README.md 5.38 KB
Newer Older
1
2
3
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.
4
5
6
7
8
9


# Installation

## System requirements

VIGNET Pierre's avatar
VIGNET Pierre committed
10
CADBIOM is mainly developed in Python 2.7.
11
12
Before running Cadbiom, the following system packages have to be installed from
the distribution packages library (or similar, depending on your operating system):
13
14

* python-gtksourceview2
VIGNET Pierre's avatar
VIGNET Pierre committed
15
* python2.7-dev
16
17
* libxml2-dev
* libxslt1-dev
18
19
20
21
* libgraphviz-dev
* pkg-config (fix errors when installing pygraphviz and when config is not loaded...)
* python-glade2
* python-gtk2
22

23
24
You can install these dependencies with the following command (on Debian systems):

25
    sudo apt-get install python-gtksourceview2 python2.7-dev libxml2-dev libxslt1-dev libxslt1-dev libgraphviz-dev pkg-config python-glade2 python-gtk2
26

27
28
29

## Python requirements

30
Before using `cadbiom` library, the following Python packages
VIGNET Pierre's avatar
VIGNET Pierre committed
31
have to be installed from pypi repository:
32

33
34
35
* lxml
* networkx
* pygraphviz
36
* pycryptosat
37
38

Note: Cadbiom software requires a SAT solver which is
39
proposed as a Python wrapper by an independant library (pycryptosat).
40
41


42
For the library itself:
43

44
* From Python Package Index:
45

46
    pip install cadbiom_cmd
47
48


49
* From the current repository
50

51
52
    cd library && make install
    cd ../command_line && make install
53
54


55
For the command line tool:
56
57


58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
* 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.
93
94


95
# Utilization
96
97
98

## Command line

ysard's avatar
ysard committed
99
### General:
100

101
    $ cadbiom_cmd -h
102

103
    usage: cadbiom_cmd [-h] [-vv [VERBOSE]]
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
                        {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>


ysard's avatar
ysard committed
133
### compute_macs:
134

135
    usage: cadbiom_cmd compute_macs [-h] [--input_file [INPUT_FILE]]
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
                                    [--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]


ysard's avatar
ysard committed
158
### parse_trajectories:
159

160
    usage: cadbiom_cmd parse_trajectories [-h] chart_file sol_file
161
162
163
164
165
166

    positional arguments:
    chart_file
    sol_file

<br>
ysard's avatar
ysard committed
167
* Result:
168

169
170
[image](examples/graph_example_with_legend.png)

ysard's avatar
ysard committed
171
* Cytoscape styles:
172
173
174
175

[file](examples/styles.xml)


ysard's avatar
ysard committed
176
### sort_solutions:
177
178
179
180
181
182
183

    usage: cadbiom_cmd sort_solutions [-h] sol_file

    positional arguments:
    sol_file


ysard's avatar
ysard committed
184
### merge_cams:
185
186
187
188
189
190
191
192
193
194
195
196
197

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

    positional arguments:
    solutions_directory


## Graphical User Interface

Usage:

    $ cadbiom

198

ysard's avatar
ysard committed
199
200
201
202
203
204
205
206
207
## 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.


208
209
210
# License

CADBIOM is freely available on cadbiom.genouest.org,
ysard's avatar
ysard committed
211
and distributed under the terms of the GNU General Public License.