ma5oud180 / simbrain

A SimGrid-based simulator of protein spread in the brain

SimBrain

A SimGrid-based simulator of protein spread in the brain.

Simulation of misfolded protein propagation in the brain as a distributed computing system

We model the brain as a distributed system where computing nodes represent brain regions and network links transport misfolded proteins (MPs). Nodes may produce, clear, and store MPs using similar processes as described in (Iturria-Medina et al. 2014). We leverage the SimGrid (Casanova et al. 2013) toolkit, the most advanced simulator for distributed systems, to simulate such a system. We compare our discrete-event simulation to the simulator in (Iturria-Medina et al. 2014).

Prerequisites

• SimGrid 3.17
• C

Instalation

• Under Debian, Ubuntu and similar systems, you can simply get the latest version of SimGrid from your distribution. For example, simply type the following in a terminal (as root):

  apt-get install simgrid

• You could also use the SimGrid docker container and get your code into the container, by typing the following in a terminal:

  sudo docker run --rm -it -v /path/to/local/directory:/SimBrain path/to/container/directory /bin/bash

  • example:sudo docker run --rm -it -v /home/masoud/Desktop/SimBrain:/SimBrain bigdatalabteam/simgriddocker /bin/bash

Usage

Type the following in a terminal:

1. List files (ls)

2. Change directory to (cd) SimBrain

3. List files. Then, you will see the following files inside of it: simbrain.c simbrain.xml simbrain_d.xml

4. LD_LIBRARY_PATH=/simgrid/lib

5. export LD_LIBRARY_PATH

6. Compile the C code using the following:

   gcc simbrain.c -I/simgrid/include -L/simgrid/lib -lsimgrid -lm -o simbrain

7. List files. You will see the binary file has been built: simbrain simbrain.c simbrain.xml simbrain_d.xml

8. Run the binary file using the following: ./simbrain ./simbrain.xml ./simbrain_d.xml

License

This project is licensed under the GNU General Public License v3.0 - see the LICENSE file for details.