@
+@article{Meshkat2014Combos,
+  title = {On finding and using identifiable parameter combinations in nonlinear dynamic systems biology models and COMBOS: A novel web implementation},
+  author = {Meshkat, Nicolette AND Kuo, Christine Er-zhen AND DiStefano, III, Joseph},
+  journal = {PLOS ONE},
+  volume = {9},
+  number = {10},
+  pages = {1--14},
+  year = {2014},
+  doi = {10.1371/journal.pone.0110261},
+  url = {https://doi.org/10.1371/journal.pone.0110261}
+}

benchmarking/bib/Biohydrogenation_io.bib

@@ -0,0 +1,25 @@
+@article{MOATE2008731,
+  title = {Kinetics of Ruminal Lipolysis of Triacylglycerol and Biohydrogenation of Long-Chain Fatty Acids: New Insights from Old Data},
+  journal = {Journal of Dairy Science},
+  volume = {91},
+  number = {2},
+  pages = {731-742},
+  year = {2008},
+  issn = {0022-0302},
+  doi = {https://doi.org/10.3168/jds.2007-0398},
+  url = {https://www.sciencedirect.com/science/article/pii/S0022030208714176},
+  author = {P.J. Moate and R.C. Boston and T.C. Jenkins and I.J. Lean},
+}
+
+@article{MUNOZTAMAYO2018701,
+  title = {Review: To be or not to be an identifiable model. Is this a relevant question in animal science modelling?},
+  journal = {animal},
+  volume = {12},
+  number = {4},
+  pages = {701-712},
+  year = {2018},
+  issn = {1751-7311},
+  doi = {https://doi.org/10.1017/S1751731117002774},
+  url = {https://www.sciencedirect.com/science/article/pii/S1751731117002774},
+  author = {R. Muñoz-Tamayo and L. Puillet and J.B. Daniel and D. Sauvant and O. Martin and M. Taghipoor and P. Blavy},
+}

benchmarking/bib/Bruno2016.bib

@@ -0,0 +1,11 @@
+@article{Bruno2016CCD,
+  title = {Enzymatic study on AtCCD4 and AtCCD7 and their potential to form acyclic regulatory metabolites},
+  author = {Bruno, Mark and Koschmieder, Julian and Wuest, Florian and Schaub, Patrick and Fehling-Kaschek, Mirjam and Timmer, Jens and Beyer, Peter and Al-Babili, Salim},
+  journal = {Journal of Experimental Botany},
+  volume = {67},
+  number = {21},
+  pages = {5993--6005},
+  year = {2016},
+  doi = {10.1093/jxb/erw356},
+  url = {https://doi.org/10.1093/jxb/erw356}
+}

benchmarking/bib/CD8_T_cell_differentiation.bib

@@ -0,0 +1,9 @@
+@article{Girel2019UnevenPartitioning,
+	title   = {Model-Based Assessment of the Role of Uneven Partitioning of Molecular Content on Heterogeneity and Regulation of Differentiation in CD8 T-Cell Immune Responses},
+	author  = {Girel, Simon and Arpin, Christophe and Marvel, Jacqueline and Gandrillon, Olivier and Crauste, Fabien},
+	journal = {Frontiers in Immunology},
+	year    = {2019},
+	volume  = {10},
+	pages   = {230},
+	doi     = {10.3389/fimmu.2019.00230}
+}

benchmarking/bib/CGV1990.bib

@@ -0,0 +1,11 @@
+@article{Chappell1990Global,
+  title = {Global identifiability of the parameters of nonlinear systems with specified inputs: A comparison of methods},
+  author = {Chappell, Michael J. and Godfrey, Keith R. and Vajda, Sandor},
+  journal = {Mathematical Biosciences},
+  volume = {102},
+  number = {1},
+  pages = {41--73},
+  year = {1990},
+  doi = {10.1016/0025-5564(90)90055-4},
+  url = {https://doi.org/10.1016/0025-5564(90)90055-4}
+}

benchmarking/bib/Chemical_reaction_network.bib

@@ -0,0 +1,12 @@
+@article{CONRADI2018507,
+	title = {Dynamics of Posttranslational Modification Systems: Recent Progress and Future Directions},
+	journal = {Biophysical Journal},
+	volume = {114},
+	number = {3},
+	pages = {507--515},
+	year = {2018},
+	issn = {0006-3495},
+	doi = {10.1016/j.bpj.2017.11.3787},
+	url = {https://doi.org/10.1016/j.bpj.2017.11.3787},
+	author = {Carsten Conradi and Anne Shiu}
+}

benchmarking/bib/Covid_model_Gevertz_et_al.bib

@@ -0,0 +1,11 @@
+@article{Mitchell2020Prophylactic,
+  title = {Prophylactic host behaviour discourages pathogen exploitation},
+  author = {Mitchell, Evan and Wild, Geoff},
+  journal = {Journal of Theoretical Biology},
+  year = {2020},
+  volume = {503},
+  pages = {110388},
+  doi = {10.1016/j.jtbi.2020.110388},
+  url = {https://doi.org/10.1016/j.jtbi.2020.110388},
+  publisher = {Elsevier}
+}

benchmarking/bib/Covid_model_Gevertz_et_al_2.bib

@@ -0,0 +1,11 @@
+@article{Gevertz2021COVIDTherapy,
+  title = {Living with COVID-19: Balancing cost of lockdowns and health outcomes in dynamical systems models},
+  author = {Gevertz, Jana L. and Greene, James M. and Sontag, Eduardo D. and Friedman, Avner},
+  journal = {Biophysical Journal},
+  volume = {120},
+  number = {12},
+  pages = {1203--1214},
+  year = {2021},
+  doi = {10.1016/j.bpj.2020.12.033},
+  url = {https://doi.org/10.1016/j.bpj.2020.12.033}
+}

benchmarking/bib/Crauste_SI.bib

@@ -0,0 +1,12 @@
+@article{Crauste2017,
+  title        = {Identification of Nascent Memory CD8 T Cells and Modeling of Their Ontogeny},
+  author       = {Crauste, Fabien and Mafille, Julien and Boucinha, Lilia and Djebali, Sophia and Gandrillon, Olivier and Marvel, Jacqueline and Arpin, Christophe},
+  journal      = {Cell Systems},
+  year         = {2017},
+  volume       = {4},
+  number       = {3},
+  pages        = {306--317.e4},
+  doi          = {10.1016/j.cels.2017.01.014},
+  url          = {https://doi.org/10.1016/j.cels.2017.01.014},
+  note         = {Benchmarked Crauste\_SI CD8 T-cell differentiation model from Local-Global-Models repository}
+}

benchmarking/bib/EIHRD_epidemiological_model.bib

@@ -0,0 +1,12 @@
+@article{Chen2024EIHRD,
+  title = {Practical identifiability and parameter estimation of compartmental epidemiological models},
+  author = {Chen, Qianyong and Rapti, Zoi and Drossinos, Yannis and Cuevas-Maraver, Jes{\'u}s and Kevrekidis, Georgios A. and Kevrekidis, Panayotis G.},
+  journal = {arXiv},
+  year = {2024},
+  eprint = {2406.17827},
+  archivePrefix = {arXiv},
+  primaryClass = {stat.ME},
+  doi = {10.48550/arXiv.2406.17827},
+  url = {https://arxiv.org/abs/2406.17827},
+  note = {See Section on EIHRD model}
+}

benchmarking/bib/Fujita.bib

@@ -0,0 +1,11 @@
+@article{Fujita2010,
+    title   = {Decoupling of Receptor and Downstream Signals in the Akt Pathway by Its Low-Pass Filter Characteristics},
+    author  = {Fujita, K. A. and Toyoshima, Y. and Uda, S. and Ozaki, Y. I. and Kubota, H. and Kuroda, S.},
+    journal = {Science Signaling},
+    year    = {2010},
+    volume  = {3},
+    number  = {132},
+    pages   = {ra56--ra56},
+    doi     = {10.1126/scisignal.2000810},
+    url     = {https://doi.org/10.1126/scisignal.2000810}
+}

benchmarking/bib/Goodwin_oscillator.bib

@@ -0,0 +1,10 @@
+@article{Goodwin1965Oscillatory,
+	title   = {Oscillatory Behavior in Enzymatic Control Processes},
+	author  = {Goodwin, Brian C.},
+	journal = {Advances in Enzyme Regulation},
+	year    = {1965},
+	volume  = {3},
+	pages   = {425--438},
+	doi     = {10.1016/0065-2571(65)90067-1},
+	url     = {https://doi.org/10.1016/0065-2571(65)90067-1}
+}

benchmarking/bib/HIV.bib

@@ -0,0 +1,12 @@
+@article{Wodarz1999HIV,
+	title   = {Specific Therapy Regimens Could Lead to Long-Term Immunological Control of HIV},
+	author  = {Wodarz, Dominik and Nowak, Martin A.},
+	journal = {Proceedings of the National Academy of Sciences},
+	year    = {1999},
+	volume  = {96},
+	number  = {25},
+	pages   = {14464--14469},
+	month   = {Dec},
+	doi     = {10.1073/pnas.96.25.14464},
+	url     = {https://doi.org/10.1073/pnas.96.25.14464}
+}

benchmarking/bib/HIV2_io.bib

@@ -0,0 +1,11 @@
+@article{Wodarz1999Therapy,
+  title = {Specific therapy regimes could lead to long-term immunological control of HIV},
+  author = {Wodarz, Dominik and Nowak, Martin A.},
+  journal = {Proceedings of the National Academy of Sciences of the United States of America},
+  volume = {96},
+  number = {25},
+  pages = {14464--14469},
+  year = {1999},
+  doi = {10.1073/pnas.96.25.14464},
+  url = {https://doi.org/10.1073/pnas.96.25.14464}
+}

benchmarking/bib/HighDimNonLin.bib

@@ -0,0 +1,11 @@
+@article{Saccomani2010DAISY,
+  title = {Examples of testing global identifiability of biological and biomedical models with the DAISY software},
+  author = {Saccomani, Maria Pia and Audoly, Solange and Bellu, Gabriella and D'Angio, Lina},
+  journal = {Computer Methods and Programs in Biomedicine},
+  volume = {40},
+  number = {4},
+  pages = {402--407},
+  year = {2010},
+  doi = {10.1016/j.compbiomed.2010.02.002},
+  url = {https://doi.org/10.1016/j.compbiomed.2010.02.002}
+}

benchmarking/bib/Immune_response_to_influenza_MB1_model.bib

@@ -0,0 +1,11 @@
+@article{Whipple2024MB1,
+  title = {Modeling the CD8+ T cell immune response to influenza infection in adult and aged mice},
+  author = {Whipple, Benjamin and Miura, Tanya A. and Hernandez-Vargas, Esteban A.},
+  journal = {Journal of Theoretical Biology},
+  year = {2024},
+  volume = {593},
+  pages = {111898},
+  doi = {10.1016/j.jtbi.2024.111898},
+  url = {https://doi.org/10.1016/j.jtbi.2024.111898},
+  note = {Defines MB1 benchmark model}
+}

benchmarking/bib/Immune_response_to_influenza_MB2_model.bib

@@ -0,0 +1,11 @@
+@article{Whipple2024MB2,
+  title = {Modeling the CD8+ T cell immune response to influenza infection in adult and aged mice},
+  author = {Whipple, Benjamin and Miura, Tanya A. and Hernandez-Vargas, Esteban A.},
+  journal = {Journal of Theoretical Biology},
+  year = {2024},
+  volume = {593},
+  pages = {111898},
+  doi = {10.1016/j.jtbi.2024.111898},
+  url = {https://doi.org/10.1016/j.jtbi.2024.111898},
+  note = {Defines MB2 benchmark model}
+}

benchmarking/bib/Immune_response_to_influenza_MB3_model.bib

@@ -0,0 +1,11 @@
+@article{Whipple2024MB3,
+  title = {Modeling the CD8+ T cell immune response to influenza infection in adult and aged mice},
+  author = {Whipple, Benjamin and Miura, Tanya A. and Hernandez-Vargas, Esteban A.},
+  journal = {Journal of Theoretical Biology},
+  year = {2024},
+  volume = {593},
+  pages = {111898},
+  doi = {10.1016/j.jtbi.2024.111898},
+  url = {https://doi.org/10.1016/j.jtbi.2024.111898},
+  note = {Defines MB3 benchmark model}
+}

benchmarking/bib/Immune_response_to_influenza_MB4_model.bib

@@ -0,0 +1,11 @@
+@article{Whipple2024MB4,
+  title = {Modeling the CD8+ T cell immune response to influenza infection in adult and aged mice},
+  author = {Whipple, Benjamin and Miura, Tanya A. and Hernandez-Vargas, Esteban A.},
+  journal = {Journal of Theoretical Biology},
+  year = {2024},
+  volume = {593},
+  pages = {111898},
+  doi = {10.1016/j.jtbi.2024.111898},
+  url = {https://doi.org/10.1016/j.jtbi.2024.111898},
+  note = {Defines MB4 benchmark model}
+}

benchmarking/bib/Immune_response_to_influenza_MD1_model.bib

@@ -0,0 +1,11 @@
+@article{Whipple2024MD1,
+  title = {Modeling the CD8+ T cell immune response to influenza infection in adult and aged mice},
+  author = {Whipple, Benjamin and Miura, Tanya A. and Hernandez-Vargas, Esteban A.},
+  journal = {Journal of Theoretical Biology},
+  year = {2024},
+  volume = {593},
+  pages = {111898},
+  doi = {10.1016/j.jtbi.2024.111898},
+  url = {https://doi.org/10.1016/j.jtbi.2024.111898},
+  note = {Defines MD1 benchmark model}
+}

benchmarking/bib/Immune_response_to_influenza_MD2_model.bib

@@ -0,0 +1,11 @@
+@article{Whipple2024MD2,
+  title = {Modeling the CD8+ T cell immune response to influenza infection in adult and aged mice},
+  author = {Whipple, Benjamin and Miura, Tanya A. and Hernandez-Vargas, Esteban A.},
+  journal = {Journal of Theoretical Biology},
+  year = {2024},
+  volume = {593},
+  pages = {111898},
+  doi = {10.1016/j.jtbi.2024.111898},
+  url = {https://doi.org/10.1016/j.jtbi.2024.111898},
+  note = {Defines MD2 benchmark model}
+}

benchmarking/bib/Immune_response_to_influenza_MD3_model.bib

@@ -0,0 +1,11 @@
+@article{Whipple2024MD3,
+  title = {Modeling the CD8+ T cell immune response to influenza infection in adult and aged mice},
+  author = {Whipple, Benjamin and Miura, Tanya A. and Hernandez-Vargas, Esteban A.},
+  journal = {Journal of Theoretical Biology},
+  year = {2024},
+  volume = {593},
+  pages = {111898},
+  doi = {10.1016/j.jtbi.2024.111898},
+  url = {https://doi.org/10.1016/j.jtbi.2024.111898},
+  note = {Defines MD3 benchmark model}
+}

benchmarking/bib/Immune_response_to_influenza_MD4_model.bib

@@ -0,0 +1,11 @@
+@article{Whipple2024MD4,
+  title = {Modeling the CD8+ T cell immune response to influenza infection in adult and aged mice},
+  author = {Whipple, Benjamin and Miura, Tanya A. and Hernandez-Vargas, Esteban A.},
+  journal = {Journal of Theoretical Biology},
+  year = {2024},
+  volume = {593},
+  pages = {111898},
+  doi = {10.1016/j.jtbi.2024.111898},
+  url = {https://doi.org/10.1016/j.jtbi.2024.111898},
+  note = {Defines MD4 benchmark model}
+}

benchmarking/bib/JAK_STAT_1.bib

@@ -0,0 +1,11 @@
+@article{Raia2011,
+    title   = {Dynamic Mathematical Modeling of IL13-Induced Signaling in Hodgkin and Primary Mediastinal B-Cell Lymphoma Allows Prediction of Therapeutic Targets},
+    author  = {Raia, Valentina and Schilling, Marcel and B{\"o}hm, Martin and Hahn, Bettina and Kowarsch, Andreas and Raue, Andreas and Sticht, Carsten and Bohl, Sebastian and Saile, Maria and M{\"o}ller, Peter and Gretz, Norbert and Timmer, Jens and Theis, Fabian and Lehmann, Wolf-Dieter and Lichter, Peter and Klingm{"u}ller, Ursula},
+    journal = {Cancer Research},
+    year    = {2011},
+    volume  = {71},
+    number  = {3},
+    pages   = {693--704},
+    doi     = {10.1158/0008-5472.CAN-10-2987},
+    url     = {https://doi.org/10.1158/0008-5472.CAN-10-2987}
+}

benchmarking/bib/KD1999.bib

@@ -0,0 +1,11 @@
+@book{KumarDaoutidis1999,
+  title = {Control of Nonlinear Differential Algebraic Equation Systems with Applications to Chemical Processes},
+  author = {Kumar, Aditya and Daoutidis, Prodromos},
+  publisher = {Chapman and Hall/CRC},
+  address = {New York, NY},
+  year = {1999},
+  doi = {10.1201/9781003072218},
+  url = {https://doi.org/10.1201/9781003072218},
+  isbn = {9781003072218},
+  note = {First published 1999; eBook edition 2020}
+}