diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md index e5a511c..ac26c2d 100644 --- a/.github/pull_request_template.md +++ b/.github/pull_request_template.md @@ -21,7 +21,7 @@ - [ ] A visualization table is included, that can be used with the simulated data to reproduce figures from the original publication - [ ] The PEtab problem is valid (check with e.g. `petablint -vy problem.yaml`) - [ ] Labels (e.g. `parameterName` in the parameter table or `xLabel` in the visualization table) encode special characters with tex-style strings instead of unicode, e.g. use `H$_2$O` for water. -- [ ] `problems//metadata.yaml` contains a single-sentence `short_description` of the problem and passes `bmp-check-metadata` +- [ ] `problems//metadata.yaml` contains a single-sentence `short_description` of the problem and the `references` (DOI and BibTeX entry, key = problem ID) of the original publication(s), and passes `bmp-check-metadata` - [ ] The PEtab problem author(s) are assigned to the GitHub issue - [ ] The README has been updated with `bmp-create-overview --update` (requires `pip install -e src/python` from the repository root) - [ ] The new PEtab problem row in the generated table has the correct reference (and other entries) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 594c32f..6f8b79d 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -7,17 +7,16 @@ Each problem lives under `problems//`, with at least one of `v1/`/`v2 `conditions.tsv`, `measurements.tsv`, `observables.tsv`, `parameters.tsv`, and optionally `simulations.tsv` and `visualizations.tsv`. - `v2/` holds the same problem in PEtab v2 format. -- `metadata.yaml` contains version-independent metadata. Currently, this is a single-sentence - `short_description` of the problem, stating the type of model (e.g., biochemical reaction network, - compartmental epidemiological model), the biological system, and, where informative, the data. - For example: - ```yaml - short_description: Reaction network model of Epo-induced STAT5A/STAT5B phosphorylation and homo- and heterodimerization, fitted to quantitative mass spectrometry data. - ``` - The file is validated against the `ProblemMetadata` model in - [`metadata.py`](src/python/benchmark_models_petab/metadata.py) - (check with `bmp-check-metadata`); the corresponding JSON schema is - [`metadata.schema.json`](src/python/benchmark_models_petab/schemas/metadata.schema.json). +- `metadata.yaml` contains version-independent metadata: + - `short_description`: a single sentence stating the type of model (e.g., biochemical reaction + network, compartmental epidemiological model), the biological system, and, where informative, + the data. + - `references`: the publications the problem is based on, each with its `doi` and a `bibtex` + entry (one field per line, including a matching `doi` field). The first entry is the main + publication; its BibTeX key is the problem ID. + + See [`problems/Boehm_JProteomeRes2014/metadata.yaml`](problems/Boehm_JProteomeRes2014/metadata.yaml) + for an example. - `resources/` (optional) holds anything else related to the problem that isn't part of the PEtab files themselves (e.g. raw data, scripts, notebooks, figures). There's no prescribed structure — organize it however fits your problem. diff --git a/README.md b/README.md index 85729fd..5e9ea71 100644 --- a/README.md +++ b/README.md @@ -18,43 +18,43 @@ available encodings in PEtab v1 and v2. The PEtab files are available in the respective subdirectories. -| ID | PEtab v1 | PEtab v2 | Description | -|:-------------------------------------------------------------------------------------|:-------------------------------------------------------|:------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------| -| [Alkan_SciSignal2018](problems/Alkan_SciSignal2018/) | [v1](problems/Alkan_SciSignal2018/v1/) | | Reaction network model of the DNA damage response and cell fate in cancer cells treated with chemotherapeutics, fitted to signaling and cell count data. | -| [Armistead_CellDeathDis2024](problems/Armistead_CellDeathDis2024/) | [v1](problems/Armistead_CellDeathDis2024/v1/) | | Small reaction network model of sphingolipid metabolism with ceramide feedback, fitted to lipidomics data of wild-type and mutant zebrafish embryos. | -| [Bachmann_MSB2011](problems/Bachmann_MSB2011/) | [v1](problems/Bachmann_MSB2011/v1/) | | Reaction network model of Epo-induced JAK2/STAT5 signaling with two negative feedback regulators (SOCS3, CIS) in murine erythroid progenitor cells. | -| [Beer_MolBioSystems2014](problems/Beer_MolBioSystems2014/) | [v1](problems/Beer_MolBioSystems2014/v1/) | | Small kinetic model of bacterial growth and production of the blue pigment indigoidine by engineered variants of a non-ribosomal peptide synthetase. | -| [Bertozzi_PNAS2020](problems/Bertozzi_PNAS2020/) | [v1](problems/Bertozzi_PNAS2020/v1/) | | SIR compartmental epidemiological model of the early COVID-19 outbreak in New York and California. | -| [Blasi_CellSystems2016](problems/Blasi_CellSystems2016/) | [v1](problems/Blasi_CellSystems2016/v1/) | | Reaction network model of combinatorial histone H4 acetylation states generated by motif-specific acetylation reactions. | -| [Boehm_JProteomeRes2014](problems/Boehm_JProteomeRes2014/) | [v1](problems/Boehm_JProteomeRes2014/v1/) | [v2](problems/Boehm_JProteomeRes2014/v2/) | Reaction network model of Epo-induced STAT5A/STAT5B phosphorylation and homo- and heterodimerization, fitted to quantitative mass spectrometry data. | -| [Borghans_BiophysChem1997](problems/Borghans_BiophysChem1997/) | [v1](problems/Borghans_BiophysChem1997/v1/) | | Three-variable ODE model of complex calcium oscillations with Ca2+-activated IP3 degradation, fitted to measured calcium bursting in a single hepatocyte. | -| [Brannmark_JBC2010](problems/Brannmark_JBC2010/) | [v1](problems/Brannmark_JBC2010/v1/) | | Reaction network model of insulin receptor and IRS1 phosphorylation with receptor endocytosis and feedback in primary human adipocytes. | -| [Bruno_JExpBot2016](problems/Bruno_JExpBot2016/) | [v1](problems/Bruno_JExpBot2016/v1/) | | Enzyme kinetic model of the in vitro cleavage of carotenoids and apocarotenoids by Arabidopsis carotenoid cleavage dioxygenase 4 (CCD4). | -| [Chen_MSB2009](problems/Chen_MSB2009/) | [v1](problems/Chen_MSB2009/v1/) | | Large mass-action reaction network model of ErbB receptor signaling to ERK and AKT in response to EGF and heregulin. | -| [Crauste_CellSystems2017](problems/Crauste_CellSystems2017/) | [v1](problems/Crauste_CellSystems2017/v1/) | | Cell population model of CD8 T cell differentiation (naive, early/late effector, memory), fitted to cell counts in mice after vaccinia virus infection. | -| [Elowitz_Nature2000](problems/Elowitz_Nature2000/) | [v1](problems/Elowitz_Nature2000/v1/) | | Gene regulatory network model of the repressilator, a synthetic three-gene transcriptional oscillator in E. coli, fitted to a fluorescence time course. | -| [Fiedler_BMCSystBiol2016](problems/Fiedler_BMCSystBiol2016/) | [v1](problems/Fiedler_BMCSystBiol2016/v1/) | | Reaction network model of RAF/MEK/ERK signaling with ERK feedback in HeLa cells, fitted to phospho-MEK/ERK data without and with RAF or MEK inhibitors. | -| [Froehlich_CellSystems2018](problems/Froehlich_CellSystems2018/) | [v1](problems/Froehlich_CellSystems2018/v1/) | | Large-scale reaction network model of cancer signaling pathways, parameterized by cell-line-specific gene expression and fitted to drug response viability data. | -| [Fujita_SciSignal2010](problems/Fujita_SciSignal2010/) | [v1](problems/Fujita_SciSignal2010/v1/) | | Reaction network model of EGF-induced EGFR, Akt and S6 phosphorylation in PC12 cells under different EGF stimulation profiles. | -| [Giordano_Nature2020](problems/Giordano_Nature2020/) | [v1](problems/Giordano_Nature2020/v1/) | | Compartmental epidemiological model (SIDARTHE, distinguishing detected/undetected and symptom severity) of the COVID-19 epidemic in Italy. | -| [Isensee_JCB2018](problems/Isensee_JCB2018/) | [v1](problems/Isensee_JCB2018/v1/) | | Reaction network model of cAMP-induced PKA activation and phosphorylation of its regulatory subunit in rat sensory neurons under pharmacological perturbations. | -| [Lang_PLOSComputBiol2024](problems/Lang_PLOSComputBiol2024/) | [v1](problems/Lang_PLOSComputBiol2024/v1/) | | Reaction network model of the human cell cycle, generated from a rule-based model and fitted to compartment-resolved single-cell imaging data of RPE-1 cells. | -| [Laske_PLOSComputBiol2019](problems/Laske_PLOSComputBiol2019/) | [v1](problems/Laske_PLOSComputBiol2019/v1/) | | Reaction network model of intracellular influenza A virus replication, fitted to viral RNA, genome import and virus release data in human A549 cells. | -| [Liu_IFACPapersOnLine2025](problems/Liu_IFACPapersOnLine2025/) | [v1](problems/Liu_IFACPapersOnLine2025/v1/) | | Population model of oncolytic virus therapy with uninfected and infected tumor cells and virus, fitted to tumor size data in zebrafish. | -| [Lucarelli_CellSystems2018](problems/Lucarelli_CellSystems2018/) | [v1](problems/Lucarelli_CellSystems2018/v1/) | | Reaction network model of TGF-beta-induced SMAD complex formation and target gene expression. | -| [Okuonghae_ChaosSolitonsFractals2020](problems/Okuonghae_ChaosSolitonsFractals2020/) | [v1](problems/Okuonghae_ChaosSolitonsFractals2020/v1/) | | Compartmental epidemiological model of COVID-19 in Lagos, Nigeria, including asymptomatic and detected infections. | -| [Oliveira_NatCommun2021](problems/Oliveira_NatCommun2021/) | [v1](problems/Oliveira_NatCommun2021/v1/) | | Compartmental epidemiological model of COVID-19 in Bahia, Brazil (state excluding the capital Salvador), with non-detected cases, hospitalization and deaths. | -| [Perelson_Science1996](problems/Perelson_Science1996/) | [v1](problems/Perelson_Science1996/v1/) | | Within-host model of HIV-1 viral dynamics, fitted to plasma HIV-1 RNA levels after treatment with the protease inhibitor ritonavir. | -| [Rahman_MBS2016](problems/Rahman_MBS2016/) | [v1](problems/Rahman_MBS2016/v1/) | | Compartmental epidemiological model of HIV transmission with CD4+ T cell count-based infection stages and treatment, fitted to HIV prevalence in South Africa. | -| [Raia_CancerResearch2011](problems/Raia_CancerResearch2011/) | [v1](problems/Raia_CancerResearch2011/v1/) | | Reaction network model of IL-13-induced JAK2/STAT5 signaling in the primary mediastinal B-cell lymphoma cell line MedB-1. | -| [Raimundez_PCB2020](problems/Raimundez_PCB2020/) | [v1](problems/Raimundez_PCB2020/v1/) | | Reaction network model of EGFR and MET signaling to ERK and AKT in two gastric cancer cell lines in response to EGF and the anti-EGFR antibody cetuximab. | -| [SalazarCavazos_MBoC2020](problems/SalazarCavazos_MBoC2020/) | [v1](problems/SalazarCavazos_MBoC2020/v1/) | | Reaction network model of EGFR dimerization, multisite phosphorylation and binding of the adaptor proteins GRB2 and SHC1, generated from a rule-based model. | -| [Schwen_PONE2014](problems/Schwen_PONE2014/) | [v1](problems/Schwen_PONE2014/v1/) | [v2](problems/Schwen_PONE2014/v2/) | Reaction network model of insulin binding, internalization and degradation in two subpopulations of isolated hepatocytes with low and high insulin binding. | -| [Smith_BMCSystBiol2013](problems/Smith_BMCSystBiol2013/) | [v1](problems/Smith_BMCSystBiol2013/v1/) | | Large reaction network model of insulin signaling in rodent adipocytes and its regulation by oxidative stress. | -| [Sneyd_PNAS2002](problems/Sneyd_PNAS2002/) | [v1](problems/Sneyd_PNAS2002/v1/) | | Kinetic model of the type-2 IP3 receptor, fitted to time courses of calcium release from liver microsomes at varying IP3 and calcium concentrations. | -| [Weber_BMC2015](problems/Weber_BMC2015/) | [v1](problems/Weber_BMC2015/v1/) | | Reaction network model of interactions of protein kinase D, a lipid kinase (PI4KIIIbeta) and a ceramide transfer protein (CERT) at the trans-Golgi network. | -| [Zhao_QuantBiol2020](problems/Zhao_QuantBiol2020/) | [v1](problems/Zhao_QuantBiol2020/v1/) | | Compartmental epidemiological model of COVID-19 in Wuhan, Hubei and the rest of China, with quarantined and unquarantined infected individuals. | -| [Zheng_PNAS2012](problems/Zheng_PNAS2012/) | [v1](problems/Zheng_PNAS2012/v1/) | | Reaction network model of the combinatorial methylation of lysines 27 and 36 on histone H3. | +| ID | PEtab v1 | PEtab v2 | Reference | Description | +|:-------------------------------------------------------------------------------------|:-------------------------------------------------------|:------------------------------------------|:-------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------| +| [Alkan_SciSignal2018](problems/Alkan_SciSignal2018/) | [v1](problems/Alkan_SciSignal2018/v1/) | | [10.1126/scisignal.aat0229](https://doi.org/10.1126/scisignal.aat0229) | Reaction network model of the DNA damage response and cell fate in cancer cells treated with chemotherapeutics, fitted to signaling and cell count data. | +| [Armistead_CellDeathDis2024](problems/Armistead_CellDeathDis2024/) | [v1](problems/Armistead_CellDeathDis2024/v1/) | | [10.1038/s41419-024-07134-2](https://doi.org/10.1038/s41419-024-07134-2) | Small reaction network model of sphingolipid metabolism with ceramide feedback, fitted to lipidomics data of wild-type and mutant zebrafish embryos. | +| [Bachmann_MSB2011](problems/Bachmann_MSB2011/) | [v1](problems/Bachmann_MSB2011/v1/) | | [10.1038/msb.2011.50](https://doi.org/10.1038/msb.2011.50) | Reaction network model of Epo-induced JAK2/STAT5 signaling with two negative feedback regulators (SOCS3, CIS) in murine erythroid progenitor cells. | +| [Beer_MolBioSystems2014](problems/Beer_MolBioSystems2014/) | [v1](problems/Beer_MolBioSystems2014/v1/) | | [10.1039/c3mb70594c](https://doi.org/10.1039/c3mb70594c) | Small kinetic model of bacterial growth and production of the blue pigment indigoidine by engineered variants of a non-ribosomal peptide synthetase. | +| [Bertozzi_PNAS2020](problems/Bertozzi_PNAS2020/) | [v1](problems/Bertozzi_PNAS2020/v1/) | | [10.1073/pnas.2006520117](https://doi.org/10.1073/pnas.2006520117) | SIR compartmental epidemiological model of the early COVID-19 outbreak in New York and California. | +| [Blasi_CellSystems2016](problems/Blasi_CellSystems2016/) | [v1](problems/Blasi_CellSystems2016/v1/) | | [10.1016/j.cels.2016.01.002](https://doi.org/10.1016/j.cels.2016.01.002) | Reaction network model of combinatorial histone H4 acetylation states generated by motif-specific acetylation reactions. | +| [Boehm_JProteomeRes2014](problems/Boehm_JProteomeRes2014/) | [v1](problems/Boehm_JProteomeRes2014/v1/) | [v2](problems/Boehm_JProteomeRes2014/v2/) | [10.1021/pr5006923](https://doi.org/10.1021/pr5006923) | Reaction network model of Epo-induced STAT5A/STAT5B phosphorylation and homo- and heterodimerization, fitted to quantitative mass spectrometry data. | +| [Borghans_BiophysChem1997](problems/Borghans_BiophysChem1997/) | [v1](problems/Borghans_BiophysChem1997/v1/) | | [10.1016/s0301-4622(97)00010-0](https://doi.org/10.1016/s0301-4622(97)00010-0) | Three-variable ODE model of complex calcium oscillations with Ca2+-activated IP3 degradation, fitted to measured calcium bursting in a single hepatocyte. | +| [Brannmark_JBC2010](problems/Brannmark_JBC2010/) | [v1](problems/Brannmark_JBC2010/v1/) | | [10.1074/jbc.M110.106849](https://doi.org/10.1074/jbc.M110.106849) | Reaction network model of insulin receptor and IRS1 phosphorylation with receptor endocytosis and feedback in primary human adipocytes. | +| [Bruno_JExpBot2016](problems/Bruno_JExpBot2016/) | [v1](problems/Bruno_JExpBot2016/v1/) | | [10.1093/jxb/erw356](https://doi.org/10.1093/jxb/erw356) | Enzyme kinetic model of the in vitro cleavage of carotenoids and apocarotenoids by Arabidopsis carotenoid cleavage dioxygenase 4 (CCD4). | +| [Chen_MSB2009](problems/Chen_MSB2009/) | [v1](problems/Chen_MSB2009/v1/) | | [10.1038/msb.2008.74](https://doi.org/10.1038/msb.2008.74) | Large mass-action reaction network model of ErbB receptor signaling to ERK and AKT in response to EGF and heregulin. | +| [Crauste_CellSystems2017](problems/Crauste_CellSystems2017/) | [v1](problems/Crauste_CellSystems2017/v1/) | | [10.1016/j.cels.2017.01.014](https://doi.org/10.1016/j.cels.2017.01.014) | Cell population model of CD8 T cell differentiation (naive, early/late effector, memory), fitted to cell counts in mice after vaccinia virus infection. | +| [Elowitz_Nature2000](problems/Elowitz_Nature2000/) | [v1](problems/Elowitz_Nature2000/v1/) | | [10.1038/35002125](https://doi.org/10.1038/35002125) | Gene regulatory network model of the repressilator, a synthetic three-gene transcriptional oscillator in E. coli, fitted to a fluorescence time course. | +| [Fiedler_BMCSystBiol2016](problems/Fiedler_BMCSystBiol2016/) | [v1](problems/Fiedler_BMCSystBiol2016/v1/) | | [10.1186/s12918-016-0319-7](https://doi.org/10.1186/s12918-016-0319-7) | Reaction network model of RAF/MEK/ERK signaling with ERK feedback in HeLa cells, fitted to phospho-MEK/ERK data without and with RAF or MEK inhibitors. | +| [Froehlich_CellSystems2018](problems/Froehlich_CellSystems2018/) | [v1](problems/Froehlich_CellSystems2018/v1/) | | [10.1016/j.cels.2018.10.013](https://doi.org/10.1016/j.cels.2018.10.013) | Large-scale reaction network model of cancer signaling pathways, parameterized by cell-line-specific gene expression and fitted to drug response viability data. | +| [Fujita_SciSignal2010](problems/Fujita_SciSignal2010/) | [v1](problems/Fujita_SciSignal2010/v1/) | | [10.1126/scisignal.2000810](https://doi.org/10.1126/scisignal.2000810) | Reaction network model of EGF-induced EGFR, Akt and S6 phosphorylation in PC12 cells under different EGF stimulation profiles. | +| [Giordano_Nature2020](problems/Giordano_Nature2020/) | [v1](problems/Giordano_Nature2020/v1/) | | [10.1038/s41591-020-0883-7](https://doi.org/10.1038/s41591-020-0883-7) | Compartmental epidemiological model (SIDARTHE, distinguishing detected/undetected and symptom severity) of the COVID-19 epidemic in Italy. | +| [Isensee_JCB2018](problems/Isensee_JCB2018/) | [v1](problems/Isensee_JCB2018/v1/) | | [10.1083/jcb.201708053](https://doi.org/10.1083/jcb.201708053) | Reaction network model of cAMP-induced PKA activation and phosphorylation of its regulatory subunit in rat sensory neurons under pharmacological perturbations. | +| [Lang_PLOSComputBiol2024](problems/Lang_PLOSComputBiol2024/) | [v1](problems/Lang_PLOSComputBiol2024/v1/) | | [10.1371/journal.pcbi.1011151](https://doi.org/10.1371/journal.pcbi.1011151) | Reaction network model of the human cell cycle, generated from a rule-based model and fitted to compartment-resolved single-cell imaging data of RPE-1 cells. | +| [Laske_PLOSComputBiol2019](problems/Laske_PLOSComputBiol2019/) | [v1](problems/Laske_PLOSComputBiol2019/v1/) | | [10.1371/journal.pcbi.1006944](https://doi.org/10.1371/journal.pcbi.1006944) | Reaction network model of intracellular influenza A virus replication, fitted to viral RNA, genome import and virus release data in human A549 cells. | +| [Liu_IFACPapersOnLine2025](problems/Liu_IFACPapersOnLine2025/) | [v1](problems/Liu_IFACPapersOnLine2025/v1/) | | [10.1016/j.ifacol.2025.07.160](https://doi.org/10.1016/j.ifacol.2025.07.160) | Population model of oncolytic virus therapy with uninfected and infected tumor cells and virus, fitted to tumor size data in zebrafish. | +| [Lucarelli_CellSystems2018](problems/Lucarelli_CellSystems2018/) | [v1](problems/Lucarelli_CellSystems2018/v1/) | | [10.1016/j.cels.2017.11.010](https://doi.org/10.1016/j.cels.2017.11.010) | Reaction network model of TGF-beta-induced SMAD complex formation and target gene expression. | +| [Okuonghae_ChaosSolitonsFractals2020](problems/Okuonghae_ChaosSolitonsFractals2020/) | [v1](problems/Okuonghae_ChaosSolitonsFractals2020/v1/) | | [10.1016/j.chaos.2020.110032](https://doi.org/10.1016/j.chaos.2020.110032) | Compartmental epidemiological model of COVID-19 in Lagos, Nigeria, including asymptomatic and detected infections. | +| [Oliveira_NatCommun2021](problems/Oliveira_NatCommun2021/) | [v1](problems/Oliveira_NatCommun2021/v1/) | | [10.1038/s41467-020-19798-3](https://doi.org/10.1038/s41467-020-19798-3) | Compartmental epidemiological model of COVID-19 in Bahia, Brazil (state excluding the capital Salvador), with non-detected cases, hospitalization and deaths. | +| [Perelson_Science1996](problems/Perelson_Science1996/) | [v1](problems/Perelson_Science1996/v1/) | | [10.1126/science.271.5255.1582](https://doi.org/10.1126/science.271.5255.1582) | Within-host model of HIV-1 viral dynamics, fitted to plasma HIV-1 RNA levels after treatment with the protease inhibitor ritonavir. | +| [Rahman_MBS2016](problems/Rahman_MBS2016/) | [v1](problems/Rahman_MBS2016/v1/) | | [10.1016/j.mbs.2016.07.009](https://doi.org/10.1016/j.mbs.2016.07.009) | Compartmental epidemiological model of HIV transmission with CD4+ T cell count-based infection stages and treatment, fitted to HIV prevalence in South Africa. | +| [Raia_CancerResearch2011](problems/Raia_CancerResearch2011/) | [v1](problems/Raia_CancerResearch2011/v1/) | | [10.1158/0008-5472.CAN-10-2987](https://doi.org/10.1158/0008-5472.CAN-10-2987) | Reaction network model of IL-13-induced JAK2/STAT5 signaling in the primary mediastinal B-cell lymphoma cell line MedB-1. | +| [Raimundez_PCB2020](problems/Raimundez_PCB2020/) | [v1](problems/Raimundez_PCB2020/v1/) | | [10.1371/journal.pcbi.1007147](https://doi.org/10.1371/journal.pcbi.1007147) | Reaction network model of EGFR and MET signaling to ERK and AKT in two gastric cancer cell lines in response to EGF and the anti-EGFR antibody cetuximab. | +| [SalazarCavazos_MBoC2020](problems/SalazarCavazos_MBoC2020/) | [v1](problems/SalazarCavazos_MBoC2020/v1/) | | [10.1091/mbc.E19-09-0548](https://doi.org/10.1091/mbc.E19-09-0548) | Reaction network model of EGFR dimerization, multisite phosphorylation and binding of the adaptor proteins GRB2 and SHC1, generated from a rule-based model. | +| [Schwen_PONE2014](problems/Schwen_PONE2014/) | [v1](problems/Schwen_PONE2014/v1/) | [v2](problems/Schwen_PONE2014/v2/) | [10.1371/journal.pone.0133653](https://doi.org/10.1371/journal.pone.0133653) | Reaction network model of insulin binding, internalization and degradation in two subpopulations of isolated hepatocytes with low and high insulin binding. | +| [Smith_BMCSystBiol2013](problems/Smith_BMCSystBiol2013/) | [v1](problems/Smith_BMCSystBiol2013/v1/) | | [10.1186/1752-0509-7-41](https://doi.org/10.1186/1752-0509-7-41) | Large reaction network model of insulin signaling in rodent adipocytes and its regulation by oxidative stress. | +| [Sneyd_PNAS2002](problems/Sneyd_PNAS2002/) | [v1](problems/Sneyd_PNAS2002/v1/) | | [10.1073/pnas.032281999](https://doi.org/10.1073/pnas.032281999) | Kinetic model of the type-2 IP3 receptor, fitted to time courses of calcium release from liver microsomes at varying IP3 and calcium concentrations. | +| [Weber_BMC2015](problems/Weber_BMC2015/) | [v1](problems/Weber_BMC2015/v1/) | | [10.1186/s12918-015-0147-1](https://doi.org/10.1186/s12918-015-0147-1) | Reaction network model of interactions of protein kinase D, a lipid kinase (PI4KIIIbeta) and a ceramide transfer protein (CERT) at the trans-Golgi network. | +| [Zhao_QuantBiol2020](problems/Zhao_QuantBiol2020/) | [v1](problems/Zhao_QuantBiol2020/v1/) | | [10.1007/s40484-020-0199-0](https://doi.org/10.1007/s40484-020-0199-0) | Compartmental epidemiological model of COVID-19 in Wuhan, Hubei and the rest of China, with quarantined and unquarantined infected individuals. | +| [Zheng_PNAS2012](problems/Zheng_PNAS2012/) | [v1](problems/Zheng_PNAS2012/v1/) | | [10.1073/pnas.1205707109](https://doi.org/10.1073/pnas.1205707109) | Reaction network model of the combinatorial methylation of lysines 27 and 36 on histone H3. | ## License diff --git a/problems/Alkan_SciSignal2018/metadata.yaml b/problems/Alkan_SciSignal2018/metadata.yaml index abdb326..8795ee6 100644 --- a/problems/Alkan_SciSignal2018/metadata.yaml +++ b/problems/Alkan_SciSignal2018/metadata.yaml @@ -1 +1,14 @@ short_description: Reaction network model of the DNA damage response and cell fate in cancer cells treated with chemotherapeutics, fitted to signaling and cell count data. +references: + - doi: 10.1126/scisignal.aat0229 + bibtex: | + @article{Alkan_SciSignal2018, + author = {Alkan, Ozan and Schoeberl, Birgit and Shah, Millie and Koshkaryev, Alexander and Heinemann, Tim and Drummond, Daryl C. and Yaffe, Michael B. and Raue, Andreas}, + title = {Modeling chemotherapy-induced stress to identify rational combination therapies in the {DNA} damage response pathway}, + journal = {Science Signaling}, + year = {2018}, + volume = {11}, + number = {540}, + pages = {eaat0229}, + doi = {10.1126/scisignal.aat0229}, + } diff --git a/problems/Armistead_CellDeathDis2024/metadata.yaml b/problems/Armistead_CellDeathDis2024/metadata.yaml index 2631044..14c6028 100644 --- a/problems/Armistead_CellDeathDis2024/metadata.yaml +++ b/problems/Armistead_CellDeathDis2024/metadata.yaml @@ -1 +1,14 @@ short_description: Small reaction network model of sphingolipid metabolism with ceramide feedback, fitted to lipidomics data of wild-type and mutant zebrafish embryos. +references: + - doi: 10.1038/s41419-024-07134-2 + bibtex: | + @article{Armistead_CellDeathDis2024, + author = {Armistead, Joy and Höpfl, Sebastian and Goldhausen, Pierre and Müller-Hartmann, Andrea and Fahle, Evelin and Hatzold, Julia and Franzen, Rainer and Brodesser, Susanne and Radde, Nicole E. and Hammerschmidt, Matthias}, + title = {A sphingolipid rheostat controls apoptosis versus apical cell extrusion as alternative tumour-suppressive mechanisms}, + journal = {Cell Death \& Disease}, + year = {2024}, + volume = {15}, + number = {10}, + pages = {746}, + doi = {10.1038/s41419-024-07134-2}, + } diff --git a/problems/Bachmann_MSB2011/metadata.yaml b/problems/Bachmann_MSB2011/metadata.yaml index 8d62e9e..9677ef0 100644 --- a/problems/Bachmann_MSB2011/metadata.yaml +++ b/problems/Bachmann_MSB2011/metadata.yaml @@ -1 +1,14 @@ short_description: Reaction network model of Epo-induced JAK2/STAT5 signaling with two negative feedback regulators (SOCS3, CIS) in murine erythroid progenitor cells. +references: + - doi: 10.1038/msb.2011.50 + bibtex: | + @article{Bachmann_MSB2011, + author = {Bachmann, Julie and Raue, Andreas and Schilling, Marcel and Böhm, Martin E. and Kreutz, Clemens and Kaschek, Daniel and Busch, Hauke and Gretz, Norbert and Lehmann, Wolf D. and Timmer, Jens and Klingmüller, Ursula}, + title = {Division of labor by dual feedback regulators controls {JAK2/STAT5} signaling over broad ligand range}, + journal = {Molecular Systems Biology}, + year = {2011}, + volume = {7}, + number = {1}, + pages = {516}, + doi = {10.1038/msb.2011.50}, + } diff --git a/problems/Beer_MolBioSystems2014/metadata.yaml b/problems/Beer_MolBioSystems2014/metadata.yaml index c8ba170..f5e5cdd 100644 --- a/problems/Beer_MolBioSystems2014/metadata.yaml +++ b/problems/Beer_MolBioSystems2014/metadata.yaml @@ -1 +1,14 @@ short_description: Small kinetic model of bacterial growth and production of the blue pigment indigoidine by engineered variants of a non-ribosomal peptide synthetase. +references: + - doi: 10.1039/c3mb70594c + bibtex: | + @article{Beer_MolBioSystems2014, + author = {Beer, Ralf and Herbst, Konrad and Ignatiadis, Nikolaos and Kats, Ilia and Adlung, Lorenz and Meyer, Hannah and Niopek, Dominik and Christiansen, Tania and Georgi, Fanny and Kurzawa, Nils and Meichsner, Johanna and Rabe, Sophie and Riedel, Anja and Sachs, Joshua and Schessner, Julia and Schmidt, Florian and Walch, Philipp and Niopek, Katharina and Heinemann, Tim and Eils, Roland and Di Ventura, Barbara}, + title = {Creating functional engineered variants of the single-module non-ribosomal peptide synthetase {IndC} by {T} domain exchange}, + journal = {Molecular BioSystems}, + year = {2014}, + volume = {10}, + number = {7}, + pages = {1709--1718}, + doi = {10.1039/c3mb70594c}, + } diff --git a/problems/Bertozzi_PNAS2020/metadata.yaml b/problems/Bertozzi_PNAS2020/metadata.yaml index 846f7d4..ad7000c 100644 --- a/problems/Bertozzi_PNAS2020/metadata.yaml +++ b/problems/Bertozzi_PNAS2020/metadata.yaml @@ -1 +1,14 @@ short_description: SIR compartmental epidemiological model of the early COVID-19 outbreak in New York and California. +references: + - doi: 10.1073/pnas.2006520117 + bibtex: | + @article{Bertozzi_PNAS2020, + author = {Bertozzi, Andrea L. and Franco, Elisa and Mohler, George and Short, Martin B. and Sledge, Daniel}, + title = {The challenges of modeling and forecasting the spread of {COVID-19}}, + journal = {Proceedings of the National Academy of Sciences}, + year = {2020}, + volume = {117}, + number = {29}, + pages = {16732--16738}, + doi = {10.1073/pnas.2006520117}, + } diff --git a/problems/Blasi_CellSystems2016/metadata.yaml b/problems/Blasi_CellSystems2016/metadata.yaml index 18d5f69..2cbae89 100644 --- a/problems/Blasi_CellSystems2016/metadata.yaml +++ b/problems/Blasi_CellSystems2016/metadata.yaml @@ -1 +1,14 @@ short_description: Reaction network model of combinatorial histone H4 acetylation states generated by motif-specific acetylation reactions. +references: + - doi: 10.1016/j.cels.2016.01.002 + bibtex: | + @article{Blasi_CellSystems2016, + author = {Blasi, Thomas and Feller, Christian and Feigelman, Justin and Hasenauer, Jan and Imhof, Axel and Theis, Fabian J. and Becker, Peter B. and Marr, Carsten}, + title = {Combinatorial Histone Acetylation Patterns Are Generated by Motif-Specific Reactions}, + journal = {Cell Systems}, + year = {2016}, + volume = {2}, + number = {1}, + pages = {49--58}, + doi = {10.1016/j.cels.2016.01.002}, + } diff --git a/problems/Boehm_JProteomeRes2014/metadata.yaml b/problems/Boehm_JProteomeRes2014/metadata.yaml index 6242d33..7d878f1 100644 --- a/problems/Boehm_JProteomeRes2014/metadata.yaml +++ b/problems/Boehm_JProteomeRes2014/metadata.yaml @@ -1 +1,14 @@ short_description: Reaction network model of Epo-induced STAT5A/STAT5B phosphorylation and homo- and heterodimerization, fitted to quantitative mass spectrometry data. +references: + - doi: 10.1021/pr5006923 + bibtex: | + @article{Boehm_JProteomeRes2014, + author = {Boehm, Martin E. and Adlung, Lorenz and Schilling, Marcel and Roth, Susanne and Klingmüller, Ursula and Lehmann, Wolf D.}, + title = {Identification of Isoform-Specific Dynamics in Phosphorylation-Dependent {STAT5} Dimerization by Quantitative Mass Spectrometry and Mathematical Modeling}, + journal = {Journal of Proteome Research}, + year = {2014}, + volume = {13}, + number = {12}, + pages = {5685--5694}, + doi = {10.1021/pr5006923}, + } diff --git a/problems/Borghans_BiophysChem1997/metadata.yaml b/problems/Borghans_BiophysChem1997/metadata.yaml index 5bad55b..6e9734d 100644 --- a/problems/Borghans_BiophysChem1997/metadata.yaml +++ b/problems/Borghans_BiophysChem1997/metadata.yaml @@ -1 +1,14 @@ short_description: Three-variable ODE model of complex calcium oscillations with Ca2+-activated IP3 degradation, fitted to measured calcium bursting in a single hepatocyte. +references: + - doi: 10.1016/s0301-4622(97)00010-0 + bibtex: | + @article{Borghans_BiophysChem1997, + author = {Borghans, José A. M. and Dupont, Geneviève and Goldbeter, Albert}, + title = {Complex intracellular calcium oscillations. {A} theoretical exploration of possible mechanisms}, + journal = {Biophysical Chemistry}, + year = {1997}, + volume = {66}, + number = {1}, + pages = {25--41}, + doi = {10.1016/s0301-4622(97)00010-0}, + } diff --git a/problems/Brannmark_JBC2010/metadata.yaml b/problems/Brannmark_JBC2010/metadata.yaml index c6acdef..177c70b 100644 --- a/problems/Brannmark_JBC2010/metadata.yaml +++ b/problems/Brannmark_JBC2010/metadata.yaml @@ -1 +1,14 @@ short_description: Reaction network model of insulin receptor and IRS1 phosphorylation with receptor endocytosis and feedback in primary human adipocytes. +references: + - doi: 10.1074/jbc.M110.106849 + bibtex: | + @article{Brannmark_JBC2010, + author = {Brännmark, Cecilia and Palmér, Robert and Glad, S. Torkel and Cedersund, Gunnar and Strålfors, Peter}, + title = {Mass and Information Feedbacks through Receptor Endocytosis Govern Insulin Signaling as Revealed Using a Parameter-free Modeling Framework}, + journal = {Journal of Biological Chemistry}, + year = {2010}, + volume = {285}, + number = {26}, + pages = {20171--20179}, + doi = {10.1074/jbc.M110.106849}, + } diff --git a/problems/Bruno_JExpBot2016/metadata.yaml b/problems/Bruno_JExpBot2016/metadata.yaml index 71343bf..4b1a343 100644 --- a/problems/Bruno_JExpBot2016/metadata.yaml +++ b/problems/Bruno_JExpBot2016/metadata.yaml @@ -1 +1,14 @@ short_description: Enzyme kinetic model of the in vitro cleavage of carotenoids and apocarotenoids by Arabidopsis carotenoid cleavage dioxygenase 4 (CCD4). +references: + - doi: 10.1093/jxb/erw356 + bibtex: | + @article{Bruno_JExpBot2016, + 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}, + title = {Enzymatic study on {AtCCD4} and {AtCCD7} and their potential to form acyclic regulatory metabolites}, + journal = {Journal of Experimental Botany}, + year = {2016}, + volume = {67}, + number = {21}, + pages = {5993--6005}, + doi = {10.1093/jxb/erw356}, + } diff --git a/problems/Chen_MSB2009/metadata.yaml b/problems/Chen_MSB2009/metadata.yaml index 9f773fd..d3a800a 100644 --- a/problems/Chen_MSB2009/metadata.yaml +++ b/problems/Chen_MSB2009/metadata.yaml @@ -1 +1,14 @@ short_description: Large mass-action reaction network model of ErbB receptor signaling to ERK and AKT in response to EGF and heregulin. +references: + - doi: 10.1038/msb.2008.74 + bibtex: | + @article{Chen_MSB2009, + author = {Chen, William W. and Schoeberl, Birgit and Jasper, Paul J. and Niepel, Mario and Nielsen, Ulrik B. and Lauffenburger, Douglas A. and Sorger, Peter K.}, + title = {Input–output behavior of {ErbB} signaling pathways as revealed by a mass action model trained against dynamic data}, + journal = {Molecular Systems Biology}, + year = {2009}, + volume = {5}, + number = {1}, + pages = {239}, + doi = {10.1038/msb.2008.74}, + } diff --git a/problems/Crauste_CellSystems2017/metadata.yaml b/problems/Crauste_CellSystems2017/metadata.yaml index 7dddb22..acdf089 100644 --- a/problems/Crauste_CellSystems2017/metadata.yaml +++ b/problems/Crauste_CellSystems2017/metadata.yaml @@ -1 +1,14 @@ short_description: Cell population model of CD8 T cell differentiation (naive, early/late effector, memory), fitted to cell counts in mice after vaccinia virus infection. +references: + - doi: 10.1016/j.cels.2017.01.014 + bibtex: | + @article{Crauste_CellSystems2017, + author = {Crauste, Fabien and Mafille, Julien and Boucinha, Lilia and Djebali, Sophia and Gandrillon, Olivier and Marvel, Jacqueline and Arpin, Christophe}, + title = {Identification of Nascent Memory {CD8} {T} Cells and Modeling of Their Ontogeny}, + journal = {Cell Systems}, + year = {2017}, + volume = {4}, + number = {3}, + pages = {306--317.e4}, + doi = {10.1016/j.cels.2017.01.014}, + } diff --git a/problems/Elowitz_Nature2000/metadata.yaml b/problems/Elowitz_Nature2000/metadata.yaml index 7141a5a..fbc1d84 100644 --- a/problems/Elowitz_Nature2000/metadata.yaml +++ b/problems/Elowitz_Nature2000/metadata.yaml @@ -1 +1,14 @@ short_description: Gene regulatory network model of the repressilator, a synthetic three-gene transcriptional oscillator in E. coli, fitted to a fluorescence time course. +references: + - doi: 10.1038/35002125 + bibtex: | + @article{Elowitz_Nature2000, + author = {Elowitz, Michael B. and Leibler, Stanislas}, + title = {A synthetic oscillatory network of transcriptional regulators}, + journal = {Nature}, + year = {2000}, + volume = {403}, + number = {6767}, + pages = {335--338}, + doi = {10.1038/35002125}, + } diff --git a/problems/Fiedler_BMCSystBiol2016/metadata.yaml b/problems/Fiedler_BMCSystBiol2016/metadata.yaml index a3bf4ce..49d574b 100644 --- a/problems/Fiedler_BMCSystBiol2016/metadata.yaml +++ b/problems/Fiedler_BMCSystBiol2016/metadata.yaml @@ -1 +1,14 @@ short_description: Reaction network model of RAF/MEK/ERK signaling with ERK feedback in HeLa cells, fitted to phospho-MEK/ERK data without and with RAF or MEK inhibitors. +references: + - doi: 10.1186/s12918-016-0319-7 + bibtex: | + @article{Fiedler_BMCSystBiol2016, + author = {Fiedler, Anna and Raeth, Sebastian and Theis, Fabian J. and Hausser, Angelika and Hasenauer, Jan}, + title = {Tailored parameter optimization methods for ordinary differential equation models with steady-state constraints}, + journal = {BMC Systems Biology}, + year = {2016}, + volume = {10}, + number = {1}, + pages = {80}, + doi = {10.1186/s12918-016-0319-7}, + } diff --git a/problems/Froehlich_CellSystems2018/metadata.yaml b/problems/Froehlich_CellSystems2018/metadata.yaml index 09997e1..f551038 100644 --- a/problems/Froehlich_CellSystems2018/metadata.yaml +++ b/problems/Froehlich_CellSystems2018/metadata.yaml @@ -1 +1,14 @@ short_description: Large-scale reaction network model of cancer signaling pathways, parameterized by cell-line-specific gene expression and fitted to drug response viability data. +references: + - doi: 10.1016/j.cels.2018.10.013 + bibtex: | + @article{Froehlich_CellSystems2018, + author = {Fröhlich, Fabian and Kessler, Thomas and Weindl, Daniel and Shadrin, Alexey and Schmiester, Leonard and Hache, Hendrik and Muradyan, Artur and Schütte, Moritz and Lim, Ji-Hyun and Heinig, Matthias and Theis, Fabian J. and Lehrach, Hans and Wierling, Christoph and Lange, Bodo and Hasenauer, Jan}, + title = {Efficient Parameter Estimation Enables the Prediction of Drug Response Using a Mechanistic Pan-Cancer Pathway Model}, + journal = {Cell Systems}, + year = {2018}, + volume = {7}, + number = {6}, + pages = {567--579.e6}, + doi = {10.1016/j.cels.2018.10.013}, + } diff --git a/problems/Fujita_SciSignal2010/metadata.yaml b/problems/Fujita_SciSignal2010/metadata.yaml index df8148f..b9581c8 100644 --- a/problems/Fujita_SciSignal2010/metadata.yaml +++ b/problems/Fujita_SciSignal2010/metadata.yaml @@ -1 +1,14 @@ short_description: Reaction network model of EGF-induced EGFR, Akt and S6 phosphorylation in PC12 cells under different EGF stimulation profiles. +references: + - doi: 10.1126/scisignal.2000810 + bibtex: | + @article{Fujita_SciSignal2010, + author = {Fujita, Kazuhiro A. and Toyoshima, Yu and Uda, Shinsuke and Ozaki, Yu-ichi and Kubota, Hiroyuki and Kuroda, Shinya}, + title = {Decoupling of Receptor and Downstream Signals in the {Akt} Pathway by Its Low-Pass Filter Characteristics}, + journal = {Science Signaling}, + year = {2010}, + volume = {3}, + number = {132}, + pages = {ra56}, + doi = {10.1126/scisignal.2000810}, + } diff --git a/problems/Giordano_Nature2020/metadata.yaml b/problems/Giordano_Nature2020/metadata.yaml index 193160f..4472327 100644 --- a/problems/Giordano_Nature2020/metadata.yaml +++ b/problems/Giordano_Nature2020/metadata.yaml @@ -1 +1,14 @@ short_description: Compartmental epidemiological model (SIDARTHE, distinguishing detected/undetected and symptom severity) of the COVID-19 epidemic in Italy. +references: + - doi: 10.1038/s41591-020-0883-7 + bibtex: | + @article{Giordano_Nature2020, + author = {Giordano, Giulia and Blanchini, Franco and Bruno, Raffaele and Colaneri, Patrizio and Di Filippo, Alessandro and Di Matteo, Angela and Colaneri, Marta}, + title = {Modelling the {COVID-19} epidemic and implementation of population-wide interventions in {Italy}}, + journal = {Nature Medicine}, + year = {2020}, + volume = {26}, + number = {6}, + pages = {855--860}, + doi = {10.1038/s41591-020-0883-7}, + } diff --git a/problems/Isensee_JCB2018/metadata.yaml b/problems/Isensee_JCB2018/metadata.yaml index d030491..8269803 100644 --- a/problems/Isensee_JCB2018/metadata.yaml +++ b/problems/Isensee_JCB2018/metadata.yaml @@ -1 +1,14 @@ short_description: Reaction network model of cAMP-induced PKA activation and phosphorylation of its regulatory subunit in rat sensory neurons under pharmacological perturbations. +references: + - doi: 10.1083/jcb.201708053 + bibtex: | + @article{Isensee_JCB2018, + author = {Isensee, Jörg and Kaufholz, Melanie and Knape, Matthias J. and Hasenauer, Jan and Hammerich, Hanna and Gonczarowska-Jorge, Humberto and Zahedi, René P. and Schwede, Frank and Herberg, Friedrich W. and Hucho, Tim}, + title = {{PKA-RII} subunit phosphorylation precedes activation by {cAMP} and regulates activity termination}, + journal = {Journal of Cell Biology}, + year = {2018}, + volume = {217}, + number = {6}, + pages = {2167--2184}, + doi = {10.1083/jcb.201708053}, + } diff --git a/problems/Lang_PLOSComputBiol2024/metadata.yaml b/problems/Lang_PLOSComputBiol2024/metadata.yaml index 50ec321..412a28e 100644 --- a/problems/Lang_PLOSComputBiol2024/metadata.yaml +++ b/problems/Lang_PLOSComputBiol2024/metadata.yaml @@ -1 +1,14 @@ short_description: Reaction network model of the human cell cycle, generated from a rule-based model and fitted to compartment-resolved single-cell imaging data of RPE-1 cells. +references: + - doi: 10.1371/journal.pcbi.1011151 + bibtex: | + @article{Lang_PLOSComputBiol2024, + author = {Lang, Paul F. and Penas, David R. and Banga, Julio R. and Weindl, Daniel and Novak, Bela}, + title = {Reusable rule-based cell cycle model explains compartment-resolved dynamics of 16 observables in {RPE-1} cells}, + journal = {PLOS Computational Biology}, + year = {2024}, + volume = {20}, + number = {1}, + pages = {e1011151}, + doi = {10.1371/journal.pcbi.1011151}, + } diff --git a/problems/Laske_PLOSComputBiol2019/metadata.yaml b/problems/Laske_PLOSComputBiol2019/metadata.yaml index 60a5792..7cee2a5 100644 --- a/problems/Laske_PLOSComputBiol2019/metadata.yaml +++ b/problems/Laske_PLOSComputBiol2019/metadata.yaml @@ -1 +1,14 @@ short_description: Reaction network model of intracellular influenza A virus replication, fitted to viral RNA, genome import and virus release data in human A549 cells. +references: + - doi: 10.1371/journal.pcbi.1006944 + bibtex: | + @article{Laske_PLOSComputBiol2019, + author = {Laske, Tanja and Bachmann, Mandy and Dostert, Melanie and Karlas, Alexander and Wirth, Dagmar and Frensing, Timo and Meyer, Thomas F. and Hauser, Hansjörg and Reichl, Udo}, + title = {Model-based analysis of influenza {A} virus replication in genetically engineered cell lines elucidates the impact of host cell factors on key kinetic parameters of virus growth}, + journal = {PLOS Computational Biology}, + year = {2019}, + volume = {15}, + number = {4}, + pages = {e1006944}, + doi = {10.1371/journal.pcbi.1006944}, + } diff --git a/problems/Liu_IFACPapersOnLine2025/metadata.yaml b/problems/Liu_IFACPapersOnLine2025/metadata.yaml index 6d7e1ec..a52c202 100644 --- a/problems/Liu_IFACPapersOnLine2025/metadata.yaml +++ b/problems/Liu_IFACPapersOnLine2025/metadata.yaml @@ -1 +1,14 @@ short_description: Population model of oncolytic virus therapy with uninfected and infected tumor cells and virus, fitted to tumor size data in zebrafish. +references: + - doi: 10.1016/j.ifacol.2025.07.160 + bibtex: | + @article{Liu_IFACPapersOnLine2025, + author = {Liu, Yuhong and Pathirana, Dilan and Hasenauer, Jan}, + title = {Parameter Estimation and Model Selection for the Quantitative Analysis of Oncolytic Virus Therapy in Zebrafish}, + journal = {IFAC-PapersOnLine}, + year = {2025}, + volume = {59}, + number = {6}, + pages = {289--294}, + doi = {10.1016/j.ifacol.2025.07.160}, + } diff --git a/problems/Lucarelli_CellSystems2018/metadata.yaml b/problems/Lucarelli_CellSystems2018/metadata.yaml index c36659d..3892807 100644 --- a/problems/Lucarelli_CellSystems2018/metadata.yaml +++ b/problems/Lucarelli_CellSystems2018/metadata.yaml @@ -1 +1,14 @@ short_description: Reaction network model of TGF-beta-induced SMAD complex formation and target gene expression. +references: + - doi: 10.1016/j.cels.2017.11.010 + bibtex: | + @article{Lucarelli_CellSystems2018, + author = {Lucarelli, Philippe and Schilling, Marcel and Kreutz, Clemens and Vlasov, Artyom and Boehm, Martin E. and Iwamoto, Nao and Steiert, Bernhard and Lattermann, Susen and Wäsch, Marvin and Stepath, Markus and Matter, Matthias S. and Heikenwälder, Mathias and Hoffmann, Katrin and Deharde, Daniela and Damm, Georg and Seehofer, Daniel and Muciek, Maria and Gretz, Norbert and Lehmann, Wolf D. and Timmer, Jens and Klingmüller, Ursula}, + title = {Resolving the Combinatorial Complexity of {Smad} Protein Complex Formation and Its Link to Gene Expression}, + journal = {Cell Systems}, + year = {2018}, + volume = {6}, + number = {1}, + pages = {75--89.e11}, + doi = {10.1016/j.cels.2017.11.010}, + } diff --git a/problems/Okuonghae_ChaosSolitonsFractals2020/metadata.yaml b/problems/Okuonghae_ChaosSolitonsFractals2020/metadata.yaml index ff043e6..10a8ff9 100644 --- a/problems/Okuonghae_ChaosSolitonsFractals2020/metadata.yaml +++ b/problems/Okuonghae_ChaosSolitonsFractals2020/metadata.yaml @@ -1 +1,13 @@ short_description: Compartmental epidemiological model of COVID-19 in Lagos, Nigeria, including asymptomatic and detected infections. +references: + - doi: 10.1016/j.chaos.2020.110032 + bibtex: | + @article{Okuonghae_ChaosSolitonsFractals2020, + author = {Okuonghae, D. and Omame, A.}, + title = {Analysis of a mathematical model for {COVID-19} population dynamics in {Lagos}, {Nigeria}}, + journal = {Chaos, Solitons \& Fractals}, + year = {2020}, + volume = {139}, + pages = {110032}, + doi = {10.1016/j.chaos.2020.110032}, + } diff --git a/problems/Oliveira_NatCommun2021/metadata.yaml b/problems/Oliveira_NatCommun2021/metadata.yaml index 6c16909..d3d608e 100644 --- a/problems/Oliveira_NatCommun2021/metadata.yaml +++ b/problems/Oliveira_NatCommun2021/metadata.yaml @@ -1 +1,14 @@ short_description: Compartmental epidemiological model of COVID-19 in Bahia, Brazil (state excluding the capital Salvador), with non-detected cases, hospitalization and deaths. +references: + - doi: 10.1038/s41467-020-19798-3 + bibtex: | + @article{Oliveira_NatCommun2021, + author = {Oliveira, Juliane F. and Jorge, Daniel C. P. and Veiga, Rafael V. and Rodrigues, Moreno S. and Torquato, Matheus F. and da Silva, Nivea B. and Fiaccone, Rosemeire L. and Cardim, Luciana L. and Pereira, Felipe A. C. and de Castro, Caio P. and Paiva, Aureliano S. S. and Amad, Alan A. S. and Lima, Ernesto A. B. F. and Souza, Diego S. and Pinho, Suani T. R. and Ramos, Pablo Ivan P. and Andrade, Roberto F. S.}, + title = {Mathematical modeling of {COVID-19} in 14.8 million individuals in {Bahia}, {Brazil}}, + journal = {Nature Communications}, + year = {2021}, + volume = {12}, + number = {1}, + pages = {333}, + doi = {10.1038/s41467-020-19798-3}, + } diff --git a/problems/Perelson_Science1996/metadata.yaml b/problems/Perelson_Science1996/metadata.yaml index 41fa767..a185ce7 100644 --- a/problems/Perelson_Science1996/metadata.yaml +++ b/problems/Perelson_Science1996/metadata.yaml @@ -1 +1,14 @@ short_description: Within-host model of HIV-1 viral dynamics, fitted to plasma HIV-1 RNA levels after treatment with the protease inhibitor ritonavir. +references: + - doi: 10.1126/science.271.5255.1582 + bibtex: | + @article{Perelson_Science1996, + author = {Perelson, Alan S. and Neumann, Avidan U. and Markowitz, Martin and Leonard, John M. and Ho, David D.}, + title = {{HIV-1} Dynamics in Vivo: Virion Clearance Rate, Infected Cell Life-Span, and Viral Generation Time}, + journal = {Science}, + year = {1996}, + volume = {271}, + number = {5255}, + pages = {1582--1586}, + doi = {10.1126/science.271.5255.1582}, + } diff --git a/problems/Rahman_MBS2016/metadata.yaml b/problems/Rahman_MBS2016/metadata.yaml index e65e1b1..7b6d045 100644 --- a/problems/Rahman_MBS2016/metadata.yaml +++ b/problems/Rahman_MBS2016/metadata.yaml @@ -1 +1,13 @@ short_description: Compartmental epidemiological model of HIV transmission with CD4+ T cell count-based infection stages and treatment, fitted to HIV prevalence in South Africa. +references: + - doi: 10.1016/j.mbs.2016.07.009 + bibtex: | + @article{Rahman_MBS2016, + author = {Rahman, S. M. Ashrafur and Vaidya, Naveen K. and Zou, Xingfu}, + title = {Impact of early treatment programs on {HIV} epidemics: An immunity-based mathematical model}, + journal = {Mathematical Biosciences}, + year = {2016}, + volume = {280}, + pages = {38--49}, + doi = {10.1016/j.mbs.2016.07.009}, + } diff --git a/problems/Raia_CancerResearch2011/metadata.yaml b/problems/Raia_CancerResearch2011/metadata.yaml index 6c2f454..e9a5935 100644 --- a/problems/Raia_CancerResearch2011/metadata.yaml +++ b/problems/Raia_CancerResearch2011/metadata.yaml @@ -1 +1,14 @@ short_description: Reaction network model of IL-13-induced JAK2/STAT5 signaling in the primary mediastinal B-cell lymphoma cell line MedB-1. +references: + - doi: 10.1158/0008-5472.CAN-10-2987 + bibtex: | + @article{Raia_CancerResearch2011, + author = {Raia, Valentina and Schilling, Marcel and Böhm, Martin and Hahn, Bettina and Kowarsch, Andreas and Raue, Andreas and Sticht, Carsten and Bohl, Sebastian and Saile, Maria and Möller, Peter and Gretz, Norbert and Timmer, Jens and Theis, Fabian and Lehmann, Wolf-Dieter and Lichter, Peter and Klingmüller, Ursula}, + title = {Dynamic Mathematical Modeling of {IL13}-Induced Signaling in {Hodgkin} and Primary Mediastinal {B}-Cell Lymphoma Allows Prediction of Therapeutic Targets}, + journal = {Cancer Research}, + year = {2011}, + volume = {71}, + number = {3}, + pages = {693--704}, + doi = {10.1158/0008-5472.CAN-10-2987}, + } diff --git a/problems/Raimundez_PCB2020/metadata.yaml b/problems/Raimundez_PCB2020/metadata.yaml index 6525abc..a661b32 100644 --- a/problems/Raimundez_PCB2020/metadata.yaml +++ b/problems/Raimundez_PCB2020/metadata.yaml @@ -1 +1,14 @@ short_description: Reaction network model of EGFR and MET signaling to ERK and AKT in two gastric cancer cell lines in response to EGF and the anti-EGFR antibody cetuximab. +references: + - doi: 10.1371/journal.pcbi.1007147 + bibtex: | + @article{Raimundez_PCB2020, + author = {Raimúndez, Elba and Keller, Simone and Zwingenberger, Gwen and Ebert, Karolin and Hug, Sabine and Theis, Fabian J. and Maier, Dieter and Luber, Birgit and Hasenauer, Jan}, + title = {Model-based analysis of response and resistance factors of cetuximab treatment in gastric cancer cell lines}, + journal = {PLOS Computational Biology}, + year = {2020}, + volume = {16}, + number = {3}, + pages = {e1007147}, + doi = {10.1371/journal.pcbi.1007147}, + } diff --git a/problems/SalazarCavazos_MBoC2020/metadata.yaml b/problems/SalazarCavazos_MBoC2020/metadata.yaml index 9b8d8f1..bbf707b 100644 --- a/problems/SalazarCavazos_MBoC2020/metadata.yaml +++ b/problems/SalazarCavazos_MBoC2020/metadata.yaml @@ -1 +1,14 @@ short_description: Reaction network model of EGFR dimerization, multisite phosphorylation and binding of the adaptor proteins GRB2 and SHC1, generated from a rule-based model. +references: + - doi: 10.1091/mbc.E19-09-0548 + bibtex: | + @article{SalazarCavazos_MBoC2020, + author = {Salazar-Cavazos, Emanuel and Nitta, Carolina Franco and Mitra, Eshan D. and Wilson, Bridget S. and Lidke, Keith A. and Hlavacek, William S. and Lidke, Diane S.}, + title = {Multisite {EGFR} phosphorylation is regulated by adaptor protein abundances and dimer lifetimes}, + journal = {Molecular Biology of the Cell}, + year = {2020}, + volume = {31}, + number = {7}, + pages = {695--708}, + doi = {10.1091/mbc.E19-09-0548}, + } diff --git a/problems/Schwen_PONE2014/metadata.yaml b/problems/Schwen_PONE2014/metadata.yaml index 1a9a5ea..1507a73 100644 --- a/problems/Schwen_PONE2014/metadata.yaml +++ b/problems/Schwen_PONE2014/metadata.yaml @@ -1 +1,14 @@ short_description: Reaction network model of insulin binding, internalization and degradation in two subpopulations of isolated hepatocytes with low and high insulin binding. +references: + - doi: 10.1371/journal.pone.0133653 + bibtex: | + @article{Schwen_PONE2014, + author = {Schwen, Lars Ole and Schenk, Arne and Kreutz, Clemens and Timmer, Jens and Bartolomé Rodríguez, María Matilde and Kuepfer, Lars and Preusser, Tobias}, + title = {Representative Sinusoids for Hepatic Four-Scale Pharmacokinetics Simulations}, + journal = {PLOS ONE}, + year = {2015}, + volume = {10}, + number = {7}, + pages = {e0133653}, + doi = {10.1371/journal.pone.0133653}, + } diff --git a/problems/Smith_BMCSystBiol2013/metadata.yaml b/problems/Smith_BMCSystBiol2013/metadata.yaml index ff36c4d..96091b2 100644 --- a/problems/Smith_BMCSystBiol2013/metadata.yaml +++ b/problems/Smith_BMCSystBiol2013/metadata.yaml @@ -1 +1,14 @@ short_description: Large reaction network model of insulin signaling in rodent adipocytes and its regulation by oxidative stress. +references: + - doi: 10.1186/1752-0509-7-41 + bibtex: | + @article{Smith_BMCSystBiol2013, + author = {Smith, Graham R. and Shanley, Daryl P.}, + title = {Computational modelling of the regulation of Insulin signalling by oxidative stress}, + journal = {BMC Systems Biology}, + year = {2013}, + volume = {7}, + number = {1}, + pages = {41}, + doi = {10.1186/1752-0509-7-41}, + } diff --git a/problems/Sneyd_PNAS2002/metadata.yaml b/problems/Sneyd_PNAS2002/metadata.yaml index fe97b22..dab381d 100644 --- a/problems/Sneyd_PNAS2002/metadata.yaml +++ b/problems/Sneyd_PNAS2002/metadata.yaml @@ -1 +1,14 @@ short_description: Kinetic model of the type-2 IP3 receptor, fitted to time courses of calcium release from liver microsomes at varying IP3 and calcium concentrations. +references: + - doi: 10.1073/pnas.032281999 + bibtex: | + @article{Sneyd_PNAS2002, + author = {Sneyd, James and Dufour, Jean-François}, + title = {A dynamic model of the type-2 inositol trisphosphate receptor}, + journal = {Proceedings of the National Academy of Sciences}, + year = {2002}, + volume = {99}, + number = {4}, + pages = {2398--2403}, + doi = {10.1073/pnas.032281999}, + } diff --git a/problems/Weber_BMC2015/metadata.yaml b/problems/Weber_BMC2015/metadata.yaml index a7ab06f..39952d0 100644 --- a/problems/Weber_BMC2015/metadata.yaml +++ b/problems/Weber_BMC2015/metadata.yaml @@ -1 +1,14 @@ short_description: Reaction network model of interactions of protein kinase D, a lipid kinase (PI4KIIIbeta) and a ceramide transfer protein (CERT) at the trans-Golgi network. +references: + - doi: 10.1186/s12918-015-0147-1 + bibtex: | + @article{Weber_BMC2015, + author = {Weber, Patrick and Hornjik, Mariana and Olayioye, Monilola A. and Hausser, Angelika and Radde, Nicole E.}, + title = {A computational model of {PKD} and {CERT} interactions at the trans-{Golgi} network of mammalian cells}, + journal = {BMC Systems Biology}, + year = {2015}, + volume = {9}, + number = {1}, + pages = {9}, + doi = {10.1186/s12918-015-0147-1}, + } diff --git a/problems/Zhao_QuantBiol2020/metadata.yaml b/problems/Zhao_QuantBiol2020/metadata.yaml index a580bb1..cf2b723 100644 --- a/problems/Zhao_QuantBiol2020/metadata.yaml +++ b/problems/Zhao_QuantBiol2020/metadata.yaml @@ -1 +1,14 @@ short_description: Compartmental epidemiological model of COVID-19 in Wuhan, Hubei and the rest of China, with quarantined and unquarantined infected individuals. +references: + - doi: 10.1007/s40484-020-0199-0 + bibtex: | + @article{Zhao_QuantBiol2020, + author = {Zhao, Shilei and Chen, Hua}, + title = {Modeling the epidemic dynamics and control of {COVID-19} outbreak in {China}}, + journal = {Quantitative Biology}, + year = {2020}, + volume = {8}, + number = {1}, + pages = {11--19}, + doi = {10.1007/s40484-020-0199-0}, + } diff --git a/problems/Zheng_PNAS2012/metadata.yaml b/problems/Zheng_PNAS2012/metadata.yaml index ee3dece..f630836 100644 --- a/problems/Zheng_PNAS2012/metadata.yaml +++ b/problems/Zheng_PNAS2012/metadata.yaml @@ -1 +1,14 @@ short_description: Reaction network model of the combinatorial methylation of lysines 27 and 36 on histone H3. +references: + - doi: 10.1073/pnas.1205707109 + bibtex: | + @article{Zheng_PNAS2012, + author = {Zheng, Yupeng and Sweet, Steve M. M. and Popovic, Relja and Martinez-Garcia, Eva and Tipton, Jeremiah D. and Thomas, Paul M. and Licht, Jonathan D. and Kelleher, Neil L.}, + title = {Total kinetic analysis reveals how combinatorial methylation patterns are established on lysines 27 and 36 of histone {H3}}, + journal = {Proceedings of the National Academy of Sciences}, + year = {2012}, + volume = {109}, + number = {34}, + pages = {13549--13554}, + doi = {10.1073/pnas.1205707109}, + } diff --git a/src/python/benchmark_models_petab/__init__.py b/src/python/benchmark_models_petab/__init__.py index c901db2..d4faeea 100644 --- a/src/python/benchmark_models_petab/__init__.py +++ b/src/python/benchmark_models_petab/__init__.py @@ -7,7 +7,7 @@ from . import v1, v2 from .v1 import get_problem, get_problem_yaml_path, get_simulation_df from .C import MODEL_DIRS, MODELS, MODELS_DIR -from .metadata import ProblemMetadata, get_metadata +from .metadata import ProblemMetadata, get_bibtex, get_metadata from .overview import get_overview_df from importlib.metadata import PackageNotFoundError, version diff --git a/src/python/benchmark_models_petab/_site/build.py b/src/python/benchmark_models_petab/_site/build.py index 07f8dc0..2b41b50 100644 --- a/src/python/benchmark_models_petab/_site/build.py +++ b/src/python/benchmark_models_petab/_site/build.py @@ -14,7 +14,7 @@ V1_DIRNAME, V2_DIRNAME, ) -from ..metadata import get_metadata +from ..metadata import get_bibtex, get_metadata REPO_URL = f"https://github.com/{GITHUB_REPO}" LOGO_URL = ( @@ -22,6 +22,8 @@ f"/{GITHUB_DEFAULT_BRANCH}/gfx/logo.svg" ) CONTRIBUTING_URL = f"{REPO_URL}/blob/{GITHUB_DEFAULT_BRANCH}/CONTRIBUTING.md" +#: File name of the BibTeX entries of all problems, next to the page. +BIBTEX_FILENAME = "references.bib" #: Rendering of the columns that are not plain text, by column name. #: Other columns of integer dtype are rendered as numbers. @@ -170,6 +172,9 @@ def get_summary_tiles(v1_df: pd.DataFrame, v2_df: pd.DataFrame) -> list: def create_overview_page(dest: Path) -> None: """Create the HTML page with the v1 and v2 overview tables. + The BibTeX entries of all problems' main publications are written to + `BIBTEX_FILENAME` in the same directory, linked from the page. + :param dest: Path to the output HTML file. """ from jinja2 import Environment, PackageLoader, select_autoescape @@ -184,6 +189,7 @@ def create_overview_page(dest: Path) -> None: repo_url=REPO_URL, logo_url=LOGO_URL, contributing_url=CONTRIBUTING_URL, + bibtex_url=BIBTEX_FILENAME, summary_tiles=get_summary_tiles(v1_df, v2_df), tables={ "v2": get_table( @@ -202,3 +208,4 @@ def create_overview_page(dest: Path) -> None: ) dest.parent.mkdir(parents=True, exist_ok=True) dest.write_text(html, encoding="utf-8") + (dest.parent / BIBTEX_FILENAME).write_text(get_bibtex(), encoding="utf-8") diff --git a/src/python/benchmark_models_petab/_site/templates/index.html.j2 b/src/python/benchmark_models_petab/_site/templates/index.html.j2 index 278ddd8..9c5a6be 100644 --- a/src/python/benchmark_models_petab/_site/templates/index.html.j2 +++ b/src/python/benchmark_models_petab/_site/templates/index.html.j2 @@ -361,6 +361,8 @@ footer { >10, <=5, or 10-100. Click a table and press Ctrl+C to copy its visible rows, including the column headers. + BibTeX entries of the publications the problems are based on: + {{ bibtex_url }}.