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@@ -1 +1,47 @@
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-# Instructions on use
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+# Instructions
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+
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+## Install code
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+
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+Install with
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+
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+```bash
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+git clone https://git0.fmf.uni-lj.si/studen/PBPK_public.git
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+```
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+
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+Use [GIT][GITinstaller] for Windows. More instructions on the web page.
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+
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+## Dependencies
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+
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+On top of python, you'll need numpy and scipy. Install using pip
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+
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+```
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+pip3 install numpy,scipy
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+```
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+
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+Use windows terminal (ie. cmd.exe)
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+
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+## Use
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+
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+Follow `cDiazepam.json`. Basic instructions:
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+- `runSolver.main(setup,model,parameters,jobDir,srcDir)`
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+ This constructs a model from the model file, sets it up with parameters from parameters file, uses the setup to drive calculation which it stores in jobDir. If srcDir is not a string NONE, it takes the solution from srcDir and continues it until tmax in setup is reached.
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+
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+- `runSolver.loadSolutionFromDir(jobDir,True)`
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+ Read solution from dir jobDir. Returns a dict with fields
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+ t,sol,se,qt,sOut,lut,lutSE,setup,model,parameters,qt,sOut where:
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+
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+ - t is the sequence of time points
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+ - sol is the list of solutions for each compartment at each time point
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+ - se is the error
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+ - lut is the look up table of named containers / indices pairs where index points to a list in solution, ie `['sol'][lut[containerName],j]` is the concentration of containerName at time point j
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+ - lutSE is the lookup table of parameters
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+ - setup is the parsed setup file
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+ - parameters are the parsed parameters
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+ - model is the model parse model
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+
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+
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+
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+
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+
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+[GITinstaller]: https://www.git-scm.com/download/win
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+
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