DBNODECoupler

Full name SMRUCC.genomics.Analysis.BNLearn.DBN.DBNODECoupler Assembly SMRUCC.genomics.Analysis.BNLearn Members 7

Coupling interface between the DBN and metabolic network ODEs. Provides a clean interface for bidirectional data exchange.

Usage in the virtual cell simulation loop:

Dim coupler As New DBNODECoupler(dbn) For Each timeStep In simulation ' ODEs -> DBN: pass metabolite and TF abundances Dim result = coupler.Step(metaboliteConcentrations, tfAbundances)

' DBN -> ODEs: get transcription rates for ODE integration Dim transcriptionRates = coupler.GetRNATranscriptionRates(result)

' Use transcriptionRates in ODE solver: dR/dt = k_syn rate - k_deg R ... integrate ODEs for one time step ... Next

01 Syntax

SMRUCC.genomics.Analysis.BNLearn.DBN.DBNODECoupler

02 Methods

Name	Overloads	Summary
.ctor	1	Create a coupler for the given DBN
Step	1	ODEs -> DBN: Execute one prediction step.
GetRNATranscriptionRates	1	DBN -> ODEs: Get RNA transcript abundance change rates for ODE integration.
GetGeneTranscriptionRate	1	DBN -> ODEs: Get RNA abundance change for a specific gene.
UpdateParametersOnline	1	ODEs -> DBN: Provide observed gene states for online parameter update.
Reset	1	Reset the coupler's internal state (gene state tracking)

03 Properties

Name	Overloads	Summary
DBN	1	The underlying DBN

04 Members

method .ctor #

#ctor(DynamicBayesianNetwork)

Create a coupler for the given DBN

method Step #

Step(Dictionary(Of String, Double), Dictionary(Of String, Double))

ODEs -> DBN: Execute one prediction step.

Takes metabolite concentrations and TF abundances from the ODEs, runs DBN inference, and returns the prediction result.

The coupler internally tracks gene states between steps for nodes that lack direct evidence (e.g., genes that are also TFs).

Parameters

Name	Type	Description
`metaboliteAbundances`	`Dictionary(Of String, Double)`	Metabolite ID -> concentration (from ODEs)
`tfAbundances`	`Dictionary(Of String, Double)`	TF ID -> abundance (from ODEs)

Returns

Prediction result with gene states and RNA abundance changes

method GetRNATranscriptionRates #

GetRNATranscriptionRates(DBNPredictionResult)

DBN -> ODEs: Get RNA transcript abundance change rates for ODE integration.

Returns a dictionary mapping each gene ID to its expected transcription rate. Genes in the same operon share the same rate (co-transcribed).

Usage in ODEs: dR_gene/dt = k_synthesis transcriptionRates(gene) - k_degradation R_gene

method GetGeneTranscriptionRate #

GetGeneTranscriptionRate(DBNPredictionResult, String)

DBN -> ODEs: Get RNA abundance change for a specific gene. Convenience method for accessing a single gene's transcription rate.

method UpdateParametersOnline #

UpdateParametersOnline(Dictionary(Of String, String), Dictionary(Of String, String))

ODEs -> DBN: Provide observed gene states for online parameter update.

After observing actual gene expression (e.g., from RNAseq or reporter assays), call this method to incrementally update the DBN's CPT parameters.

Parameters

Name	Type	Description
`currentStates`	`Dictionary(Of String, String)`	Discrete states at time t
`nextStates`	`Dictionary(Of String, String)`	Discrete states at time t+1

method Reset #

Reset

Reset the coupler's internal state (gene state tracking)

property DBN #

DBN

The underlying DBN