Commit 1986884b authored by VIGNET Pierre's avatar VIGNET Pierre
Browse files

Rewrite first part of the workflow; Add real examples and files

parent bac2df36
......@@ -39,7 +39,7 @@ The generated model will be placed in the ``./output`` folder;
we will focus on the model with specific alterations
intended to optimize the operation of Cadbiom and its solver: ``./output/model_without_scc.bcx``.
TODO: (Download link: `model.bcx <./***.bcx>`_)
(Download link: :download:`pid_model_without_scc.bcx <./_static/demo_files/pid_model_without_scc.bcx>`)
.. note:: Small graphs can be queried and converted from the GUI of Cadbiom.
......@@ -76,7 +76,7 @@ To get information about the model, the subcommand ``model_info``
of the model, and a full summary about the model itself (boundaries, transitions, events, entities locations, entities types).
:Example of file (Download link\: `model_summary.json <model_summary.json>`_):
:Example of JSON file (Download link\: `model_summary.json <_static/demo_files/model_summary.json>`_):
.. code-block:: javascript
......@@ -116,7 +116,7 @@ Such a file could facilitate a work of visualization or a possible mapping of id
because it centralizes in a standardized manner most of the information about BioPAX entities.
:Simplified example of CSV file (Download link\: `all_entities.csv <all_entities.csv>`_):
:Simplified example of CSV file (Download link\: :download:`all_entities.csv <_static/demo_files/all_entities.csv>`):
.. csv-table::
:header: cadbiomName, names, uri, entityType, entityRef, uniprot knowledgebase, chebi, hgnc symbol
......@@ -133,8 +133,7 @@ in the model and thus its analysis by the solver.
Get information and graph based on the model
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
To build a graph based on the model and get information about it,
the subcommand ``model_graph``
To build a graph based on the model and get information about it, the subcommand ``model_graph``
(see `the documentation of the model_graph command <./command_line_usage.html#model_graph>`_) can be used:
.. code-block:: bash
......@@ -149,10 +148,8 @@ the subcommand ``model_graph``
* ``--json``: Create a JSON formated file containing a summary of the graph based on the model.
.. note:: Examples of use and style for Cytoscape are available on the repository: `examples <https://gitlab.inria.fr/pvignet/cadbiom/tree/master/examples>`_
:Example of file (Download link\: `graph_summary.json <graph_summary.json>`_):
:Example of JSON file (Download link\: `graph_summary.json <_static/demo_files/graph_summary.json>`_):
.. code-block:: javascript
......@@ -188,6 +185,11 @@ the subcommand ``model_graph``
}
}
The corresponding GraphML file can be downloaded here :download:`PID_GraphML.graphml <_static/demo_files/PID_GraphML.graphml>`.
.. note:: Examples of use and style dedicated to opening the GraphML file in cytoscape are available
on the repository: `examples <https://gitlab.inria.fr/pvignet/cadbiom/tree/master/examples>`_
Search for molecules of interest
================================
......@@ -198,15 +200,24 @@ With a given model, Cadbiom allows to explain how to obtain an entity or a set o
Ultimately, the software answers to the question: *"Is it possible to find an initialization
such that the given state/property happens?"*
The subcommand ``compute_macs`` `doc <./command_line_usage.html#compute_macs>`_ is designed to compute MACs.
Searching a complex query with a combination of entities requires to express it
in a boolean formula with the names of the entities as variables.
The logical operators available are ``or``, ``and``, ``not``.
The subcommand `solutions_search <./command_line_usage.html#solutions_search>`_ is designed to compute MACs.
:Example\: We are looking for entities involved in the production of extracellular matrix molecules:
:Example\: Search for all the paths explaining the production of the SRP9 protein:
Some combinations of these entities are gathered in the following file: :download:`logical_formulas.txt <_static/demo_files/logical_formulas.txt>`.
This file is then loaded in the solver:
.. code-block:: bash
$ cadbiom_cmd compute_macs model.bcx SRP9 --all_macs --steps 7 --continue
$ cadbiom_cmd solutions_search model_without_scc.bcx --input_file logical_formulas.txt --all_macs --steps 7 --continue
TODO: exemple réel
**Arguments:**
......@@ -214,6 +225,10 @@ Most of the time, the number of steps to reach a solution is significant and the
the necessary computation time ensues. Fortunately, it can be limited with ``--steps``.
Moreover, a stopped calculation can be resumed later thanks to ``--continue``.
* ``--input_file``: Multiple jobs can be launched in parallel if the user provides a file with one
boolean formula per line. In this case, each processor core will be dedicated to
the calculation of one boolean formula (within the limit of the number of available cores).
* ``--all_macs``: Solver will try to search all macs with 0 to the maximum of allowed steps.
* ``--steps``: Maximum of allowed steps to find macs.
......@@ -225,39 +240,40 @@ Moreover, a stopped calculation can be resumed later thanks to ``--continue``.
The program produces two categories of files:
* ``*cam.txt`` files: Each line contains a MAC solution.
Ex: XXXX
* ``*cam.txt`` files: Each line contains a MAC solution. Here is an example taken from the file
corresponding to the query ``COL1A1 and COL3A1 and COL5A1 and MMP2 and not PERP``
(:download:`cam file <_static/demo_files/model_without_scc_COL1A1 and COL3A1 and COL5A1 and MMP2 and not PERP_cam.txt>`).
.. code-block:: text
COL1A1_gene COL3A1_gene COL5A1_gene dNp63a__tetramer__nucleus_v2 ET1_extracellular_region ETA FOXM1B_nucleus GTF3A MMP2_gene
COL1A1_gene COL3A1_gene COL5A1_gene dNp63a__tetramer__nucleus_v2 ET1_extracellular_region ETA Fra1_1O_2O_nucleus GTF3A JUN_2O_2O_nucleus MMP2_gene
* ``*cam_complete.txt`` files: Each MAC solution is followed by the successions of events
fired at each step to obtain them.
Ex: XXXX
fired at each step to obtain them. Here is an example taken from the file
corresponding to the query ``COL1A1 and COL3A1 and COL5A1 and MMP2 and not PERP``
(:download:`cam_complete file <_static/demo_files/model_without_scc_COL1A1 and COL3A1 and COL5A1 and MMP2 and not PERP_cam_complete.txt>`).
Chapter `Processing of the results files <./examples.html#processing-of-the-results-files>`_
will discuss how to use the high-level features available to handle these files.
.. code-block:: text
COL1A1_gene COL3A1_gene COL5A1_gene dNp63a__tetramer__nucleus_v2 ET1_extracellular_region ETA FOXM1B_nucleus GTF3A MMP2_gene
% _h_5848 _h_1070 _h_4563 _h_4049
% _h_5603 _h_1051
COL1A1_gene COL3A1_gene COL5A1_gene dNp63a__tetramer__nucleus_v2 ET1_extracellular_region ETA Fra1_1O_2O_nucleus GTF3A JUN_2O_2O_nucleus MMP2_gene
% _h_5848 _h_1070 _h_4283
% _h_4174 _h_4049 _h_1051
Advanced search
---------------
Searching a complex with a combination of entities requires to express its query
in a boolean formula with the names of the entities as variables.
The logical operators available are ``OR``, ``AND``, ``NOT``.
:Example\: Search for all the paths explaining the production of multiple proteins:
As we can see, these files are not particularly meaningful, which is why the next chapter
`Processing of the results files <./examples.html#processing-of-the-results-files>`_
will discuss how to use the high-level features available to handle them.
.. code-block:: bash
$ cadbiom_cmd compute_macs model.bcx XXXXX --all_macs --steps 7 --continue
TODO: exemple réel
Multiple jobs can be launched in parallel if the user provides a file with one
boolean formula per line. In this case, a processor of the computer will be
dedicated to the calculation of each boolean formula
(within the limit of the number of available processors).
Processing of the results files
......
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