MAJ terminée. Nous sommes passés en version 14.6.2 . Pour consulter les "releases notes" associées c'est ici :

https://about.gitlab.com/releases/2022/01/11/security-release-gitlab-14-6-2-released/
https://about.gitlab.com/releases/2022/01/04/gitlab-14-6-1-released/

Commit 95e4280c authored by VIGNET Pierre's avatar VIGNET Pierre
Browse files

[doc] Fix typos

parent ffcfe214
......@@ -323,7 +323,7 @@ To get information about the biological entities in the model, the subcommand ``
of the model, and a full summary about the model itself (boundaries, transitions, events, entities locations, entities types).
:Example of JSON file (Download link\: `model_summary.json <_static/demo_files/model_summary.json>`_):
Example of JSON file (Download link\: `model_summary.json <_static/demo_files/model_summary.json>`_):
.. code-block:: javascript
......@@ -363,7 +363,7 @@ 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\: :download:`all_entities.csv <_static/demo_files/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 , location , uniprot knowledgebase , chebi
......@@ -396,7 +396,7 @@ To build a graph based on the model and get information about it, the subcommand
* ``--json``: Create a JSON formated file containing a summary of the graph based on the model.
:Example of JSON file (Download link\: `graph_summary.json <_static/demo_files/graph_summary.json>`_):
Example of JSON file (Download link\: `graph_summary.json <_static/demo_files/graph_summary.json>`_):
.. code-block:: javascript
......@@ -454,7 +454,7 @@ external identifier.
* ``--external_identifiers``: Multiple external identifiers to be mapped.
:Example of CSV file (Download link\: :download:`mapping.csv <_static/demo_files/mapping_examples.csv>`):
Example of CSV file (Download link\: :download:`mapping.csv <_static/demo_files/mapping_examples.csv>`):
.. csv-table::
:header: External identifiers, Cadbiom identifiers
......@@ -481,7 +481,7 @@ 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\: We are looking for entities involved in the production of extracellular matrix molecules:
Some combinations of these entities are gathered in the following file: :download:`logical_formulas.txt <_static/demo_files/logical_formulas.txt>`.
......@@ -563,7 +563,7 @@ This command requires the model and solution files of type ``*.mac_complete.txt`
We will take the example of the file seen in the previous chapter.
:Example:
Example:
.. code-block:: bash
......@@ -619,7 +619,7 @@ solutions_2_common_graph
interest.
:Example:
Example:
.. code-block:: bash
......@@ -652,7 +652,7 @@ solutions_2_json
attributes involved in a solution.
:Example:
Example:
.. code-block:: bash
......@@ -676,7 +676,7 @@ json_2_interaction_graph
interest, the genes and other frontier
places/boundaries found among all the solutions.
:Example:
Example:
.. code-block:: bash
......@@ -708,7 +708,7 @@ solutions_2_occcurrences_matrix
path.
:Example:
Example:
.. code-block:: bash
......
......@@ -20,8 +20,8 @@ without heavy design changes to GTK3 that is specific to Python 3.
.. https://stackoverflow.com/questions/27542828/is-it-possible-to-create-gtk2-x-applications-using-python-3
We use standard Python application packaging by hosting our program on the PyPI platform.
This simple and light but well-proven system allows to quickly deploy and install an application.
We use standard Python application packaging by hosting our program on the PyPI (Python Package Index) platform.
This simple and light but well-proven system allows quickly deploying, and installing an application.
The procedure is described in the next chapter.
.. seealso:: `Working with Cadbiom source code <./dev_work_with_source.html#working-with-cadbiom-source-code>`_
......
......@@ -82,14 +82,14 @@ The GUI provides a graph editor to build and explore models;
it purposes a simple query interface to analyse the dynamics of a model (i.e. search properties and
conduct discrete time simulations).
The command line allows users to search trajectories, and necessary and sufficient sets of boundaries
The command line module allows searching trajectories, and necessary and sufficient sets of boundaries
related to the states of the places of interest mentioned in a logical formula built by the user.
These sets are also called Minimal Activation Conditions.
Output files from Cadbiom can be difficult to exploit by hand
(See `Cadbiom file format specification <./file_format_specification.html>`_);
they contain the sequences of transitions necessary to satisfy a problem.
We have developed sub modules that allow to work with these files from the command line.
We have developed sub commands that allow to work with these files from the command line.
..
Nous sommes ainsi capables de générer des graphes de trajectoires depuis les places frontières jusqu'aux entités d'intérêt.
......
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