Version 7.0.0

@msevestre msevestre released this Jan 31, 2017 · 59 commits to master since this release


Release Notes for the Open Systems Pharmacology Suite 7.0.0

Software Suite

Open Systems Pharmacology Suite (formerly known as Systems Biology Software Suite) is now distributed under GNU GENERAL PUBLIC LICENSE v2 plus clarifying addendum.

PK-Sim and MoBi

Calculation of time profile confidence intervals as output of parameter identification. Three different types of confidence intervals are supported:

  • Confidence Interval: Corresponds to the model error, which is based on the uncertainty of estimated parameters. This uncertainty is based on an estimation of the difference between the mean value of used observed data compared with the mean value of the (unknown) total data.
    01_6 3 2_pi_confidenceinterval
  • Visual Predictive Check Interval: Corresponds to the uncertainty based on the data error. The data error is the standard deviation of the distribution of the used observed data.
    02_6 3 2_pi_vpccheckinterval
  • Prediction Interval: Corresponds to the combination of the model error and the data error. It shows how much future measured data are expected to differ from the model predictions.
    03_6 3 2_pi_predictioninterval

Sensitivity of PK-Parameters (AUC, CMax, …) vs. simulation parameters.

Because PBPK models can be complex and contain numerous input parameters, it would be useful to know which input parameters have the most impact on the output curves. The Sensitivity Analysis tool provides an answer to this question.
For a chosen simulation, the relative impact of selected - or all - input parameters on the PK parameters of the output curves is calculated and displayed. In addition, the input parameters can be ranked by their impact on a certain PK parameter of an output. Results of Sensitivity Analysis can be shown as:

  • Sensitivity table:
    04_6 3 2_sa_results1
  • Ranking of most sensitive simulation parameters. Most sensitive parameters comprise all parameters that contribute to 90% of total sensitivity.
    05_6 3 2_sa_ranking1

Fixed issues and Improvements

PK-Sim and MoBi

  • 46-7335 Graphical display of Parameter Identification results should match log/lin selection
  • 47-8156 Default Visual Feedback Height little bit to small
  • 46-7325 Only log plots in Parameter Identification
  • 47-8190 Parameter Identification: Weights should all be >=0
  • 47-8185 Covariance matrix and Correlation Matrix should only be calculated for residuals with weight >0
  • 46-7339 Applying default templates to PI charts always hides the Simulation column in data browser
  • 46-7332 Parameter Identification aborted - "Do you really want to import the identified parameters?" shows only "OK"
  • 47-8196 NaN in observed data should be ignored in Parameter Identification
  • 47-8173 Crash showing Covariance/Correlation matrix after removing identification parameters
  • 47-8176 PI Analysis charts: After rerun of Parameter Identification Chart settings/options are reset to default
  • 47-8312 PI Analysis charts: Concentration outputs not shown in mass units


  • 47-7496 Enable output of concentration/amount in feces
  • 47-8227 Error exporting PK parameter table from comparison plot of individual simulations
  • 47-8148 Population Simulation Time Profile figures sometimes show too many observed data sets
  • 47-8079 Observed data "Amount in Urine/Feces" cannot be mapped to observers
  • 47-6533 "Plasma protein scale factor" is not variable in a population
  • 47-8199 “Export PK-Analysis” missing in ribbon for export of population simulation
  • 47-8195 PI finishes but PK-Sim does not notice that project has changed when closing
  • 47-8287 Specific binding reaction uses wrong concentration if fraction unbound defined in compound is <1


  • 46-7319 Using Ctrl/C on an empty parameter list crashes MoBi
  • 46-7323 Re-creating (or deleting) simulation produces error in Parameter Identification
  • 46-7328 Simulation Diagram is messed up after update from Building Block
  • 46-7260 After Update of Building Block in Simulation from Building Blocks Symbols remain partly red
  • 46-7333 Change of "GFR Fraction" in Simulation not committable to Passive Transports Building Block

MoBi Toolbox for Matlab

  • 26-5517 Unicode problems in SaveSimulationToXML
  • 26-5516 Error in getPKParametersForConcentration when calculating Vd or Vss for multiple individuals
  • 26-5503 XML file is saved encrypted
  • 47-8296 Ontogenies cannot be set in MoBi Toolbox for Matlab