A valuable Old Timer

General Electric’s BiodMet is a Java PBPK simulator which is quite old now. It appears in 2008 and did not receive any improvements  at least since 2013. Indeed there are ferocious competitors like Certara’s SimCyp and many others.

However it is still an impressive software, with a GUI providing a detailed simulation of many organs seemingly up to cell level. Indeed not everything is perfect, there is nothing about eyes, the circulatory system is very basic, there is only one lung or kidney, genital organs simulation is not implemented, but for a free to use software it is nevertheless awesome. When the software runs a simulation it says it uses 2126 ODEs equation, which is extremely impressive.

In order to test the veracity of this claim, we used the same approach as in last post. It turns out this claim is somehow true.

Actually the body itself is simulated with 52 equations (mostly for modeling blood usage by organs at cell level and modeling a few to model inter-organ fluid exchanges). There are also for each organ a set of 82 ODEs to model how the drug moves from one compartment to the next and how it is transformed. The pattern is to model how the drug moves from vasculature to organs interstitial medium, and from there back to  vasculature and to cell’s cytosol and from there to each compartment of the cell.

BiodMet is still available at: http://pdsl.research.ge.com/

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When software does not deliver what it advertizes

We are interested in competitors performance.

Most PBPK simulators follow a pattern where a GUI is used to design a physiology model in order to construct ODEs that are solved by an ODE solver. The trick is to make it easy for the user to think in physiology terms, when she enters model’s parameters or reads simulation’s results, while at the same time enable the code to manage an ODE solver accordingly to this model.

Understanding what a solver really does is not so easy, particularly if the source code is not available. But even if it is available, what can be deduced is not very informative, as a model is something which is instantiated at run time, and not something written out in the source code. Most of simulator’s code is used in the GUI, the solver is often provided by a third party such as Numerical recipes (http://numerical.recipes/). Even for the GUI, there is reliance on existing libraries such as Java’s DefaultMutableTreeNode or JFreeChart. To understand what the solver does, one has to observe the user provided function that the ODE solver calls to progress from one step to the next.

We took a small free PBPK modeler. The literature about it is sparse but presents it in a favourable manner. The reader understands this software is a labour of love, minuscule details seems to be taken in account. Its GUI follows the form paradigm and is quite complex.

After decompiling the binaries, we logged each call to the user function, rebuilt the software and ran it with the default values. At the end, it was apparent that this simulator only uses 5 ODEs on only two compartments: Lung and liver. Nothing is computed about  kidney, muscle or heart even if their models are described with much details in this software’s literature.