Tutorial A simulation

General

Simulation

Most of our main simulation scripts are intended to run on clusters with queuing systems. Up to now we support SLURM and PBS. That is the reason while most of them bear the prefix "submit".

To get help about the programs used in this tutorial use them with the -h flag. Exemplarily for the network creation you should get an output similar to:

usage: submitVesselgeneration [-h] [-t TYPE [TYPE ...]] [-p VESSELPARAMSET] [-w WIDTH_CUBE] [-i ITER_H] [-e ENSEMBLE_SIZE]

Compute an artificial blood vessel network.

optional arguments:

-h, --help show this help message and exit

-t TYPE [TYPE ...], --type TYPE [TYPE ...] Type of root node configurations, range from 0 to 8

-p VESSELPARAMSET, --VesselParamSet VESSELPARAMSET specify Parameterset for creation, possible configs are found in /krebsjobs/parameters/vesselGenParams.py

-w WIDTH_CUBE, --width_cube WIDTH_CUBE Size of vesselcube you want to create

-i ITER_H, --iter_h ITER_H Number of hieracial iterations

-e ENSEMBLE_SIZE, --ensemble_size ENSEMBLE_SIZE Number of realizations

Parameters

We stored parameters as python dict. For most simulations you need to provide a valid parameter set names which could be found in the corresponding folder at py/krebsjobs/parameters.

Output

The output files are in the hdf format and could easily be inspected with the help of hdfview (https://support.hdfgroup.org/products/java/hdfview/) or various other data handling software supporting that format.

Vesselgenerator

To create a simple vesselnetwork system with the default parameter set run:

submitVesselgeneration -p default -t 8 -w 2000

If everything is set up properly this will create the file vessels-default-typeI-15x19L130-sample00.h5 which we need as input for the following simulations.

Faketumor

Here we assume a simple tumor model for the sake of computational time. Again submitFakeTum -h could be helpful. In the following line we calculate a fake tumor with the parameter set name "default". The parameters corresponding to this type of simulation can be found in the file /py/krebsjobs/parameters/fakeTumorParams.py

submitFakeTum default vessels-default-typeI-15x19L130-sample00.h5

will run the simulation an create an outputfile called fakeTum-default-typeI-sample00-default.h5

Bulk tissue tumor

Run submitBulkTissue -h to get help.

submitBulkTissue bulktissue_tutorial vessels-default-typeI-15x19L130-sample00.h5

will start the simulation. NOTE: on desktop PC this will take a few minutes. Analogously to the the fake tumor the parameterset 'bulktissue_tutorial' could be found in the file /py/krebsjobs/parameters/tumorParameters.py.

The outputfile tumBulk-default-typeI-sample00-bulktissue_tutorial.h5 should be created afterwards.

#Extented oxygen model Run submitDetailedO2 to get help.

submitDetailedO2 default_o2 vessels-default-typeI-15x19L130-sample00.h5 vessels

will launch a simulation. Again parameters could be found and modified in /py/krebsjobs/parameters/parameterSetsO2.py.

The outputfile o2_vessels-default-typeI-15x19L130-sample00_default.h5 should be created.