convert parameter files to pure ASCII

Author: murrayrm

biocrnpyler/mechanisms/transport_parameters.tsv

@@ -1,29 +1,29 @@
-mechanism	part_id	param_name	value	units	comments
-membrane_protein_integration		kb_oligomer	2E-03		Arbitrary value for the binding integration step if protein is an oligomer
-membrane_protein_integration		ku_oligomer	2E-10		Arbitrary value for the unbinding integration steps if protein is an oligomer 
-membrane_protein_integration		kex	1E+01		Arbitrary value for the integration of protein into membrane
-membrane_protein_integration		kcat	5E-01		Arbitrary value for the integration of protein into membrane
-simple_diffusion		k_diff	2E-04		Arbitrary value for the diffusion of molecule through membrane
-simple_membrane_protein_transport		k_trnsp	1E-01		Arbitrary value for the simple transport of molecule through membrane pore 
-facilitated_membrane_protein_transport		kb_subMC	1E-01		Arbitrary value for the binding of signal substrate and membrane carrier
-facilitated_membrane_protein_transport		ku_subMC	1E-01		Arbitrary value for the unbinding of signal substrate and membrane carrier
-facilitated_membrane_protein_transport		k_trnspMC	1E-02		Arbitrary value for the facilitated transport of molecule using membrane carrier
-facilitated_membrane_protein_transport		ku_prodMC	1E-01		Arbitrary value for the unbinding of product and membrane pump
-active_membrane_protein_transport		kb_subMP	1E-01		Arbitrary value for the binding of signal substrate and membrane pump
-active_membrane_protein_transport		ku_subMP	1E-01		Arbitrary value for the unbinding of signal substrate and membrane pump
-active_membrane_protein_transport		kb_subMPnATP	1E-01		Arbitrary value for the binding of signal substrate and membrane pump to energy
-active_membrane_protein_transport		ku_subMPnATP	1E-02		Arbitrary value for the unbinding of signal substrate and membrane pump to energy
-active_membrane_protein_transport		k_trnspMP	1E-02		Arbitrary value for the active transport of molecule using membrane pump
-active_membrane_protein_transport		ku_prodMP	1E-01		Arbitrary value for the unbinding of product and membrane pump
-active_membrane_protein_transport		ku_MP	1E-01		Arbitrary value for the unbinding of waste and membrane pump
-two_component_membrane_signaling		kb_sigMS	2E-03		Arbitrary value for the binding of signal substrate and membrane sensor
-two_component_membrane_signaling		ku_sigMS	2E-10		Arbitrary value for the unbinding of signal substrate and membrane sensor
-two_component_membrane_signaling		kb_autoPhos	2E-03		Arbitrary value for the binding of ATP and membrane sensor
-two_component_membrane_signaling		ku_autoPhos	2E-10		Arbitrary value for the unbinding of ATP and membrane sensor
-two_component_membrane_signaling		k_hydro	1E-01		Arbitrary value for the hydrolysis
-two_component_membrane_signaling		ku_waste	8E-01		Arbitrary value for the unbinding of waste product from hydrolyzed membrane sensor
-two_component_membrane_signaling		kb_phosRP	2E-03		Arbitrary value for the binding of phosphorylated membrane sensor and response protein
-two_component_membrane_signaling		ku_phosRP	1E-10		Arbitrary value for the unbinding of phosphorylated membrane sensor and response protein
-two_component_membrane_signaling		k_phosph	1E-01		Arbitrary value for the phosphorylation of response protein
-two_component_membrane_signaling		ku_activeRP	2E-01		Arbitrary value for the unbinding of response protein and membrane sensor
-two_component_membrane_signaling		ku_dephos	2E-10		Arbitrary value for the dephosphorylation of response protein
+mechanism	part_id	param_name	value	units	comments
+membrane_protein_integration		kb_oligomer	2E-03		Arbitrary value for the binding integration step if protein is an oligomer
+membrane_protein_integration		ku_oligomer	2E-10		Arbitrary value for the unbinding integration steps if protein is an oligomer 
+membrane_protein_integration		kex	1E+01		Arbitrary value for the integration of protein into membrane
+membrane_protein_integration		kcat	5E-01		Arbitrary value for the integration of protein into membrane
+simple_diffusion		k_diff	2E-04		Arbitrary value for the diffusion of molecule through membrane
+simple_membrane_protein_transport		k_trnsp	1E-01		Arbitrary value for the simple transport of molecule through membrane pore 
+facilitated_membrane_protein_transport		kb_subMC	1E-01		Arbitrary value for the binding of signal substrate and membrane carrier
+facilitated_membrane_protein_transport		ku_subMC	1E-01		Arbitrary value for the unbinding of signal substrate and membrane carrier
+facilitated_membrane_protein_transport		k_trnspMC	1E-02		Arbitrary value for the facilitated transport of molecule using membrane carrier
+facilitated_membrane_protein_transport		ku_prodMC	1E-01		Arbitrary value for the unbinding of product and membrane pump
+active_membrane_protein_transport		kb_subMP	1E-01		Arbitrary value for the binding of signal substrate and membrane pump
+active_membrane_protein_transport		ku_subMP	1E-01		Arbitrary value for the unbinding of signal substrate and membrane pump
+active_membrane_protein_transport		kb_subMPnATP	1E-01		Arbitrary value for the binding of signal substrate and membrane pump to energy
+active_membrane_protein_transport		ku_subMPnATP	1E-02		Arbitrary value for the unbinding of signal substrate and membrane pump to energy
+active_membrane_protein_transport		k_trnspMP	1E-02		Arbitrary value for the active transport of molecule using membrane pump
+active_membrane_protein_transport		ku_prodMP	1E-01		Arbitrary value for the unbinding of product and membrane pump
+active_membrane_protein_transport		ku_MP	1E-01		Arbitrary value for the unbinding of waste and membrane pump
+two_component_membrane_signaling		kb_sigMS	2E-03		Arbitrary value for the binding of signal substrate and membrane sensor
+two_component_membrane_signaling		ku_sigMS	2E-10		Arbitrary value for the unbinding of signal substrate and membrane sensor
+two_component_membrane_signaling		kb_autoPhos	2E-03		Arbitrary value for the binding of ATP and membrane sensor
+two_component_membrane_signaling		ku_autoPhos	2E-10		Arbitrary value for the unbinding of ATP and membrane sensor
+two_component_membrane_signaling		k_hydro	1E-01		Arbitrary value for the hydrolysis
+two_component_membrane_signaling		ku_waste	8E-01		Arbitrary value for the unbinding of waste product from hydrolyzed membrane sensor
+two_component_membrane_signaling		kb_phosRP	2E-03		Arbitrary value for the binding of phosphorylated membrane sensor and response protein
+two_component_membrane_signaling		ku_phosRP	1E-10		Arbitrary value for the unbinding of phosphorylated membrane sensor and response protein
+two_component_membrane_signaling		k_phosph	1E-01		Arbitrary value for the phosphorylation of response protein
+two_component_membrane_signaling		ku_activeRP	2E-01		Arbitrary value for the unbinding of response protein and membrane sensor
+two_component_membrane_signaling		ku_dephos	2E-10		Arbitrary value for the dephosphorylation of response protein

biocrnpyler/mixtures/extract_parameters.tsv

@@ -5,13 +5,13 @@
 # otherwise noted:
 #
 #   [TX-TL 2.0] Garamella, Jonathan, Ryan Marshall, Mark Rustad, and Vincent
-#   Noireaux. “The All E. Coli TX-TL Toolbox 2.0: A Platform for Cell-Free
-#   Synthetic Biology”. ACS Synthetic Biology 5, no. 4 (2016):344–55.
+#   Noireaux. "The All E. Coli TX-TL Toolbox 2.0: A Platform for Cell-Free
+#   Synthetic Biology". ACS Synthetic Biology 5, no. 4 (2016):344-55.
 #   https://doi.org/10.1021/acssynbio.5b00296.
 #
 #   [txtlsim] Singhal, Vipul, Zoltan A Tuza, Zachary Z Sun, and Richard
-#   M Murray. “A MATLAB Toolbox for Modeling Genetic Circuits in Cell-Free
-#   Systems”. Synthetic Biology 6, no. 1 (2021):ysab007.
+#   M Murray. "A MATLAB Toolbox for Modeling Genetic Circuits in Cell-Free
+#   Systems". Synthetic Biology 6, no. 1 (2021):ysab007.
 #   https://doi.org/10.1093/synbio/ysab007.
 #
 # The parameters for the most complex mechanisms are listed first, with