Mercurial > repos > tduigou > neo4jsbml

comparison neo4jsbml.xml @ 3:7f1f5eedfbfc draft default tip

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planemo upload for repository https://github.com/brsynth/neo4jsbml commit 513db7f056db275f3f5d8d1337d39ff66012d89f
author tduigou
date Fri, 29 Sep 2023 11:37:37 +0000
parents eea256ad4d7f
children
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2:eea256ad4d7f 3:7f1f5eedfbfc
57 ========= 57 =========
58 58
59 Step 1 59 Step 1
60 ------ 60 ------
61 61
62 Create a schema with [arrows](https://arrows.app), following these rules: 62 Create a schema with `Arrows <https://arrows.app>`_
63 .. image:: ${static_path}/images/PathwayModelisation-1.0.0.arrows.png
64 :width: 90 %
65 :align: center
66 63
67 Rules: 64 Rules:
68 * Nodes are labelled based on SBML object name as defined in the `SBML specification <https://sbml.org>`_ 65 - Nodes are labelled based on SBML object name as defined in the `SBML specification <https://sbml.org>`_
69 * Properties are labelled based on SBML object properties as defined the `SBML specification <https://sbml.org>`_ 66 - Properties are labelled based on SBML object properties as defined the `SBML specification <https://sbml.org>`_
70 67
71 Step 2 68 Step 2
72 ------ 69 ------
73 Export your schema at the JSON format. 70 Export your schema at the JSON format.
74 .. image:: ${static_path}/images/arrows.dwl.png
75 :width: 90 %
76 :align: center
77 71
78 Step 3 72 Step 3
79 ------ 73 ------
80 74
81 Import your data with `neo4jsbml` into Neo4j. 75 Import your data with `neo4jsbml` into Neo4j.
82 * Use either a configuration file `ini` or individual parameters 76 - Use either a configuration file `ini` or individual parameters
83 * Password needs to be store in a file for safety security 77 - Password needs to be store in a file for safety security
84 * If you have multiple model in the database, pass a `tag` to identify the model loaded into the database if you want to avoid collision 78 - If you have multiple model in the database, pass a `tag` to identify the model loaded into the database if you want to avoid collision
85
86 79
87 Inputs 80 Inputs
88 ------ 81 ------
89 82
90 Database parameters 83 Database parameters
91 * **Protocol**: choose the protocol (default: neo4j) 84 - **Protocol**: choose the protocol (default: neo4j)
92 * **Url of the database**: define the url of the database 85 - **Url of the database**: define the url of the database
93 * **Port of the database**: define the port of the database (default: 7687) 86 - **Port of the database**: define the port of the database (default: 7687)
94 * **Username of the database**: User name of the database 87 - **Username of the database**: User name of the database
95 * **Password of the database**: file with the password 88 - **Password of the database**: file with the password
96 * **Database name**: database name 89 - **Database name**: database name
97 90
98 Input 91 Input
99 * **SBML model**: SBML model 92 - **SBML model**: SBML model
100 * **Identifier of the model**: Associate an ID to the nodes 93 - **Identifier of the model**: Associate an ID to the nodes
101 * **Arrow's schema**: Schema created with Arrow 94 - **Arrow's schema**: Schema created with Arrow
102 95
103 Ouput 96 Ouput
104 ----- 97 -----
105 98
106 * Traceback of the tool 99 - Traceback of the tool
107 ]]></help> 100 ]]></help>
108 <citations> 101 <citations>
109 <citation type="bibtex"> 102 <citation type="bibtex">
110 @unpublished{neo4jsbml 103 @unpublished{neo4jsbml
111 author = {Guillaume Gricourt, Thomas Duigou, Sandra Dérozier, Jean-Loup Faulon}, 104 author = {Guillaume Gricourt, Thomas Duigou, Sandra Dérozier, Jean-Loup Faulon},