Add master readme & make commands

Makefile

+all: install unit_tests clean
+
+clean:
+	cd command_line && make clean
+	cd library && make clean
+	cd gui && make clean
+
+install:
+	cd command_line && make install
+	cd library && make install
+	cd gui && make install
+
+uninstall:
+	-cd command_line && make uninstall
+	-cd library && make uninstall
+	-cd gui && make uninstall
+
+unit_tests:
+	-cd command_line && make unit_tests
+	-cd library && make unit_tests

README.md

+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.
+
+
+# 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):
+
+* python-gtksourceview2
+* python2.7-dev
+* libxml2-dev
+* libxslt1-dev
+* libgraphviz-dev
+* pkg-config (fix errors when installing pygraphviz and when config is not loaded...)
+* python-glade2
+* python-gtk2
+
+You can install these dependencies with the following command (on Debian systems):
+
+    sudo apt-get install python-gtksourceview2 python2.7-dev libxml2-dev libxslt1-dev libxslt1-dev libgraphviz-dev pkg-config python-glade2 python-gtk2
+
+
+## Python requirements
+
+Before using `cadbiom` library, the following Python packages
+have to be installed from pypi repository:
+
+* lxml
+* networkx
+* pygraphviz
+* pycryptosat
+
+Note: Cadbiom software requires a SAT solver which is
+proposed as a Python wrapper by an independant library (pycryptosat).
+
+
+For the library itself:
+
+* From Python Package Index:
+
+    pip install cadbiom_cmd
+
+
+* From the current repository
+
+    cd library && make install
+    cd ../command_line && 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_cams}
+                        ...
+
+    optional arguments:
+    -h, --help            show this help message and exit
+    -vv [VERBOSE], --verbose [VERBOSE]
+
+    subcommands:
+    {compute_macs,sort_solutions,parse_trajectories,merge_cams}
+        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_cams          Merge solutions to a csv file. .. note:: CSV file:
+                            <Final property formula>;<cam>
+
+
+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/styles.xml)
+
+
+sort_solutions:
+
+    usage: cadbiom_cmd sort_solutions [-h] sol_file
+
+    positional arguments:
+    sol_file
+
+
+merge_cams:
+
+    usage: cadbiom_cmd merge_cams [-h] [--output [OUTPUT]] [solutions_directory]
+
+    positional arguments:
+    solutions_directory
+
+
+## Graphical User Interface
+
+Usage:
+
+    $ cadbiom
+
+
+# License
+
+CADBIOM is freely available on cadbiom.genouest.org,
+distributed under the terms of the GNU General Public License.