Results

Fitting

In its most simple use the Cumulus system can be used to characterize promoters. The example below shows how this can be done for the Pbad Promoter with flowcytometry data. The measurements points in this case are generated by comparing as measurement of an unknown part against two measurements from a well characterized one.

movie

 Dim Arabinose As Compound = New Protein(ParameterSetting, "Arabinose")
 Dim GFP As Compound = New Protein(ParameterSetting, "GFP")

 Dim GFPGene As Gene = New Gene(ParameterSetting, "GFPGene", GFP)
 Dim PbadPromoter As AdditiveHillPromoter = New AdditiveHillPromoter(ParameterSetting, "Pbad Promoter", "Arabinose")

 Dim GFPTranscript As Transcript = New RegularTranscript(ParameterSetting, "GFP Transcript", GFPGene)
 Dim PbadSequence As Sequence = New Sequence(ParameterSetting, "Pbad Sequence", PbadPromoter, GFPTranscript)
 
 Dim Sequences As List(Of Sequence) = New List(Of Sequence)
 Sequences.Add(PbadSequence)

 Dim Compounds As List(Of Compound) = New List(Of Compound)
 Compounds.Add(Arabinose)
 Compounds.Add(GFP)

 Dim Environmentals As List(Of Environmental) = New List(Of Environmental)
 Environmentals.Add(New ExtracellularConcentration(ParameterSetting, "Arabinose"))

 ' Output
 Dim SensorBase As Double = 0
 Dim SensorMultiplier As Double = 500
 Environmentals.Add(New Luminescence(ParameterSetting, "Green Fluorescence", "GFP", SensorBase, SensorMultiplier))

 Dim Cell As Cell = New Cell(Sequences, Compounds, Environmentals)
 Return New Model(Cell)

           Public Overrides Function GetInitialParameters() As ParameterSetting
               Dim ParameterSetting As ParameterSetting = New ParameterSetting()
               ParameterSetting.Add("Pbad Promoter", "LeakageActivation", 0.0001, 0, 0.01)
               ParameterSetting.Add("Pbad Promoter", "MaximumActivation", 0.02, 0.01, 0.02)
               ParameterSetting.Add("Pbad Promoter", "KMid", 20000, 10000, 40000)
               ParameterSetting.Add("Pbad Promoter", "Cooperativety", 2, 1, 3)

               ParameterSetting.Add("Arabinose", "Halflife", 2520, 600, 3600)
               ParameterSetting.Add("GFP", "Halflife", 2520, 600, 3600)

               ParameterSetting.Add("GFP Transcript", "Halflife", 240, 180, 300)
               ParameterSetting.Add("GFP Transcript", "RIBS", 0.02, 0, 0.1)
               ParameterSetting.Add("GFP Transcript", "Delay", 300, 120, 600)

               ParameterSetting.Add("Pbad Sequence", "CopyNumber", 10, 9, 11)
               ParameterSetting.Add("Pbad Sequence", "TranscriptionTime", 300, 120, 600)

               ParameterSetting.Add("Extracellular Arabinose", "TransportRate", 0.00001, 0, 1)

               Return ParameterSetting

Visulisation of out model

Because we did not manage to finish our model we decided to try to model our system in the Cumulus system. One of the main problems in assembling our system seemed to be the defective hybB promoter. For this reason in this model we replaced it with a LacI promoter. In order to operate our system we also assume that we can remove both arabinose and IPTG from the medium in an effcient way.

This figure shows a simulation of our full model. As you can see in the bottomleft corner we induce twice with IPTG for ten minutes, once after 5000 seconds and a second time after 15000 seconds, finally reset the system with a long exposure to arabinose in the medium after 25000

Speedup

The Cumulus system allows for large speedups by parallelization through both the cloud and added machines. We tried this with some typical cloud intances and some local machines in the lab, the results are listed below. The benchmarking was done the the Pbad characterization task described above.