cadbiom 0.1.8

Cadbiom library

CADBIOM (Computer Aided Design of Biological Models) is an open source modelling software.
Based on Guarded transition semantic, it gives a formal framework to help the modelling of
biological systems such as cell signaling network.

Official website: [link](http://cadbiom.genouest.org/)


# Installation

## System requirements

CADBIOM is mainly developed in Python 2.7.
Before running Cadbiom, the following system packages have to be installed from
the distribution packages library (or similar, depending on your operating system).<br>
**Most of these packages are already installed on basic GNU/Linux systems.**

### Debian-like systems (Ubuntu):

* python2.7-dev
* libxml2-dev
* libxslt1-dev (Library providing the Gnome XSLT engine)
* pkg-config (Fix errors when installing pygraphviz and when config is not loaded)
* libgraphviz-dev (GUI layouts)
* python-gtk2 (GUI)
* python-glade2 (GUI)
* python-gtksourceview2 (GUI)
* python-tk (GUI)

You can install these dependencies with the following command:

sudo apt-get install python-gtksourceview2 python2.7-dev libxml2-dev libxslt1-dev \
libxslt1-dev libgraphviz-dev pkg-config python-glade2 python-gtk2 python-tk

On some old systems you may have to install also `python-pip`.
When installing pygraphviz on some systems, you may have this error:

_graphviz.so: undefined symbol: Agundirected

...which is solved by:

pip install --upgrade pygraphviz --install-option="--include-path=/usr/include/graphviz" \
--install-option="--library-path=/usr/lib/graphviz/"

### Red Hat-like systems (Fedora/CentOS)

* python-devel
* libxml-devel
* redhat-rpm-config (lxml config)
* libxslt-devel (Library providing the Gnome XSLT engine)
* graphviz-devel (GUI layouts)
* pygtk2 (GUI)
* pygtk2-libglade (GUI)
* pygtksourceview (GUI)

You can install these dependencies with the following command:

sudo dnf install python-devel libxml-devel redhat-rpm-config libxslt-devel graphviz-devel \
pygtk2 pygtk2-libglade pygtksourceview


## Python requirements

When `cadbiom` library is installed, the following Python packages
**are automatically** installed from pypi repository:

* lxml
* networkx
* pygraphviz
* numpy
* pycryptosat


### Virtual environment

This is not a mandatory step but it is a good practice to use virtual environments
to separate projects from each other.

* Install virtualenvwrapper:

pip install virtualenvwrapper


* Edit your .bashrc or .zshrc file to source the virtualenvwrapper.sh script with these lines:

export WORKON_HOME=~/.virtualenvs
mkdir -p $WORKON_HOME
source /usr/bin/virtualenvwrapper.sh

The location of this script may vary depending on your Linux distro


* Restart your terminal or run:

source /usr/bin/virtualenvwrapper.sh


* Create your virtualenv:

mkvirtualenv cadbiom -p /usr/bin/python2.7


* Later if you want to reactivate the virtualenv:

workon cadbiom


### SAT solver

Cadbiom software requires a SAT solver which is
proposed as a Python wrapper by an independant library (pycryptosat).

*For now, an non official version of pycryptosat is on pypi and it is used by packages;

Source of the fork if you want to compile it manually:
[Cryptominisat repository](https://gitlab.inria.fr/pvignet/pycryptosat/tree/5.0.1_cmake_dev)*

Here you will find the installation commands of the pycryptosat package:

git clone --branch 5.0.1_cmake_dev [e-mail]:0000B8EG/pycryptosat.git
cd pycryptosat
mkdir build && cd build && cmake ../
make python_interface_install


### Cadbiom

If you want to install from pypi, just do:

pip install cadbiom-cmd
pip install cadbiom-gui


If you want to install the library with its GUI, and command line in one command,
after the git clone step, just do:

make install

---

For the library itself:

* From Python Package Index:

pip install cadbiom_cmd


* From the current repository

cd library && make install


For the command line tool:


* From Python Package Index:

pip install cadbiom_cmd


* From the current repository

cd library && make install
cd ../command_line && make install


For the GUI:

* From Python Package Index:

pip install cadbiom_gui


* From the current repository

cd library && make install
cd ../gui && make install


# Structure of packages

The library contains the cadbiom folder with 4 modules:

antlr3 (folder)
bio_models (folder)
models (folder)

The command line tool exposes the command `cadbiom_cmd` to the current context.

The gui package exposes the command `cadbiom` to the current context.


# Utilization

## Command line

### General:

$ cadbiom_cmd -h

usage: cadbiom_cmd [-h] [-vv [VERBOSE]]
{compute_macs,sort_solutions,parse_trajectories,merge_macs}
...

optional arguments:
-h, --help show this help message and exit
-vv [VERBOSE], --verbose [VERBOSE]

subcommands:
{compute_macs,sort_solutions,parse_trajectories,merge_macs}
compute_macs Parse arguments and launch Cadbiom search of MACs
(Minimal Activation Conditions). - If there is no
input file, there will be only one process. - If an
input file is given, there will be 1 process per line
(per logical formula on each line). - all_macs: Solver
will try to search all macs with 0 to the maximum of
steps allowed. - continue: If there is a mac file from
a previous work, last frontier places will be
reloaded.
sort_solutions Parse a solution file and sort all frontier places in
alphabetical order.
parse_trajectories Parse a complete solution file and make a
representation of trajectories.
The output is in graphml file format and is exported
in 'graphs' directory. .. note:: Requires the
model file.
merge_macs Merge solutions to a csv file. .. note:: CSV file:
<Final property formula>;<mac>
model_comp Model consistency checking. Check if the 2 given
models have the same topology, nodes & edges
attributes/roles. .. note:: You can export a graphml
file for the 2 models.
model_infos Model informations. Get number of nodes, edges,
centralities (degree, closeness, betweenness). ..
note:: You can export a graphml file for model.


### compute_macs:

usage: cadbiom_cmd compute_macs [-h] [--input_file [INPUT_FILE]]
[--combinations] [--steps [STEPS]]
[--all_macs] [--continue]
[--start_prop [START_PROP]]
[--inv_prop [INV_PROP]] [--output [OUTPUT]]
chart_file [final_prop]

positional arguments:
chart_file
final_prop

optional arguments:
-h, --help show this help message and exit
--input_file [INPUT_FILE]
--combinations
--steps [STEPS]
--all_macs
--continue
--start_prop [START_PROP]
--inv_prop [INV_PROP]
--output [OUTPUT]


### parse_trajectories:

usage: cadbiom_cmd parse_trajectories [-h] chart_file sol_file

positional arguments:
chart_file
sol_file

<br>
* Result:

[image](examples/graph_example_with_legend.png)

* Cytoscape styles:

[file](examples/cytoscape_styles.xml)


### sort_solutions:

usage: cadbiom_cmd sort_solutions [-h] sol_file

positional arguments:
sol_file


### merge_macs:

usage: cadbiom_cmd merge_macs [-h] [--output [OUTPUT]] [solutions_directory]

positional arguments:
solutions_directory


### model_comp:

usage: cadbiom_cmd model_comp [-h] [--make_graphs] model_file_1 model_file_2

positional arguments:
model_file_1
model_file_2

optional arguments:
-h, --help show this help message and exit
--graphs
--json
--output [OUTPUT]

<br>

Usage in scripts:

>>> from cadbiom_cmd.solution_repr import graph_isomorph_test
>>> print(graph_isomorph_test('test.bcx', 'test2.bcx', output_dir='graphs/',
make_graphs=False, make_json=False))
INFO: 3 transitions loaded
INFO: 3 transitions loaded
INFO: BUILD GRAPH FOR SOL: Connexin_32_0 Connexin_26_0
INFO: BUILD GRAPH FOR SOL: Connexin_32_0 Connexin_26_0
INFO: Topology checking: True
INFO: Nodes checking: True
INFO: Edges checking: True
{u'nodes': True, u'edges': True, u'topology': True}


### model_infos

usage: cadbiom_cmd model_infos [-h] [--graph] [--json] [--output [OUTPUT]]
model_file

positional arguments:
model_file

optional arguments:
-h, --help show this help message and exit
--graph
--json
--output [OUTPUT]


## Graphical User Interface

Usage:

$ cadbiom


## Logging

Logs are stored in the system temporary dictory:

* On Windows, the directories C:\TEMP, C:\TMP, \TEMP, and \TMP, in that order.
* On all other platforms, the directories /tmp, /var/tmp, and /usr/tmp, in that order.
* As a last resort, the current working directory.


# License

CADBIOM is freely available on cadbiom.genouest.org,
and distributed under the terms of the GNU General Public License.