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satya-arjunan committed Jan 9, 2015
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Expand Up @@ -51,16 +51,17 @@ environment variables:
::

$ source ~/.bashrc
$ ecell3-session-monitor (try opening it, the window shown in Figure 1 should appear, and then close it)
$ ecell3-session-monitor

We can now attempt to run a simple 1D diffusion model in the E-Cell Model (EM)
language, simple.em:
The window shown in Figure 1 should appear. Congratulations! You have now
sucessfully installed Spatiocyte. We can now attempt to run a simple 1D
diffusion model in written in python, 1D.py:

::

$ cd $HOME/wrk/spatiocyte/examples/1D
$ ecell3-session 1D.py
$ spatiocyte

The Spatiocyte package includes the MinDE model (see Figure 2)
reported in (Arjunan and Tomita, 2010). We can now attempt to run the
Expand Down Expand Up @@ -128,8 +129,7 @@ get some debugging information using the Valgrind tool:

::

$ valgrind --tool=memcheck --num-callers=40 --leak-check=full python
$ HOME/root/bin/ecell3-session -f modelFileName.eml
$ valgrind --tool=memcheck --num-callers=40 --leak-check=full python $HOME/root/bin/ecell3-session -f modelFileName.eml


.. image:: https://raw.github.com/ecell/spatiocyte-docs/master/images/image12.png
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