The program digitalroot version 1.0 is written by

Kirsten ten Tusscher
Theoretical Biology and Bioinformatics Group
Department of Biology
Faculty of Science
Utrecht University

This program was developed in close collaboration with the experimental groups of Prof. Ben Scheres at Wageningen University and Dr. Ari Pekka Mahonen at the University of Helsinki

All below information can also be found in the file README.doc.

Conditions of use:

By downloading the program you implicitly agree to the following conditions of use: At all times, be it on websites, in presentations, lectures, articles or books, when the program or adapted versions of the program have been used a full reference should be made to the following article:
A.P. Mahonen et al., PLETHORA gradient formation mechanism separates auxin responses, Nature ....., 2014

Furthermore, the program is made available under the GNU General Public License (see the file GNUGeneralPublicLicense.doc), and as such all associated further conditions apply.

General information:

The program simulates the regulation of growth and developmental zonation dynamics by the phytohormone auxin and the PLETHORA transcription factors in a simplified, two dimensional model of the Arabidopsis root.

The program is written in C++. As a consequence, you may need to install a C++ compiler to configure the program and C++ libraries needed by the program. The program is developed under an Ubuntu Linux environment. No platform independence can be garantueed.

To install the program:

1. create a directory "digitalroot"

2. download the file "digitalroot.tar.gz" in this directory

3. unpack the file using "tar -xvf digitalroot.tar.gz"

If all went well you now have in the directory digitalroot a file called "Makefile" and the subdirectories "src" "include" "bin" and "obj". The makefile in the directory digitalroot and the secondary makefile in the subdirectory "obj" are needed to reconfigure (compile) the program after changes have been made. The *.cc source code files can be found in the directory "src". In the directory "include" you can find the file "Header.hh" which contains the parameter settings of the model as well as switches to choose the type of simulation you want to perform. In addition it contains all function definitions.

To use the program:

1. make the desired changes in the file "Header.hh" in the directory "include"

2. to configure the changed program type "make" in the directory "digitalroot" this produces an executable called "digitalroot" in the subdirectory "bin" (as well as a number of so-called object files in the subdirectory "obj")

3. to run the simulation:
a. create in the directory digitalroot a subdirectory in which you want simulation results to be put
b. type "./bin/digitalroot name-of-subdirectory-you-created &"

4. to view simulation results:
a. go to the subdirectory you created
b. use a program capable of viewing *.png picture files to look at snapshots of auxin, PLT, growth, zonation etc. dynamics
c. use a program capable of plotting graphs to visualize the output written in files called "Totalauxin", "GridResolutionxxx", "Spatialdynamicsxx" or "TemporalDynamicsxxx" containing the tissues total auxin content over time, or the longitudinal and transversal distributions of auxin, PLT, differentiation levels at particular time points, etc. To find what data exactly is written to these files look in the source code file "src/".

To simulate different conditions and interpret program output:

Please note that when not using the option "restart" (see in directory "include" the file "Header.hh" and the explanation given there), simulations start from scratch and auxin gradients, PLT expression and protein domains, and cellular differentiation profiles need a considerable while before approximately steady state conditions have developed. (Whether or not you have reached steady state conditions can be checked by plotting the contents of the file TotalAuxin and seeing whether total tissue auxin content is approaching approximately -after all there is growth- constant levels). It is only after steady state conditions have developed that program output can be subjected to sensible biological interpretation.

To test out model behaviour for different simulation conditions proceed as follows:

1. First perform an equilibriation simulation: Run the model under it's default conditions (original settings of the provided code) for a long time (>250000 simulated time), ensuring that steady state zonation and growth dynamics have been reached. Note that the program will automatically store its entiry state at certain intervals in files called "DumpPlantStateAtxxx", where xxx is the time at which the state was saved.

2. Next perform a test simulation, in which you test the effect of a particular condition. For this you need to do the following:
a. Change the file "Header.hh" to the conditions you wish to test
b. Copy a "DumpPlantStateAtxxx" file from the output directory of the equilibration simulation to the output directory for the new test simulation. Make sure that you use a "DumpPlantStateAtxxx" file corresponding to steady state growth and zonation dynamics, that is xxx>250000
c. In the file "Header.hh" (in directory include) activate the define statement "RESTART", now the simulation will not start from scratch but instead restart from the provided "DumpPlantStateAtxxx" file.
d. In the file "" at line 133 ensure that starttime has the correct value, that is corresponding to the xxx in the name of the "DumpPlantStateAtxxx" file. Now the program knows which restart file it has too look for.