diff --git a/.gitignore b/.gitignore
index 759fe810..515b6346 100644
--- a/.gitignore
+++ b/.gitignore
@@ -31,4 +31,6 @@ Manifest.toml
 # VSCode settings
 .vscode/
 
+benchmarking/local
+
 # End of https://www.toptal.com/developers/gitignore/api/julia
diff --git a/benchmarking/benchmarks.jl b/benchmarking/benchmarks.jl
index 6775b7ea..fd9921db 100644
--- a/benchmarking/benchmarks.jl
+++ b/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
diff --git a/benchmarking/bib/Akt_pathway.bib b/benchmarking/bib/Akt_pathway.bib
new file mode 100644
index 00000000..2b288de4
--- /dev/null
+++ b/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}
+}
diff --git a/benchmarking/bib/Bilirubin2_io.bib b/benchmarking/bib/Bilirubin2_io.bib
new file mode 100644
index 00000000..47a53efd
--- /dev/null
+++ b/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}
+}
diff --git a/benchmarking/bib/Biohydrogenation_io.bib b/benchmarking/bib/Biohydrogenation_io.bib
new file mode 100644
index 00000000..ced7d3d5
--- /dev/null
+++ b/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},
+}
diff --git a/benchmarking/bib/Bruno2016.bib b/benchmarking/bib/Bruno2016.bib
new file mode 100644
index 00000000..d1d2e4f0
--- /dev/null
+++ b/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}
+}
diff --git a/benchmarking/bib/CD8_T_cell_differentiation.bib b/benchmarking/bib/CD8_T_cell_differentiation.bib
new file mode 100644
index 00000000..ad108be9
--- /dev/null
+++ b/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}
+}
diff --git a/benchmarking/bib/CGV1990.bib b/benchmarking/bib/CGV1990.bib
new file mode 100644
index 00000000..75aedf05
--- /dev/null
+++ b/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}
+}
diff --git a/benchmarking/bib/Chemical_reaction_network.bib b/benchmarking/bib/Chemical_reaction_network.bib
new file mode 100644
index 00000000..5f2e5e16
--- /dev/null
+++ b/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}
+}
diff --git a/benchmarking/bib/Covid_model_Gevertz_et_al.bib b/benchmarking/bib/Covid_model_Gevertz_et_al.bib
new file mode 100644
index 00000000..dd0059a2
--- /dev/null
+++ b/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}
+}
diff --git a/benchmarking/bib/Covid_model_Gevertz_et_al_2.bib b/benchmarking/bib/Covid_model_Gevertz_et_al_2.bib
new file mode 100644
index 00000000..55b6c7b3
--- /dev/null
+++ b/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}
+}
diff --git a/benchmarking/bib/Crauste_SI.bib b/benchmarking/bib/Crauste_SI.bib
new file mode 100644
index 00000000..32126300
--- /dev/null
+++ b/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}
+}
diff --git a/benchmarking/bib/EIHRD_epidemiological_model.bib b/benchmarking/bib/EIHRD_epidemiological_model.bib
new file mode 100644
index 00000000..e37b8f80
--- /dev/null
+++ b/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}
+}
diff --git a/benchmarking/bib/Fujita.bib b/benchmarking/bib/Fujita.bib
new file mode 100644
index 00000000..40c4f353
--- /dev/null
+++ b/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}
+}
diff --git a/benchmarking/bib/Goodwin_oscillator.bib b/benchmarking/bib/Goodwin_oscillator.bib
new file mode 100644
index 00000000..7655fcf9
--- /dev/null
+++ b/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}
+}
diff --git a/benchmarking/bib/HIV.bib b/benchmarking/bib/HIV.bib
new file mode 100644
index 00000000..df2fac03
--- /dev/null
+++ b/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}
+}
diff --git a/benchmarking/bib/HIV2_io.bib b/benchmarking/bib/HIV2_io.bib
new file mode 100644
index 00000000..0604cbea
--- /dev/null
+++ b/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}
+}
diff --git a/benchmarking/bib/HighDimNonLin.bib b/benchmarking/bib/HighDimNonLin.bib
new file mode 100644
index 00000000..36b005a0
--- /dev/null
+++ b/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}
+}
diff --git a/benchmarking/bib/Immune_response_to_influenza_MB1_model.bib b/benchmarking/bib/Immune_response_to_influenza_MB1_model.bib
new file mode 100644
index 00000000..d310f1b3
--- /dev/null
+++ b/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}
+}
diff --git a/benchmarking/bib/Immune_response_to_influenza_MB2_model.bib b/benchmarking/bib/Immune_response_to_influenza_MB2_model.bib
new file mode 100644
index 00000000..17cb5138
--- /dev/null
+++ b/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}
+}
diff --git a/benchmarking/bib/Immune_response_to_influenza_MB3_model.bib b/benchmarking/bib/Immune_response_to_influenza_MB3_model.bib
new file mode 100644
index 00000000..09281385
--- /dev/null
+++ b/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}
+}
diff --git a/benchmarking/bib/Immune_response_to_influenza_MB4_model.bib b/benchmarking/bib/Immune_response_to_influenza_MB4_model.bib
new file mode 100644
index 00000000..667cc178
--- /dev/null
+++ b/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}
+}
diff --git a/benchmarking/bib/Immune_response_to_influenza_MD1_model.bib b/benchmarking/bib/Immune_response_to_influenza_MD1_model.bib
new file mode 100644
index 00000000..1ea8f0b8
--- /dev/null
+++ b/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}
+}
diff --git a/benchmarking/bib/Immune_response_to_influenza_MD2_model.bib b/benchmarking/bib/Immune_response_to_influenza_MD2_model.bib
new file mode 100644
index 00000000..32ccfc67
--- /dev/null
+++ b/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}
+}
diff --git a/benchmarking/bib/Immune_response_to_influenza_MD3_model.bib b/benchmarking/bib/Immune_response_to_influenza_MD3_model.bib
new file mode 100644
index 00000000..a1a4b1c9
--- /dev/null
+++ b/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}
+}
diff --git a/benchmarking/bib/Immune_response_to_influenza_MD4_model.bib b/benchmarking/bib/Immune_response_to_influenza_MD4_model.bib
new file mode 100644
index 00000000..8d2fcc41
--- /dev/null
+++ b/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}
+}
diff --git a/benchmarking/bib/JAK_STAT_1.bib b/benchmarking/bib/JAK_STAT_1.bib
new file mode 100644
index 00000000..55f2da17
--- /dev/null
+++ b/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}
+}
diff --git a/benchmarking/bib/KD1999.bib b/benchmarking/bib/KD1999.bib
new file mode 100644
index 00000000..997e7f98
--- /dev/null
+++ b/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}
+}
diff --git a/benchmarking/bib/LLW1987_io.bib b/benchmarking/bib/LLW1987_io.bib
new file mode 100644
index 00000000..ed094a27
--- /dev/null
+++ b/benchmarking/bib/LLW1987_io.bib
@@ -0,0 +1,10 @@
+@inproceedings{Lecourtier1987Unidentifiable,
+  title = {A method to prove that nonlinear models can be unidentifiable},
+  author = {Lecourtier, Yves and Lamnabhi-Lagarrigue, Francoise and Walter, Eric},
+  booktitle = {Proceedings of the 26th IEEE Conference on Decision and Control},
+  pages = {2144--2145},
+  year = {1987},
+  publisher = {IEEE},
+  doi = {10.1109/CDC.1987.272543},
+  url = {https://doi.org/10.1109/CDC.1987.272543}
+}
diff --git a/benchmarking/bib/LeukaemiaLeon2021.bib b/benchmarking/bib/LeukaemiaLeon2021.bib
new file mode 100644
index 00000000..d87320e4
--- /dev/null
+++ b/benchmarking/bib/LeukaemiaLeon2021.bib
@@ -0,0 +1,10 @@
+@article{LeonTriana2021CART,
+  title = {CAR T cell therapy in B-cell acute lymphoblastic leukaemia: Insights from mathematical models},
+  author = {Leon-Triana, Oscar and Sabir, Salman and Calvo, Gelesan F. and Belmonte-Beitia, Juan and Chulian, Sandra and Martinez-Rubio, Angel and Rosa, Miguel and Perez-Martinez, Antonio and Ramirez-Orellana, Miriam and Perez-Garcia, Victor M.},
+  journal = {Communications in Nonlinear Science and Numerical Simulation},
+  volume = {94},
+  pages = {105570},
+  year = {2021},
+  doi = {10.1016/j.cnsns.2020.105570},
+  url = {https://doi.org/10.1016/j.cnsns.2020.105570}
+}
diff --git a/benchmarking/bib/Linear_compartment_hard_1.bib b/benchmarking/bib/Linear_compartment_hard_1.bib
new file mode 100644
index 00000000..4ed1d423
--- /dev/null
+++ b/benchmarking/bib/Linear_compartment_hard_1.bib
@@ -0,0 +1,10 @@
+@article{Jia2024HardCases,
+  title = {Hard-to-detect unidentifiability in linear compartment models},
+  author = {Jia, Zhe and Voldum-Clark, Jim and Cobo, Ademir and Wu, Danilo and Massonis, Guillermo and Villaverde, Alejandro F.},
+  journal = {Journal of Theoretical Biology},
+  volume = {591},
+  pages = {111898},
+  year = {2024},
+  doi = {10.1016/j.jtbi.2024.111898},
+  url = {https://doi.org/10.1016/j.jtbi.2024.111898}
+}
diff --git a/benchmarking/bib/Linear_compartment_hard_2.bib b/benchmarking/bib/Linear_compartment_hard_2.bib
new file mode 100644
index 00000000..4ed1d423
--- /dev/null
+++ b/benchmarking/bib/Linear_compartment_hard_2.bib
@@ -0,0 +1,10 @@
+@article{Jia2024HardCases,
+  title = {Hard-to-detect unidentifiability in linear compartment models},
+  author = {Jia, Zhe and Voldum-Clark, Jim and Cobo, Ademir and Wu, Danilo and Massonis, Guillermo and Villaverde, Alejandro F.},
+  journal = {Journal of Theoretical Biology},
+  volume = {591},
+  pages = {111898},
+  year = {2024},
+  doi = {10.1016/j.jtbi.2024.111898},
+  url = {https://doi.org/10.1016/j.jtbi.2024.111898}
+}
diff --git a/benchmarking/bib/MAPK_model_5_outputs.bib b/benchmarking/bib/MAPK_model_5_outputs.bib
new file mode 100644
index 00000000..2d840cb1
--- /dev/null
+++ b/benchmarking/bib/MAPK_model_5_outputs.bib
@@ -0,0 +1,12 @@
+@article{Manrai2008MAPK5,
+	title   = {The Geometry of Multisite Phosphorylation},
+	author  = {Manrai, Arjun Kumar and Gunawardena, Jeremy},
+	journal = {Biophysical Journal},
+	year    = {2008},
+	volume  = {95},
+	number  = {12},
+	pages   = {5533--5543},
+	month   = {Dec},
+	doi     = {10.1529/biophysj.108.140632},
+	url     = {https://doi.org/10.1529/biophysj.108.140632}
+}
diff --git a/benchmarking/bib/MAPK_model_5_outputs_bis.bib b/benchmarking/bib/MAPK_model_5_outputs_bis.bib
new file mode 100644
index 00000000..cc8c4785
--- /dev/null
+++ b/benchmarking/bib/MAPK_model_5_outputs_bis.bib
@@ -0,0 +1,12 @@
+@article{Manrai2008MAPK5bis,
+	title   = {The Geometry of Multisite Phosphorylation},
+	author  = {Manrai, Arjun Kumar and Gunawardena, Jeremy},
+	journal = {Biophysical Journal},
+	year    = {2008},
+	volume  = {95},
+	number  = {12},
+	pages   = {5533--5543},
+	month   = {Dec},
+	doi     = {10.1529/biophysj.108.140632},
+	url     = {https://doi.org/10.1529/biophysj.108.140632}
+}
diff --git a/benchmarking/bib/MAPK_model_6_outputs.bib b/benchmarking/bib/MAPK_model_6_outputs.bib
new file mode 100644
index 00000000..5024640e
--- /dev/null
+++ b/benchmarking/bib/MAPK_model_6_outputs.bib
@@ -0,0 +1,12 @@
+@article{Manrai2008MAPK,
+	title   = {The Geometry of Multisite Phosphorylation},
+	author  = {Manrai, Arjun Kumar and Gunawardena, Jeremy},
+	journal = {Biophysical Journal},
+	year    = {2008},
+	volume  = {95},
+	number  = {12},
+	pages   = {5533--5543},
+	month   = {Dec},
+	doi     = {10.1529/biophysj.108.140632},
+	url     = {https://doi.org/10.1529/biophysj.108.140632}
+}
diff --git a/benchmarking/bib/Modified_LV_for_testing.bib b/benchmarking/bib/Modified_LV_for_testing.bib
new file mode 100644
index 00000000..e69de29b
diff --git a/benchmarking/bib/NFkB.bib b/benchmarking/bib/NFkB.bib
new file mode 100644
index 00000000..31f49dc3
--- /dev/null
+++ b/benchmarking/bib/NFkB.bib
@@ -0,0 +1,10 @@
+@article{BalsaCanto2010NFkB,
+	title   = {An Iterative Identification Procedure for Dynamic Modeling of Biochemical Networks},
+	author  = {Balsa-Canto, Eva and Alonso, Antonio A. and Banga, Julio R.},
+	journal = {BMC Systems Biology},
+	year    = {2010},
+	volume  = {4},
+	pages   = {11},
+	doi     = {10.1186/1752-0509-4-11},
+	url     = {https://doi.org/10.1186/1752-0509-4-11}
+}
diff --git a/benchmarking/bib/Ovarian_follicle_population_dynamics.bib b/benchmarking/bib/Ovarian_follicle_population_dynamics.bib
new file mode 100644
index 00000000..8972d063
--- /dev/null
+++ b/benchmarking/bib/Ovarian_follicle_population_dynamics.bib
@@ -0,0 +1,12 @@
+@article{Ballif2024Ovarian,
+  title = {Nonlinear compartmental modeling to monitor ovarian follicle population dynamics on the whole lifespan},
+  author = {Ballif, Guillaume and Cl{\'e}ment, Fr{\'e}d{\'e}rique and Yvinec, Romain},
+  journal = {Journal of Mathematical Biology},
+  year = {2024},
+  volume = {89},
+  number = {9},
+  pages = {43},
+  doi = {10.1007/s00285-024-02108-6},
+  url = {https://doi.org/10.1007/s00285-024-02108-6},
+  note = {Section 3.2 provides the ODE system used in the benchmark}
+}
diff --git a/benchmarking/bib/Pharm.bib b/benchmarking/bib/Pharm.bib
new file mode 100644
index 00000000..206d0efa
--- /dev/null
+++ b/benchmarking/bib/Pharm.bib
@@ -0,0 +1,11 @@
+@article{Demignot1987Pharm,
+	title   = {Effect of Prosthetic Sugar Groups on the Pharmacokinetics of Glucose-Oxidase},
+	author  = {Demignot, S. and Domurado, D.},
+	journal = {Drug Design and Delivery},
+	year    = {1987},
+	volume  = {1},
+	number  = {4},
+	pages   = {333--348},
+	month   = {May},
+	url     = {https://pubmed.ncbi.nlm.nih.gov/2855567/}
+}
\ No newline at end of file
diff --git a/benchmarking/bib/Pivastatin.bib b/benchmarking/bib/Pivastatin.bib
new file mode 100644
index 00000000..f6d71ba5
--- /dev/null
+++ b/benchmarking/bib/Pivastatin.bib
@@ -0,0 +1,11 @@
+@article{Carter2020Pitavastatin,
+  title = {Prediction of Clinical Transporter-Mediated Drug--Drug Interactions via Comeasurement of Pitavastatin and Eltrombopag in Human Hepatocyte Models},
+  author = {Carter, S. J. and Chouhan, B. and Sharma, P. and Chappell, M. J.},
+  journal = {CPT: Pharmacometrics \& Systems Pharmacology},
+  year = {2020},
+  volume = {9},
+  number = {4},
+  pages = {211--221},
+  doi = {10.1002/psp4.12505},
+  url = {https://doi.org/10.1002/psp4.12505}
+}
diff --git a/benchmarking/bib/QWWC.bib b/benchmarking/bib/QWWC.bib
new file mode 100644
index 00000000..65cafa45
--- /dev/null
+++ b/benchmarking/bib/QWWC.bib
@@ -0,0 +1,11 @@
+@article{Qi2008Hyperchaotic,
+	title   = {On a New Hyperchaotic System},
+	author  = {Qi, Guoyuan and van Wyk, Micha{\"e}l Antonie and van Wyk, Barend Jacobus and Chen, Guanrong},
+	journal = {Physics Letters A},
+	year    = {2008},
+	volume  = {372},
+	number  = {2},
+	pages   = {124--136},
+	doi     = {10.1016/j.physleta.2007.10.082},
+	url     = {https://doi.org/10.1016/j.physleta.2007.10.082}
+}
diff --git a/benchmarking/bib/Ruminal_lipolysis.bib b/benchmarking/bib/Ruminal_lipolysis.bib
new file mode 100644
index 00000000..eceebf02
--- /dev/null
+++ b/benchmarking/bib/Ruminal_lipolysis.bib
@@ -0,0 +1,12 @@
+@article{Moate2008Lipolysis,
+  title   = {Kinetics of Ruminal Lipolysis of Triacylglycerol and Biohydrogenation of Long-Chain Fatty Acids: New Insights from Old Data},
+  author  = {Moate, Peter J. and Boston, Raymond C. and Jenkins, Thomas C. and Lean, Ian J.},
+  journal = {Journal of Dairy Science},
+  year    = {2008},
+  volume  = {91},
+  number  = {2},
+  pages   = {731--742},
+  doi     = {10.3168/jds.2007-0398},
+  url     = {https://doi.org/10.3168/jds.2007-0398},
+  note    = {Source for Ruminal lipolysis benchmark (Local-Global-Models)}
+}
diff --git a/benchmarking/bib/SEAIJRC_Covid_model.bib b/benchmarking/bib/SEAIJRC_Covid_model.bib
new file mode 100644
index 00000000..7b3ca210
--- /dev/null
+++ b/benchmarking/bib/SEAIJRC_Covid_model.bib
@@ -0,0 +1,12 @@
+@article{Roosa2019SEAIJRC,
+	title     = {Assessing Parameter Identifiability in Compartmental Dynamic Models Using a Computational Approach: Application to Infectious Disease Transmission Models},
+	author    = {Roosa, Kimberlyn and Chowell, Gerardo},
+	journal   = {Theoretical Biology and Medical Modelling},
+	year      = {2019},
+	volume    = {16},
+	number    = {1},
+	pages     = {1},
+	month     = {Jan},
+	doi       = {10.1186/s12976-018-0097-6},
+	url       = {https://tbiomed.biomedcentral.com/articles/10.1186/s12976-018-0097-6}
+}
diff --git a/benchmarking/bib/SEIR2T.bib b/benchmarking/bib/SEIR2T.bib
new file mode 100644
index 00000000..1c2fdd1c
--- /dev/null
+++ b/benchmarking/bib/SEIR2T.bib
@@ -0,0 +1,11 @@
+@article{Roosa2019SEIR2T,
+    title   = {Assessing Parameter Identifiability in Compartmental Dynamic Models Using a Computational Approach: Application to Infectious Disease Transmission Models},
+    author  = {Roosa, Kimberlyn and Chowell, Gerardo},
+    journal = {Theoretical Biology and Medical Modelling},
+    year    = {2019},
+    volume  = {16},
+    number  = {1},
+    pages   = {1},
+    doi     = {10.1186/s12976-018-0097-6},
+    url     = {https://tbiomed.biomedcentral.com/articles/10.1186/s12976-018-0097-6}
+}
diff --git a/benchmarking/bib/SEIRT.bib b/benchmarking/bib/SEIRT.bib
new file mode 100644
index 00000000..0a986873
--- /dev/null
+++ b/benchmarking/bib/SEIRT.bib
@@ -0,0 +1,11 @@
+@article{Sauer2022SEIRT,
+	title   = {Identifiability of Infection Model Parameters Early in an Epidemic},
+	author  = {Sauer, Timothy and Berry, Tyrus and Ebeigbe, Donald and Norton, Michael M. and Whalen, Andrew J. and Schiff, Steven J.},
+	journal = {SIAM Journal on Control and Optimization},
+	year    = {2022},
+	volume  = {60},
+	number  = {2},
+	pages   = {S27--S48},
+	doi     = {10.1137/20M1353289},
+	url     = {https://doi.org/10.1137/20M1353289}
+}
diff --git a/benchmarking/bib/SEIR_1_io.bib b/benchmarking/bib/SEIR_1_io.bib
new file mode 100644
index 00000000..b15760da
--- /dev/null
+++ b/benchmarking/bib/SEIR_1_io.bib
@@ -0,0 +1,10 @@
+@article{Zha2020,
+    title   = {Research about the optimal strategies for prevention and control of varicella outbreak in a school in a central city of China: based on an SEIR dynamic model},
+    author  = {Zha, Wen-ting and Pang, Fen-rui and Zhou, Nan and Wu, Bin and Liu, Ying and Du, Yan-bing and Hong, Xiu-qin and Lv, Yuan},
+    journal = {Epidemiology and Infection},
+    year    = {2020},
+    volume  = {148},
+    pages   = {e56},
+    doi     = {10.1017/S0950268819002188},
+    url     = {https://doi.org/10.1017/S0950268819002188}
+}
diff --git a/benchmarking/bib/SEIR_34.bib b/benchmarking/bib/SEIR_34.bib
new file mode 100644
index 00000000..4bf69bc2
--- /dev/null
+++ b/benchmarking/bib/SEIR_34.bib
@@ -0,0 +1,9 @@
+@article{Massonis2020SEIR34,
+	title   = {Structural Identifiability and Observability of Compartmental Models of the COVID-19 Pandemic},
+	author  = {Massonis, Gemma and Banga, Julio R. and Villaverde, Alejandro F.},
+	journal = {arXiv preprint arXiv:2006.14295},
+	year    = {2020},
+	doi     = {10.48550/arXiv.2006.14295},
+	url     = {https://arxiv.org/abs/2006.14295},
+	note    = {Preprint}
+}
diff --git a/benchmarking/bib/SEIR_36_ref.bib b/benchmarking/bib/SEIR_36_ref.bib
new file mode 100644
index 00000000..c7bd2f9c
--- /dev/null
+++ b/benchmarking/bib/SEIR_36_ref.bib
@@ -0,0 +1,9 @@
+@article{Massonis2020SEIR36,
+	title   = {Structural Identifiability and Observability of Compartmental Models of the COVID-19 Pandemic},
+	author  = {Massonis, Gemma and Banga, Julio R. and Villaverde, Alejandro F.},
+	journal = {arXiv preprint arXiv:2006.14295},
+	year    = {2020},
+	doi     = {10.48550/arXiv.2006.14295},
+	url     = {https://arxiv.org/abs/2006.14295},
+	note    = {Preprint}
+}
diff --git a/benchmarking/bib/SEUIR.bib b/benchmarking/bib/SEUIR.bib
new file mode 100644
index 00000000..af3dfac2
--- /dev/null
+++ b/benchmarking/bib/SEUIR.bib
@@ -0,0 +1,11 @@
+@article{Sauer2022SEUIR,
+	title   = {Identifiability of Infection Model Parameters Early in an Epidemic},
+	author  = {Sauer, Timothy and Berry, Tyrus and Ebeigbe, Donald and Norton, Michael M. and Whalen, Andrew J. and Schiff, Steven J.},
+	journal = {SIAM Journal on Control and Optimization},
+	year    = {2022},
+	volume  = {60},
+	number  = {2},
+	pages   = {S27--S48},
+	doi     = {10.1137/20M1353289},
+	url     = {https://doi.org/10.1137/20M1353289}
+}
diff --git a/benchmarking/bib/SIRS_forced.bib b/benchmarking/bib/SIRS_forced.bib
new file mode 100644
index 00000000..bb7d31f6
--- /dev/null
+++ b/benchmarking/bib/SIRS_forced.bib
@@ -0,0 +1,12 @@
+@article{Capistran2009SIRS,
+	title   = {Parameter Estimation of Some Epidemic Models: The Case of Recurrent Epidemics Caused by Respiratory Syncytial Virus},
+	author  = {Capistr{\'a}n, Marcos A. and Moreles, Miguel A. and Lara, Bruno},
+	journal = {Bulletin of Mathematical Biology},
+	year    = {2009},
+	volume  = {71},
+	number  = {8},
+	pages   = {1890--1901},
+	month   = {Nov},
+	doi     = {10.1007/s11538-009-9429-3},
+	url     = {https://link.springer.com/article/10.1007/s11538-009-9429-3}
+}
diff --git a/benchmarking/bib/SIR_19.bib b/benchmarking/bib/SIR_19.bib
new file mode 100644
index 00000000..896dc5a7
--- /dev/null
+++ b/benchmarking/bib/SIR_19.bib
@@ -0,0 +1,11 @@
+@article{Gaeta2021,
+    title   = {A Simple SIR Model with a Large Set of Asymptomatic Infectives},
+    author  = {Gaeta, Giuseppe},
+    journal = {Mathematics in Engineering},
+    year    = {2021},
+    volume  = {3},
+    number  = {2},
+    pages   = {1--39},
+    doi     = {10.3934/mine.2021013},
+    url     = {https://doi.org/10.3934/mine.2021013}
+}
diff --git a/benchmarking/bib/SIR_21.bib b/benchmarking/bib/SIR_21.bib
new file mode 100644
index 00000000..e7876dff
--- /dev/null
+++ b/benchmarking/bib/SIR_21.bib
@@ -0,0 +1,10 @@
+@article{Roda2020,
+    title   = {Why is it Difficult to Accurately Predict the COVID-19 Epidemic?},
+    author  = {Roda, Weston C. and Varughese, Marie B. and Han, Donglin and Li, Michael Y.},
+    journal = {Infectious Disease Modelling},
+    year    = {2020},
+    volume  = {5},
+    pages   = {271--281},
+    doi     = {10.1016/j.idm.2020.03.001},
+    url     = {https://doi.org/10.1016/j.idm.2020.03.001}
+}
diff --git a/benchmarking/bib/SIR_24.bib b/benchmarking/bib/SIR_24.bib
new file mode 100644
index 00000000..adbc7fff
--- /dev/null
+++ b/benchmarking/bib/SIR_24.bib
@@ -0,0 +1,11 @@
+@article{Kim1995,
+    title   = {A Mathematical Model of Epidemics with Screening and Variable Infectivity},
+    author  = {Kim, M. Y. and Milner, F. A.},
+    journal = {Mathematical and Computer Modelling},
+    year    = {1995},
+    volume  = {21},
+    number  = {7},
+    pages   = {29--42},
+    doi     = {10.1016/0895-7177(95)00029-2},
+    url     = {https://doi.org/10.1016/0895-7177(95)00029-2}
+}
diff --git a/benchmarking/bib/SIR_6.bib b/benchmarking/bib/SIR_6.bib
new file mode 100644
index 00000000..1cf8e9c3
--- /dev/null
+++ b/benchmarking/bib/SIR_6.bib
@@ -0,0 +1,9 @@
+@article{Zheng2020TVR,
+	title   = {Total Variation Regularization for Compartmental Epidemic Models with Time-Varying Dynamics},
+	author  = {Zheng, Wenjie},
+	journal = {arXiv preprint arXiv:2004.00412},
+	year    = {2020},
+	doi     = {10.48550/arXiv.2004.00412},
+	url     = {https://arxiv.org/abs/2004.00412},
+	note    = {Preprint}
+}
diff --git a/benchmarking/bib/SIWR_original.bib b/benchmarking/bib/SIWR_original.bib
new file mode 100644
index 00000000..ae3a331e
--- /dev/null
+++ b/benchmarking/bib/SIWR_original.bib
@@ -0,0 +1,10 @@
+@article{Lee2017Cholera,
+	title   = {Model Distinguishability and Inference Robustness in Mechanisms of Cholera Transmission and Loss of Immunity},
+	author  = {Lee, Elizabeth C. and Kelly, Michael R. Jr and Ochocki, Brad M. and Akinwumi, Segun M. and Hamre, Karen E. S. and Tien, Joseph H. and Eisenberg, Marisa C.},
+	journal = {Journal of Theoretical Biology},
+	year    = {2017},
+	volume  = {420},
+	pages   = {68--81},
+	doi     = {10.1016/j.jtbi.2017.01.032},
+	url     = {https://doi.org/10.1016/j.jtbi.2017.01.032}
+}
diff --git a/benchmarking/bib/SIWR_with_extra_output.bib b/benchmarking/bib/SIWR_with_extra_output.bib
new file mode 100644
index 00000000..ae3a331e
--- /dev/null
+++ b/benchmarking/bib/SIWR_with_extra_output.bib
@@ -0,0 +1,10 @@
+@article{Lee2017Cholera,
+	title   = {Model Distinguishability and Inference Robustness in Mechanisms of Cholera Transmission and Loss of Immunity},
+	author  = {Lee, Elizabeth C. and Kelly, Michael R. Jr and Ochocki, Brad M. and Akinwumi, Segun M. and Hamre, Karen E. S. and Tien, Joseph H. and Eisenberg, Marisa C.},
+	journal = {Journal of Theoretical Biology},
+	year    = {2017},
+	volume  = {420},
+	pages   = {68--81},
+	doi     = {10.1016/j.jtbi.2017.01.032},
+	url     = {https://doi.org/10.1016/j.jtbi.2017.01.032}
+}
diff --git a/benchmarking/bib/SLIQR.bib b/benchmarking/bib/SLIQR.bib
new file mode 100644
index 00000000..7e2c9eb6
--- /dev/null
+++ b/benchmarking/bib/SLIQR.bib
@@ -0,0 +1,9 @@
+@article{Fosu2020SLIQR,
+	title   = {Construction of Compartmental Models for {COVID}-19 with Quarantine, Lockdown and Vaccine Interventions},
+	author  = {Fosu, Gabriel Obed and Opong, Joseph M. and Appati, Justice K.},
+	journal = {SSRN Electronic Journal},
+	year    = {2020},
+	doi     = {10.2139/ssrn.3574020},
+	url     = {https://doi.org/10.2139/ssrn.3574020},
+	note    = {Preprint}
+}
diff --git a/benchmarking/bib/Transfection_4State.bib b/benchmarking/bib/Transfection_4State.bib
new file mode 100644
index 00000000..0cc48242
--- /dev/null
+++ b/benchmarking/bib/Transfection_4State.bib
@@ -0,0 +1,9 @@
+@mastersthesis{Lechtenberg2015,
+  title        = {Model selection in deterministic models of mRNA transfection},
+  author       = {Lechtenberg, Laura},
+  school       = {Ludwig-Maximilians-Universit\"at M\"unchen},
+  type         = {Master's thesis},
+  year         = {2015},
+  note         = {Model described in the GenSSI Transfection\_4State documentation},
+  url          = {https://github.com/genssi-developer/genssi/blob/main/Examples/Transfection_4State/Transfection_4State.m}
+}
diff --git a/benchmarking/bib/Treatment_io.bib b/benchmarking/bib/Treatment_io.bib
new file mode 100644
index 00000000..963c5b9c
--- /dev/null
+++ b/benchmarking/bib/Treatment_io.bib
@@ -0,0 +1,10 @@
+@article{Tuncer2018,
+    title   = {Structural and Practical Identifiability Analysis of Outbreak Models},
+    author  = {Tuncer, Necibe and Le, Trang T.},
+    journal = {Mathematical Biosciences},
+    year    = {2018},
+    volume  = {299},
+    pages   = {1--18},
+    doi     = {10.1016/j.mbs.2018.02.004},
+    url     = {https://doi.org/10.1016/j.mbs.2018.02.004}
+}
diff --git a/benchmarking/bib/TumorHu2019.bib b/benchmarking/bib/TumorHu2019.bib
new file mode 100644
index 00000000..e924163b
--- /dev/null
+++ b/benchmarking/bib/TumorHu2019.bib
@@ -0,0 +1,11 @@
+@article{Hu2019Tumor,
+	title   = {Modeling Pancreatic Cancer Dynamics with Immunotherapy},
+	author  = {Hu, Xiaochuan and Ke, Guoyi and Jang, Sophia R.-J.},
+	journal = {Bulletin of Mathematical Biology},
+	year    = {2019},
+	volume  = {81},
+	number  = {6},
+	pages   = {1885--1915},
+	doi     = {10.1007/s11538-019-00591-3},
+	url     = {https://doi.org/10.1007/s11538-019-00591-3}
+}
diff --git a/benchmarking/bib/TumorPillis2007.bib b/benchmarking/bib/TumorPillis2007.bib
new file mode 100644
index 00000000..ccc3a08c
--- /dev/null
+++ b/benchmarking/bib/TumorPillis2007.bib
@@ -0,0 +1,11 @@
+@article{dePillis2008Optimal,
+	title   = {Optimal Control of Mixed Immunotherapy and Chemotherapy of Tumors},
+	author  = {de Pillis, L. G. and Fister, K. R. and Gu, W. and Head, Tiffany and Maples, Kenny and Neal, Todd and Murugan, Anand and Kozai, Kenji},
+	journal = {Journal of Biological Systems},
+	year    = {2008},
+	volume  = {16},
+	number  = {1},
+	pages   = {51--80},
+	doi     = {10.1142/S0218339008002435},
+	url     = {https://doi.org/10.1142/S0218339008002435}
+}
diff --git a/benchmarking/bib/cLV1_1o.bib b/benchmarking/bib/cLV1_1o.bib
new file mode 100644
index 00000000..a93c0dda
--- /dev/null
+++ b/benchmarking/bib/cLV1_1o.bib
@@ -0,0 +1,12 @@
+@article{Joseph2020cLV1OneOutput,
+  title        = {Compositional Lotka-Volterra Describes Microbial Dynamics in the Simplex},
+  author       = {Joseph, Tyler A. and Shenhav, Liat and Xavier, Joao B. and Halperin, Eran and Pe'er, Itsik},
+  journal      = {PLOS Computational Biology},
+  year         = {2020},
+  volume       = {16},
+  number       = {5},
+  pages        = {e1007917},
+  doi          = {10.1371/journal.pcbi.1007917},
+  url          = {https://doi.org/10.1371/journal.pcbi.1007917},
+  note         = {Source for cLV1 compositional Lotka-Volterra benchmark (single output)}
+}
diff --git a/benchmarking/bib/cLV1_2o.bib b/benchmarking/bib/cLV1_2o.bib
new file mode 100644
index 00000000..50c2858c
--- /dev/null
+++ b/benchmarking/bib/cLV1_2o.bib
@@ -0,0 +1,12 @@
+@article{Joseph2020cLV1,
+  title        = {Compositional Lotka-Volterra Describes Microbial Dynamics in the Simplex},
+  author       = {Joseph, Tyler A. and Shenhav, Liat and Xavier, Joao B. and Halperin, Eran and Pe'er, Itsik},
+  journal      = {PLOS Computational Biology},
+  year         = {2020},
+  volume       = {16},
+  number       = {5},
+  pages        = {e1007917},
+  doi          = {10.1371/journal.pcbi.1007917},
+  url          = {https://doi.org/10.1371/journal.pcbi.1007917},
+  note         = {Source for cLV1 compositional Lotka-Volterra benchmark (two outputs)}
+}
diff --git a/benchmarking/bib/genLV.bib b/benchmarking/bib/genLV.bib
new file mode 100644
index 00000000..008228d2
--- /dev/null
+++ b/benchmarking/bib/genLV.bib
@@ -0,0 +1,11 @@
+@article{Remien2021GLVIdentifiability,
+  title = {Structural identifiability of the generalized Lotka--Volterra model for microbiome studies},
+  author = {Remien, Christopher H. and Eckwright, Mariah J. and Ridenhour, Benjamin J.},
+  journal = {Royal Society Open Science},
+  volume = {8},
+  number = {7},
+  pages = {20378},
+  year = {2021},
+  doi = {10.1098/rsos.201378},
+  url = {https://doi.org/10.1098/rsos.201378}
+}
diff --git a/benchmarking/bib/p53.bib b/benchmarking/bib/p53.bib
new file mode 100644
index 00000000..1888bd28
--- /dev/null
+++ b/benchmarking/bib/p53.bib
@@ -0,0 +1,10 @@
+@book{DiStefano2015,
+  title     = {Dynamic Systems Biology Modeling and Simulation},
+  author    = {DiStefano III, Joseph},
+  publisher = {Academic Press},
+  year      = {2015},
+  address   = {Cambridge, MA},
+  isbn      = {978-0-12-410411-2},
+  url       = {https://www.educate.elsevier.com/book/details/9780124104112},
+  note      = {Publication date reported as 10 Jan 2015 on the Elsevier Educate product page.}
+}
diff --git a/test/benchmarks.jl b/test/benchmarks.jl
new file mode 100644
index 00000000..01c5854f
--- /dev/null
+++ b/test/benchmarks.jl
@@ -0,0 +1,14 @@
+# Test that models in benchmarking/benchmarks.jl are well-formed.
+
+benchmarking_dir = joinpath(dirname(dirname(pathof(StructuralIdentifiability))), "benchmarking")
+include(joinpath(benchmarking_dir, "benchmarks.jl"))
+
+@testset "Benchmark definitions" begin
+    for (name, bench) in benchmarks
+        @test haskey(bench, :name)
+        @test haskey(bench, :ode)
+        if haskey(bench, :cite)
+            @test isfile(joinpath(benchmarking_dir, bench[:cite]))
+        end
+    end
+end