AMMP-PDEVS

Automatic Modeling of Metabolic Pathways in Parallel DEVS

Dependencies

1. C++17 >
2. Boost 1.57 >
3. TinyXML-2
4. Cadmium
5. DESTimes
6. DEVSDiagrammer

Note: Dependencies from 3 to 6 comes in this project as submodules: git submodule update -i --recursive

Standard names

Some variables and concepts have standarized names that are used across the project code, the list of this names is:

• cid: Compartment ID
• sid: Specie ID
• eid: Enzyme ID
• rid: Reaction ID
• rsn: Reaction Set Name

Hot to install the model generator Python module

1. cd model_generator
2. python setup install

How to generate models from SBML files (once installed the model generator)

1. pmgbp_generate_model -f <sbml_file_path> Note: For a complete list of the model generator parameters do: pmgbp_generate_model --help

How to compile a generated model

1. Having the model in the project root dir (where the main.cpp file is palced) run: make all

Notes:

The directory structure format: The structure used in this project for the directory structure was taken from https://hiltmon.com/blog/2013/07/03/a-simple-c-plus-plus-project-structure/

INSTALL MongoDB C++ drivers

Source: http://mongocxx.org/mongocxx-v3/installation/

Step 1:

$sudo apt install cmake libssl-dev libsasl2-dev

Step 2 (install mongo-c-driver):

source: http://mongoc.org/libmongoc/current/installing.html

$ wget https://github.com/mongodb/mongo-c-driver/releases/download/1.17.4/mongo-c-driver-1.17.4.tar.gz $ tar xzf mongo-c-driver-1.17.4.tar.gz $ cd mongo-c-driver-1.17.4 $ mkdir cmake-build $ cd cmake-build $ cmake -DENABLE_AUTOMATIC_INIT_AND_CLEANUP=OFF .. $ make $ sudo make install

step 3 (install mongo-cxx drivers in /usr/local)

source: http://mongocxx.org/mongocxx-v3/installation/linux/

$curl -OL https://github.com/mongodb/mongo-cxx-driver/releases/download/r3.6.2/mongo-cxx-driver-r3.6.2.tar.gz $tar -xzf mongo-cxx-driver-r3.6.2.tar.gz $cd mongo-cxx-driver-r3.6.2/build

$ cmake ..
$ -DCMAKE_BUILD_TYPE=Release
$ -DCMAKE_INSTALL_PREFIX=/usr/local

$ sudo cmake --build . --target EP_mnmlstc_core $ cmake --build . $ sudo cmake --build . --target install

Note: If when running the model with memore, there is an error like this one (error while loading shared libraries: libmongocxx.so._noabi: cannot open shared object library file: No such file or directory) try to upgrade the system: $ sudo apt upgrade (this updates g++ and c++ and that is the problem)