diff --git a/biosimulators_test_suite/_version.py b/biosimulators_test_suite/_version.py index b757cf8..1ad7804 100644 --- a/biosimulators_test_suite/_version.py +++ b/biosimulators_test_suite/_version.py @@ -1 +1 @@ -__version__ = '0.1.81' +__version__ = '0.1.82' diff --git a/examples/bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ.omex b/examples/bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ.omex index 3438e8c..53b8947 100644 Binary files a/examples/bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ.omex and b/examples/bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ.omex differ diff --git a/examples/bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ/metadata.rdf b/examples/bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ/metadata.rdf index 023f306..9918867 100644 --- a/examples/bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ/metadata.rdf +++ b/examples/bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ/metadata.rdf @@ -18,7 +18,7 @@ - + Homo sapiens @@ -83,21 +83,21 @@ Jonathan Karr - + Jonathan Karr - + David W. P. Dolan, Anze Zupanic, Glyn Nelson, Philip Hall, Satomi Miwa, Thomas B. L. Kirkwood & Daryl P. Shanley. Integrated Stochastic Model of DNA Damage Repair by Non-homologous End Joining and p53/p21- Mediated Early Senescence Signalling. PLoS Comput Biol 11, 5 (2015): e1004246. - + MIT diff --git a/examples/bngl/test-bngl.omex b/examples/bngl/test-bngl.omex index f2a3d8e..9621c6f 100644 Binary files a/examples/bngl/test-bngl.omex and b/examples/bngl/test-bngl.omex differ diff --git a/examples/bngl/test-bngl/metadata.rdf b/examples/bngl/test-bngl/metadata.rdf index 94d3f20..0290b8a 100644 --- a/examples/bngl/test-bngl/metadata.rdf +++ b/examples/bngl/test-bngl/metadata.rdf @@ -24,14 +24,14 @@ Jonathan Karr - + Jonathan Karr - + MIT diff --git a/examples/cellml/Elowitz-Nature-2000-Repressilator.omex b/examples/cellml/Elowitz-Nature-2000-Repressilator.omex index ffd1ac2..dd6f505 100644 Binary files a/examples/cellml/Elowitz-Nature-2000-Repressilator.omex and b/examples/cellml/Elowitz-Nature-2000-Repressilator.omex differ diff --git a/examples/cellml/Elowitz-Nature-2000-Repressilator/metadata.rdf b/examples/cellml/Elowitz-Nature-2000-Repressilator/metadata.rdf index a73c55f..b378e86 100644 --- a/examples/cellml/Elowitz-Nature-2000-Repressilator/metadata.rdf +++ b/examples/cellml/Elowitz-Nature-2000-Repressilator/metadata.rdf @@ -26,7 +26,7 @@ - + Escherichia coli @@ -42,7 +42,7 @@ - + biomodels.db:BIOMD0000000012 @@ -60,7 +60,7 @@ Michael Elowitz - + Michael Elowitz @@ -111,7 +111,7 @@ Jonathan Karr - + Jonathan Karr @@ -119,7 +119,7 @@ - + Michael B Elowitz & Stanislas Leibler. A synthetic oscillatory network of transcriptional regulators. Nature 403, 6767 (2000) 335-338. @@ -127,7 +127,7 @@ - + CC0-1.0 @@ -151,7 +151,7 @@ - + Figure 1c diff --git a/examples/cellml/Lorenz-system.omex b/examples/cellml/Lorenz-system.omex index a6336de..f69d786 100644 Binary files a/examples/cellml/Lorenz-system.omex and b/examples/cellml/Lorenz-system.omex differ diff --git a/examples/cellml/Lorenz-system/metadata.rdf b/examples/cellml/Lorenz-system/metadata.rdf index 65e68b9..36e2157 100644 --- a/examples/cellml/Lorenz-system/metadata.rdf +++ b/examples/cellml/Lorenz-system/metadata.rdf @@ -24,21 +24,21 @@ Jonathan Karr - + Jonathan Karr - + Alan Garny & Peter J. Hunter. OpenCOR: a modular and interoperable approach to computational biology. Front Physiol 6 (2015): 26. - + GPL-3.0-only diff --git a/examples/mass/Bordbar-Cell-Syst-2015-RBC-metabolism.omex b/examples/mass/Bordbar-Cell-Syst-2015-RBC-metabolism.omex index 0db805b..dce5c7d 100644 Binary files a/examples/mass/Bordbar-Cell-Syst-2015-RBC-metabolism.omex and b/examples/mass/Bordbar-Cell-Syst-2015-RBC-metabolism.omex differ diff --git a/examples/mass/Bordbar-Cell-Syst-2015-RBC-metabolism/metadata.rdf b/examples/mass/Bordbar-Cell-Syst-2015-RBC-metabolism/metadata.rdf index 3d01fd9..22d3ca4 100644 --- a/examples/mass/Bordbar-Cell-Syst-2015-RBC-metabolism/metadata.rdf +++ b/examples/mass/Bordbar-Cell-Syst-2015-RBC-metabolism/metadata.rdf @@ -23,7 +23,7 @@ - + Homo sapiens @@ -93,7 +93,7 @@ Jonathan Karr - + Jonathan Karr @@ -101,7 +101,7 @@ - + Aarash Bordbar, Douglas McCloskey, Daniel C Zielinski, Nikolaus Sonnenschein, Neema Jamshidi & Bernhard O Palsson. Personalized Whole-Cell Kinetic Models of Metabolism for Discovery in Genomics and Pharmacodynamics. Cell Syst 1, 4 (2015): 283-292. @@ -109,7 +109,7 @@ - + MIT diff --git a/examples/neuroml-lems/Hodgkin-Huxley-cell-CVODE.omex b/examples/neuroml-lems/Hodgkin-Huxley-cell-CVODE.omex index 53d3f85..b5ab8ee 100644 Binary files a/examples/neuroml-lems/Hodgkin-Huxley-cell-CVODE.omex and b/examples/neuroml-lems/Hodgkin-Huxley-cell-CVODE.omex differ diff --git a/examples/neuroml-lems/Hodgkin-Huxley-cell-CVODE/metadata.rdf b/examples/neuroml-lems/Hodgkin-Huxley-cell-CVODE/metadata.rdf index 7ad4c77..d218fff 100644 --- a/examples/neuroml-lems/Hodgkin-Huxley-cell-CVODE/metadata.rdf +++ b/examples/neuroml-lems/Hodgkin-Huxley-cell-CVODE/metadata.rdf @@ -24,21 +24,21 @@ Jonathan Karr - + Jonathan Karr - + Robert C. Cannon, Padraig Gleeson, Sharon Crook, Gautham Ganapathy, Boris Marin, Eugenio Piasini & R. Angus Silver. LEMS: a language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2. Front Neuroinform 8 (2014): 79. - + LGPL-3.0-only diff --git a/examples/neuroml-lems/Hodgkin-Huxley-cell-Euler.omex b/examples/neuroml-lems/Hodgkin-Huxley-cell-Euler.omex index a16624e..1a2f69a 100644 Binary files a/examples/neuroml-lems/Hodgkin-Huxley-cell-Euler.omex and b/examples/neuroml-lems/Hodgkin-Huxley-cell-Euler.omex differ diff --git a/examples/neuroml-lems/Hodgkin-Huxley-cell-Euler/metadata.rdf b/examples/neuroml-lems/Hodgkin-Huxley-cell-Euler/metadata.rdf index b1dd188..99ffa94 100644 --- a/examples/neuroml-lems/Hodgkin-Huxley-cell-Euler/metadata.rdf +++ b/examples/neuroml-lems/Hodgkin-Huxley-cell-Euler/metadata.rdf @@ -24,21 +24,21 @@ Jonathan Karr - + Jonathan Karr - + Robert C. Cannon, Padraig Gleeson, Sharon Crook, Gautham Ganapathy, Boris Marin, Eugenio Piasini & R. Angus Silver. LEMS: a language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2. Front Neuroinform 8 (2014): 79. - + LGPL-3.0-only diff --git a/examples/rba/Escherichia-coli-K12-WT.omex b/examples/rba/Escherichia-coli-K12-WT.omex index 6557dd7..b5559a8 100644 Binary files a/examples/rba/Escherichia-coli-K12-WT.omex and b/examples/rba/Escherichia-coli-K12-WT.omex differ diff --git a/examples/rba/Escherichia-coli-K12-WT/metadata.rdf b/examples/rba/Escherichia-coli-K12-WT/metadata.rdf index d92224c..2ed072f 100644 --- a/examples/rba/Escherichia-coli-K12-WT/metadata.rdf +++ b/examples/rba/Escherichia-coli-K12-WT/metadata.rdf @@ -25,7 +25,7 @@ - + Escherichia coli K-12 @@ -33,7 +33,7 @@ - + Jeffrey D Orth, Tom M Conrad, Jessica Na, Joshua A Lerman, Hojung Nam, Adam M Feist & Bernhard Ø Palsson. A comprehensive genome-scale reconstruction of Escherichia coli metabolism—2011. Molecular Systems Biology 7 (2011): 535. @@ -123,7 +123,7 @@ Jonathan Karr - + Jonathan Karr @@ -131,7 +131,7 @@ - + Ana Bulović, Stephan Fischer, Marc Dinh, Felipe Golib, Wolfram Liebermeister, Christian Poirier, Laurent Tournier, Edda Klipp, Vincent Fromion & Anne Goelzer. Automated generation of bacterial resource allocation models. Metabolic Engineering 55 (2019): 12-22. @@ -139,7 +139,7 @@ - + GPL-3.0-or-later @@ -163,7 +163,7 @@ - + Figure S13 diff --git a/examples/sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex b/examples/sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex index 740d952..02c1eee 100644 Binary files a/examples/sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex and b/examples/sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex differ diff --git a/examples/sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations/metadata.rdf b/examples/sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations/metadata.rdf index 6832ef6..4063e2d 100644 --- a/examples/sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations/metadata.rdf +++ b/examples/sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations/metadata.rdf @@ -27,7 +27,7 @@ - + Homo sapiens @@ -35,7 +35,7 @@ - + Denise Kirschner & John Carl Panetta. Modeling immunotherapy of the tumor-immune interaction. Journal of Mathematical Biology 37, 3 (1998): 235-252. @@ -43,7 +43,7 @@ - + biomodels.db:BIOMD0000000912 @@ -54,7 +54,7 @@ Giulio Caravagna - + Giulio Caravagna @@ -64,7 +64,7 @@ Alberto d'Onofrio - + Alberto d'Onofrio @@ -74,7 +74,7 @@ Paolo Milazzo - + Paolo Milazzo @@ -92,7 +92,7 @@ Mohammad Umer Sharif Shohan - + Mohammad Umer Sharif Shohan @@ -102,7 +102,7 @@ Jonathan Karr - + Jonathan Karr @@ -110,7 +110,7 @@ - + Giulio Caravagna, Alberto d'Onofrio, Paolo Milazzo & Roberto Barbuti. Journal of Theoretical Biology 265, 3 (2010) 336-345. @@ -118,7 +118,7 @@ - + CC0-1.0 @@ -142,7 +142,7 @@ - + Figure 1 (bottom left) diff --git a/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex b/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex index e994636..05a983e 100644 Binary files a/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex and b/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex differ diff --git a/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg/metadata.rdf b/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg/metadata.rdf index f8bacae..3dbc1fd 100644 --- a/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg/metadata.rdf +++ b/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg/metadata.rdf @@ -29,7 +29,7 @@ - + Schizosaccharomyces pombe @@ -37,21 +37,21 @@ - + cell cycle - + anatomical structure morphogenesis - + mitotic morphogenesis checkpoint signaling @@ -59,14 +59,14 @@ - + John J. Tyson & Bela Novak. Regulation of the eukaryotic cell cycle: molecular antagonism, hysteresis, and irreversible transitions. Journal of Theoretical Biology 210 (2001): 249-263. - + Katherine C. Chen, Attila Csikasz-Nagy, Bela Gyorffy, John Val, Bela Novak & John J. Tyson. Kinetic analysis of a molecular model of the budding yeast cell cycle. Mololecular Biology of the Cell 11 (2000): 369-391. @@ -74,7 +74,7 @@ - + biomodels.db:BIOMD0000000297 @@ -92,7 +92,7 @@ Bela Novak - + Bela Novak @@ -102,7 +102,7 @@ John J. Tyson - + John J. Tyson @@ -121,7 +121,7 @@ Jonathan Karr - + Jonathan Karr @@ -129,7 +129,7 @@ - + Andrea Ciliberto, Bela Novak & John J. Tyson. Cell Biology 163, 3 (2003): 1243-1254. @@ -137,7 +137,7 @@ - + CC0-1.0 @@ -161,7 +161,7 @@ - + Figure 3 @@ -170,7 +170,7 @@ - + Figure 3a @@ -179,7 +179,7 @@ - + Figure 3b @@ -188,7 +188,7 @@ - + Figure 3c @@ -197,7 +197,7 @@ - + Figure 3d diff --git a/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex b/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex index 769aa4a..f87028c 100644 Binary files a/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex and b/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex differ diff --git a/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous/metadata.rdf b/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous/metadata.rdf index 9301543..6dd4cb0 100644 --- a/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous/metadata.rdf +++ b/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous/metadata.rdf @@ -29,7 +29,7 @@ - + Schizosaccharomyces pombe @@ -37,21 +37,21 @@ - + cell cycle - + anatomical structure morphogenesis - + mitotic morphogenesis checkpoint signaling @@ -59,14 +59,14 @@ - + John J. Tyson & Bela Novak. Regulation of the eukaryotic cell cycle: molecular antagonism, hysteresis, and irreversible transitions. Journal of Theoretical Biology 210 (2001): 249-263. - + Katherine C. Chen, Attila Csikasz-Nagy, Bela Gyorffy, John Val, Bela Novak & John J. Tyson. Kinetic analysis of a molecular model of the budding yeast cell cycle. Mololecular Biology of the Cell 11 (2000): 369-391. @@ -74,7 +74,7 @@ - + biomodels.db:BIOMD0000000297 @@ -92,7 +92,7 @@ Bela Novak - + Bela Novak @@ -102,7 +102,7 @@ John J. Tyson - + John J. Tyson @@ -121,7 +121,7 @@ Jonathan Karr - + Jonathan Karr @@ -129,7 +129,7 @@ - + Andrea Ciliberto, Bela Novak & John J. Tyson. Cell Biology 163, 3 (2003): 1243-1254. @@ -137,7 +137,7 @@ - + CC0-1.0 @@ -161,7 +161,7 @@ - + Figure 3 @@ -170,7 +170,7 @@ - + Figure 3a @@ -179,7 +179,7 @@ - + Figure 3b @@ -188,7 +188,7 @@ - + Figure 3c @@ -197,7 +197,7 @@ - + Figure 3d diff --git a/examples/sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation.omex b/examples/sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation.omex index 06318c1..2ca8922 100644 Binary files a/examples/sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation.omex and b/examples/sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation.omex differ diff --git a/examples/sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation/metadata.rdf b/examples/sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation/metadata.rdf index f8a15db..61d05c1 100644 --- a/examples/sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation/metadata.rdf +++ b/examples/sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation/metadata.rdf @@ -33,7 +33,7 @@ - + Tetronarce californica @@ -41,21 +41,21 @@ - + neuromuscular synaptic transmission - + transmission of nerve impulse - + cell surface receptor signaling pathway @@ -63,7 +63,7 @@ - + biomodels.db:BIOMD0000000002 @@ -112,7 +112,7 @@ Jonathan Karr - + Jonathan Karr @@ -120,7 +120,7 @@ - + Edelstein SJ, Schaad O, Henry E, Bertrand D & Changeux JP. A kinetic mechanism for nicotinic acetylcholine receptors based on multiple allosteric transitions. Biological cybernetics 1996, 75 (11): 361-379. @@ -128,7 +128,7 @@ - + CC0-1.0 @@ -152,7 +152,7 @@ - + Figure 4b @@ -161,7 +161,7 @@ - + Figure 4b diff --git a/examples/sbml-core/Elowitz-Nature-2000-Repressilator.omex b/examples/sbml-core/Elowitz-Nature-2000-Repressilator.omex index 3db939d..6f74d9f 100644 Binary files a/examples/sbml-core/Elowitz-Nature-2000-Repressilator.omex and b/examples/sbml-core/Elowitz-Nature-2000-Repressilator.omex differ diff --git a/examples/sbml-core/Elowitz-Nature-2000-Repressilator/metadata.rdf b/examples/sbml-core/Elowitz-Nature-2000-Repressilator/metadata.rdf index a73c55f..b378e86 100644 --- a/examples/sbml-core/Elowitz-Nature-2000-Repressilator/metadata.rdf +++ b/examples/sbml-core/Elowitz-Nature-2000-Repressilator/metadata.rdf @@ -26,7 +26,7 @@ - + Escherichia coli @@ -42,7 +42,7 @@ - + biomodels.db:BIOMD0000000012 @@ -60,7 +60,7 @@ Michael Elowitz - + Michael Elowitz @@ -111,7 +111,7 @@ Jonathan Karr - + Jonathan Karr @@ -119,7 +119,7 @@ - + Michael B Elowitz & Stanislas Leibler. A synthetic oscillatory network of transcriptional regulators. Nature 403, 6767 (2000) 335-338. @@ -127,7 +127,7 @@ - + CC0-1.0 @@ -151,7 +151,7 @@ - + Figure 1c diff --git a/examples/sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution.omex b/examples/sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution.omex index ebae874..1d52239 100644 Binary files a/examples/sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution.omex and b/examples/sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution.omex differ diff --git a/examples/sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution/metadata.rdf b/examples/sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution/metadata.rdf index 313b9b9..5d8b2cd 100644 --- a/examples/sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution/metadata.rdf +++ b/examples/sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution/metadata.rdf @@ -23,7 +23,7 @@ - + Mus musculus @@ -31,7 +31,7 @@ - + iron ion homeostasis @@ -39,7 +39,7 @@ - + biomodels.db:BIOMD0000000734 @@ -85,7 +85,7 @@ Jonathan Karr - + Jonathan Karr @@ -100,7 +100,7 @@ - + Jignesh H Parmar, Grey Davis, Hope Shevchuk & Pedro Mendes. Modeling the dynamics of mouse iron body distribution: hepcidin is necessary but not sufficient. BMC Syst Biol 11, 1 (2017): 57. @@ -108,7 +108,7 @@ - + CC0-1.0 @@ -132,7 +132,7 @@ - + Figure 3b @@ -141,7 +141,7 @@ - + Figure 3c @@ -150,7 +150,7 @@ - + Figure 3d @@ -159,7 +159,7 @@ - + Figure 3e @@ -168,7 +168,7 @@ - + Figure 3f @@ -177,7 +177,7 @@ - + Figure 3g @@ -186,7 +186,7 @@ - + Figure 3h diff --git a/examples/sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis.omex b/examples/sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis.omex index d8273dc..622a5c1 100644 Binary files a/examples/sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis.omex and b/examples/sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis.omex differ diff --git a/examples/sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis/metadata.rdf b/examples/sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis/metadata.rdf index 56844d1..590651f 100644 --- a/examples/sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis/metadata.rdf +++ b/examples/sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis/metadata.rdf @@ -15,21 +15,21 @@ - + Homo sapiens - + signaling pathway - + biomodels.db:BIOMD0000000896 @@ -57,7 +57,7 @@ Jonathan Karr - + Jonathan Karr @@ -70,14 +70,14 @@ - + Zuzanna Szymańska Z & Maciej Zylicz. Mathematical modeling of heat shock protein synthesis in response to temperature change. Journal of Theoretical Biology 259, 3 (2009): 562-569. - + CC0-1.0 @@ -98,7 +98,7 @@ - + Figure 3 diff --git a/examples/sbml-core/Tomida-EMBO-J-2003-NFAT-translocation.omex b/examples/sbml-core/Tomida-EMBO-J-2003-NFAT-translocation.omex index 9a9110d..a960475 100644 Binary files a/examples/sbml-core/Tomida-EMBO-J-2003-NFAT-translocation.omex and b/examples/sbml-core/Tomida-EMBO-J-2003-NFAT-translocation.omex differ diff --git a/examples/sbml-core/Tomida-EMBO-J-2003-NFAT-translocation/metadata.rdf b/examples/sbml-core/Tomida-EMBO-J-2003-NFAT-translocation/metadata.rdf index 8512e3f..2a45b67 100644 --- a/examples/sbml-core/Tomida-EMBO-J-2003-NFAT-translocation/metadata.rdf +++ b/examples/sbml-core/Tomida-EMBO-J-2003-NFAT-translocation/metadata.rdf @@ -16,27 +16,27 @@ - + Homo sapiens - + calcineurin-NFAT signaling cascade - + JURKAT cell - + biomodels.db:BIOMD0000000678 @@ -82,7 +82,7 @@ Jonathan Karr - + Jonathan Karr @@ -95,14 +95,14 @@ - + Taichiro Tomida, Kenzo Hirose, Azusa Takizawa, Futoshi Shibasaki & Masamitsu Iino. NFAT functions as a working memory of Ca2+ signals in decoding Ca2+ oscillation. EMBO J 22, 15 (2003): 3825-3832. - + CC0-1.0 @@ -123,7 +123,7 @@ - + Figure 3c diff --git a/examples/sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML.omex b/examples/sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML.omex index 83dcaed..3249818 100644 Binary files a/examples/sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML.omex and b/examples/sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML.omex differ diff --git a/examples/sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML/metadata.rdf b/examples/sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML/metadata.rdf index 4206cf2..c858099 100644 --- a/examples/sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML/metadata.rdf +++ b/examples/sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML/metadata.rdf @@ -14,27 +14,27 @@ - + Homo sapiens - + mTOR signaling pathway - + DEP Domain-Containing mTOR-Interacting Protein - + biomodels.db:BIOMD0000000823 @@ -62,7 +62,7 @@ Jonathan Karr - + Jonathan Karr @@ -75,14 +75,14 @@ - + Thawfeek M Varusai & Lan K Nguyen. Dynamic modelling of the mTOR signalling network reveals complex emergent behaviours conferred by DEPTOR. Sci Rep 8, 1 (2018): 643. - + CC0-1.0 @@ -103,7 +103,7 @@ - + Figure 2c diff --git a/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous.omex b/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous.omex index 80facb2..5c265a1 100644 Binary files a/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous.omex and b/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous.omex differ diff --git a/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous/metadata.rdf b/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous/metadata.rdf index a73593f..042cfd2 100644 --- a/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous/metadata.rdf +++ b/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous/metadata.rdf @@ -14,28 +14,28 @@ - + cellular organisms - + regulation of circadian rhythm - + Naama Barkai & Stanislas Leibler. Circadian clocks limited by noise. Nature 403, 6767 (2000): 267-268. - + biomodels.db:BIOMD0000000035 @@ -75,21 +75,21 @@ Jonathan Karr - + Jonathan Karr - + José M Vilar, Hao Y Kueh, Naama Barkai & Stanislas Leibler. Mechanisms of noise-resistance in genetic oscillators. Proc Natl Acad Sci USA 99, 9 (2002): 5988-5992. - + CC0-1.0 @@ -110,7 +110,7 @@ - + Figure 1a @@ -118,7 +118,7 @@ - + Figure 2ab diff --git a/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM.omex b/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM.omex index a5e3bf3..1e62bec 100644 Binary files a/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM.omex and b/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM.omex differ diff --git a/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM/metadata.rdf b/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM/metadata.rdf index 06d53b9..c457030 100644 --- a/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM/metadata.rdf +++ b/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM/metadata.rdf @@ -14,28 +14,28 @@ - + cellular organisms - + regulation of circadian rhythm - + Naama Barkai & Stanislas Leibler. Circadian clocks limited by noise. Nature 403, 6767 (2000): 267-268. - + biomodels.db:BIOMD0000000035 @@ -75,21 +75,21 @@ Jonathan Karr - + Jonathan Karr - + José M Vilar, Hao Y Kueh, Naama Barkai & Stanislas Leibler. Mechanisms of noise-resistance in genetic oscillators. Proc Natl Acad Sci USA 99, 9 (2002): 5988-5992. - + CC0-1.0 @@ -110,7 +110,7 @@ - + Figure 1c diff --git a/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA.omex b/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA.omex index f577032..5989807 100644 Binary files a/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA.omex and b/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA.omex differ diff --git a/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA/metadata.rdf b/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA/metadata.rdf index a4b9d96..aef42ba 100644 --- a/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA/metadata.rdf +++ b/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA/metadata.rdf @@ -14,28 +14,28 @@ - + cellular organisms - + regulation of circadian rhythm - + Naama Barkai & Stanislas Leibler. Circadian clocks limited by noise. Nature 403, 6767 (2000): 267-268. - + biomodels.db:BIOMD0000000035 @@ -75,21 +75,21 @@ Jonathan Karr - + Jonathan Karr - + José M Vilar, Hao Y Kueh, Naama Barkai & Stanislas Leibler. Mechanisms of noise-resistance in genetic oscillators. Proc Natl Acad Sci USA 99, 9 (2002): 5988-5992. - + CC0-1.0 @@ -110,7 +110,7 @@ - + Figure 1c diff --git a/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock.omex b/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock.omex index 7249731..00f441b 100644 Binary files a/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock.omex and b/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock.omex differ diff --git a/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock/metadata.rdf b/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock/metadata.rdf index f500330..352be22 100644 --- a/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock/metadata.rdf +++ b/examples/sbml-core/Vilar-PNAS-2002-minimal-circardian-clock/metadata.rdf @@ -14,28 +14,28 @@ - + cellular organisms - + regulation of circadian rhythm - + Naama Barkai & Stanislas Leibler. Circadian clocks limited by noise. Nature 403, 6767 (2000): 267-268. - + biomodels.db:BIOMD0000000035 @@ -75,21 +75,21 @@ Jonathan Karr - + Jonathan Karr - + José M Vilar, Hao Y Kueh, Naama Barkai & Stanislas Leibler. Mechanisms of noise-resistance in genetic oscillators. Proc Natl Acad Sci USA 99, 9 (2002): 5988-5992. - + CC0-1.0 @@ -110,7 +110,7 @@ - + Figure 1a @@ -118,7 +118,7 @@ - + Figure 1c diff --git a/examples/sbml-fbc/Escherichia-coli-core-metabolism.omex b/examples/sbml-fbc/Escherichia-coli-core-metabolism.omex index d25100d..dd0f03b 100644 Binary files a/examples/sbml-fbc/Escherichia-coli-core-metabolism.omex and b/examples/sbml-fbc/Escherichia-coli-core-metabolism.omex differ diff --git a/examples/sbml-fbc/Escherichia-coli-core-metabolism/metadata.rdf b/examples/sbml-fbc/Escherichia-coli-core-metabolism/metadata.rdf index a708296..0a59f91 100644 --- a/examples/sbml-fbc/Escherichia-coli-core-metabolism/metadata.rdf +++ b/examples/sbml-fbc/Escherichia-coli-core-metabolism/metadata.rdf @@ -8,7 +8,7 @@ - + Escherichia coli @@ -37,21 +37,21 @@ Jonathan Karr - + Jonathan Karr - + Ali Ebrahim, Joshua A Lerman, Bernhard O Palsson & Daniel R Hyduke. COBRApy: COnstraints-Based Reconstruction and Analysis for Python. BMC Syst Biol 7 (2013): 74. - + GPL-2.0 diff --git a/examples/sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling.omex b/examples/sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling.omex index 299b904..4654845 100644 Binary files a/examples/sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling.omex and b/examples/sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling.omex differ diff --git a/examples/sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling/metadata.rdf b/examples/sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling/metadata.rdf index 76dc83f..ea6f87f 100644 --- a/examples/sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling/metadata.rdf +++ b/examples/sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling/metadata.rdf @@ -12,34 +12,34 @@ - + Homo sapiens - + tumor necrosis factor-mediated signaling pathway - + epidermal growth factor receptor signaling pathway - + Aidan MacNamara, Camille Terfve, David Henriques, Beatriz Peñalver Bernabé & Julio Saez-Rodriguez. State-time spectrum of signal transduction logic models. Phys Biol 7 (2012): 045003. - + biomodels.db:BIOMD0000000562 @@ -199,21 +199,21 @@ Jonathan Karr - + Jonathan Karr - + Claudine Chaouiya, Duncan Bérenguier, Sarah M Keating, Aurélien Naldi, Martijn P van Iersel, Nicolas Rodriguez, Andreas Dräger, Finja Büchel, Thomas Cokelaer, Bryan Kowal, Benjamin Wicks, Emanuel Gonçalves, Julien Dorier, Michel Page, Pedro T Monteiro, Axel von Kamp, Ioannis Xenarios, Hidde de Jong, Michael Hucka, Steffen Klamt, Denis Thieffry, Nicolas Le Novère, Julio Saez-Rodriguez & Tomáš Helikar. SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. BMC Syst Biol 7 (2013): 135. - + CC0-1.0 @@ -234,7 +234,7 @@ - + Figure 4a diff --git a/examples/sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle.omex b/examples/sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle.omex index d67910b..9a89f99 100644 Binary files a/examples/sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle.omex and b/examples/sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle.omex differ diff --git a/examples/sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle/metadata.rdf b/examples/sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle/metadata.rdf index 40e6ca3..8cff23d 100644 --- a/examples/sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle/metadata.rdf +++ b/examples/sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle/metadata.rdf @@ -12,14 +12,14 @@ - + Saccharomyces cerevisiae - + cell cycle @@ -54,21 +54,21 @@ Jonathan Karr - + Jonathan Karr - + DJ Irons. Logical analysis of the budding yeast cell cycle. J Theor Biol 257, 4 (2009): 543-559. - + GPL-3.0-only diff --git a/examples/smoldyn/Lotka-Volterra.omex b/examples/smoldyn/Lotka-Volterra.omex index 07ec574..65dadb3 100644 Binary files a/examples/smoldyn/Lotka-Volterra.omex and b/examples/smoldyn/Lotka-Volterra.omex differ diff --git a/examples/smoldyn/Lotka-Volterra/metadata.rdf b/examples/smoldyn/Lotka-Volterra/metadata.rdf index b46782d..57ce7ff 100644 --- a/examples/smoldyn/Lotka-Volterra/metadata.rdf +++ b/examples/smoldyn/Lotka-Volterra/metadata.rdf @@ -24,21 +24,21 @@ Jonathan Karr - + Jonathan Karr - + Steven S. Andrews. Smoldyn: particle-based simulation with rule-based modeling, improved molecular interaction and a library interface. Bioinformatics 33, 5 (2017): 710-717. - + GPL-3.0-only diff --git a/examples/xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells.omex b/examples/xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells.omex index af1f82a..4aeefe5 100644 Binary files a/examples/xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells.omex and b/examples/xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells.omex differ diff --git a/examples/xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells/metadata.rdf b/examples/xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells/metadata.rdf index bee316b..c42017f 100644 --- a/examples/xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells/metadata.rdf +++ b/examples/xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells/metadata.rdf @@ -26,7 +26,7 @@ - + Rattus norvegicus @@ -34,7 +34,7 @@ - + modeldb:62272 @@ -70,7 +70,7 @@ Jonathan Karr - + Jonathan Karr @@ -78,7 +78,7 @@ - + Sheng-Nan Wu & Han-Dong Chang. Diethyl pyrocarbonate, a histidine-modifying agent, directly stimulates activity of ATP-sensitive potassium channels in pituitary GH(3) cells. Biochem Pharmacol 71, 5 (2006) 615-623. @@ -86,7 +86,7 @@ - + CC0-1.0 @@ -110,7 +110,7 @@ - + Figure 7a