Commit ff0755ad authored by ysard's avatar ysard
Browse files

Add master readme & make commands

parent ed65bfda
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
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.
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