BioCRNpyler Class	Object Type	Example Notebook
ComplexSpecies	Species	1. Building CRNs Directly.ipynb
OrderedComplexSpecies	Species	1. Building CRNs Directly.ipynb
OrderedPolymerSpecies	Species	1. Building CRNs Directly.ipynb
PolymerConformation	Species	Specialized Tutorials/4. PolymerConformation and CombinatorialConformation.ipynb
Species	Species	1. Building CRNs Directly.ipynb
GeneralPropensity	Propensity	1. Building CRNs Directly.ipynb
Hill	Propensity	1. Building CRNs Directly.ipynb
HillNegative	Propensity	1. Building CRNs Directly.ipynb
HillPositive	Propensity	1. Building CRNs Directly.ipynb
MassAction	Propensity	7. Network Plotting Examples.ipynb
Propensity	Propensity	1. Building CRNs Directly.ipynb
ProportionalHillNegative	Propensity	1. Building CRNs Directly.ipynb
ProportionalHillPositive	Propensity	1. Building CRNs Directly.ipynb
ActivatablePromoter	Component	4. Promoters Transcriptional Regulation and Gene Regulatory Networks.ipynb
CDS	Component	2. Compiling CRNs with Enzymes Catalysis and Binding.ipynb
ChemicalComplex	Component	1. Building CRNs Directly.ipynb
CombinatorialComplex	Component	2. Compiling CRNs with Enzymes Catalysis and Binding.ipynb
CombinatorialConformation	Component	Specialized Tutorials/4. PolymerConformation and CombinatorialConformation.ipynb
CombinatorialConformationPromoter	Component	Specialized Tutorials/4. PolymerConformation and CombinatorialConformation.ipynb
CombinatorialPromoter	Component	4. Promoters Transcriptional Regulation and Gene Regulatory Networks.ipynb
Component	Component	1. Building CRNs Directly.ipynb
Construct	Component	8. Developer Overview.ipynb
DNA	Component	3. DNA Assemblies gene expression transcription and translation.ipynb
DNA_construct	Component	7. Network Plotting Examples.ipynb
DNA_part	Component	9. DNA_construct Examples.ipynb
DNAassembly	Component	3. DNA Assemblies gene expression transcription and translation.ipynb
Enzyme	Component	2. Compiling CRNs with Enzymes Catalysis and Binding.ipynb
IntegraseSite	Component	9. DNA_construct Examples.ipynb
Origin	Component	7. Network Plotting Examples.ipynb
Promoter	Component	3. DNA Assemblies gene expression transcription and translation.ipynb
Protein	Component	3. DNA Assemblies gene expression transcription and translation.ipynb
RBS	Component	2. Compiling CRNs with Enzymes Catalysis and Binding.ipynb
RNA	Component	2. Compiling CRNs with Enzymes Catalysis and Binding.ipynb
RNA_construct	Component	9. DNA_construct Examples.ipynb
RegulatedPromoter	Component	4. Promoters Transcriptional Regulation and Gene Regulatory Networks.ipynb
RepressiblePromoter	Component	4. Promoters Transcriptional Regulation and Gene Regulatory Networks.ipynb
Terminator	Component	7. Network Plotting Examples.ipynb
BasicCatalysis	Mechanism	2. Compiling CRNs with Enzymes Catalysis and Binding.ipynb
Combinatorial_Cooperative_Binding	Mechanism	Specialized Tutorials/1. CombinatorialPromoter Details.ipynb
Deg_Tagged_Degradation	Mechanism	6. Global Mechanisms.ipynb
Degradation_mRNA_MM	Mechanism	3. DNA Assemblies gene expression transcription and translation.ipynb
Dilution	Mechanism	3. DNA Assemblies gene expression transcription and translation.ipynb
Mechanism	Mechanism	2. Compiling CRNs with Enzymes Catalysis and Binding.ipynb
MichaelisMenten	Mechanism	2. Compiling CRNs with Enzymes Catalysis and Binding.ipynb
MichaelisMentenReversible	Mechanism	2. Compiling CRNs with Enzymes Catalysis and Binding.ipynb
OneStepGeneExpression	Mechanism	3. DNA Assemblies gene expression transcription and translation.ipynb
One_Step_Binding	Mechanism	2. Compiling CRNs with Enzymes Catalysis and Binding.ipynb
One_Step_Cooperative_Binding	Mechanism	9. DNA_construct Examples.ipynb
SimpleTranscription	Mechanism	3. DNA Assemblies gene expression transcription and translation.ipynb
SimpleTranslation	Mechanism	3. DNA Assemblies gene expression transcription and translation.ipynb
Transcription_MM	Mechanism	3. DNA Assemblies gene expression transcription and translation.ipynb
Translation_MM	Mechanism	3. DNA Assemblies gene expression transcription and translation.ipynb
multi_tl	Mechanism	Specialized Tutorials/3, MultiOccupancyTxTl_Demo.ipynb
multi_tx	Mechanism	Specialized Tutorials/3, MultiOccupancyTxTl_Demo.ipynb
EnergyTxTlExtract	Mixture	Specialized Tutorials/5. TxTl Toolbox.ipynb
ExpressionDilutionMixture	Mixture	3. DNA Assemblies gene expression transcription and translation.ipynb
ExpressionExtract	Mixture	3. DNA Assemblies gene expression transcription and translation.ipynb
Mixture	Mixture	2. Compiling CRNs with Enzymes Catalysis and Binding.ipynb
SimpleTxTlDilutionMixture	Mixture	3. DNA Assemblies gene expression transcription and translation.ipynb
SimpleTxTlExtract	Mixture	3. DNA Assemblies gene expression transcription and translation.ipynb
TxTlDilutionMixture	Mixture	3. DNA Assemblies gene expression transcription and translation.ipynb
TxTlExtract	Mixture	3. DNA Assemblies gene expression transcription and translation.ipynb
CRNPlotter	Other	Specialized Tutorials/6. Integrase Examples.ipynb
ChemicalReactionNetwork	Other	1. Building CRNs Directly.ipynb
Compartment	Other	Specialized Tutorials/2. Membrane Models .ipynb
Complex	Other	1. Building CRNs Directly.ipynb
IntegraseRule	Other	9. DNA_construct Examples.ipynb
Integrase_Enumerator	Other	9. DNA_construct Examples.ipynb
OrderedMonomer	Other	9. DNA_construct Examples.ipynb
OrderedPolymer	Other	1. Building CRNs Directly.ipynb
Parameter	Other	1. Building CRNs Directly.ipynb
ParameterDatabase	Other	5. Parameters.ipynb
ParameterEntry	Other	1. Building CRNs Directly.ipynb
ParameterKey	Other	2. Compiling CRNs with Enzymes Catalysis and Binding.ipynb
Reaction	Other	1. Building CRNs Directly.ipynb
