WikiBot: Automatic synchronization with BioUML

2017-02-13T12:01:04Z

Automatic synchronization with BioUML

WikiBot: {{Type link}} used

2013-05-17T09:40:10Z

{{Type link}} used

WikiBot: Target element type added

2013-05-16T06:47:11Z

Target element type added

WikiBot: Plugin link added

2013-05-07T07:13:00Z

Plugin link added

WikiBot: Protected "GinSim (file format)": Autogenerated page (‎[edit=sysop] (indefinite))

2013-04-04T09:28:24Z

Protected "GinSim (file format)": Autogenerated page (‎[edit=sysop] (indefinite))

WikiBot: Added 'Autogenerated pages' category

2013-04-04T09:28:24Z

Added 'Autogenerated pages' category

WikiBot: Automatic synchronization with BioUML

2013-04-04T08:24:47Z

Automatic synchronization with BioUML

New page

=== GINsim format ===

GINsim is a software supporting the definition, the simulation and the analysis of regulatory graphs1. The underlying multilevel logical formalism leans on the definition of two types of graphs: '''regulatory graphs''', which model regulatory networks, and '''state transition graphs''', which represent their dynamical behaviour.

GINsim format (GINML) is the extension of the GXL (Graph eXchange Language) comprising new attributes and subelements for elements <code>node</code> and <code>edge</code>, and an additional element called <code>parameter</code>, where

* element <code>node</code>:
*# a new attribute <code>basevalue</code> corresponds to the "based level of expression" of the corresponding component (default value 0). In other words, it is the value of the logical parameter corresponding to the case where none of the incoming interactions if functional,
*# new subelements within a node:
*#* a list of elements <code>parameter</code> corresponding to the user defined logical parameters for this node
*#* an element <code>int</code>defining the maximum level of expression of this node.
* element <code>edge</code>:
*# a new attribute <code>sign</code> which gives the sign of the interaction (positive for an activation, negative for a repression, otherwise unknown),
*# one or two subelements int (level or interval letting the interaction functional).
* element <code>parameter</code>, is empty and has two attributes:
*# attribute <code>idActiveInteractions</code> gives the "name" of the parameter. It is the list of the functional interactions exerted upon the considered node,
*# attribute <code>val</code> is the value of the logical parameter.

==== Regulatory graphs ====

Logical regulatory graphs are defined as follow:

# The nodes (or vertices): ''G''=<nowiki>{</nowiki>''G''1,''G''2,...,''G''''n''<nowiki>}</nowiki> representing ''n'' components (regulatory products, genes, proteins...) labelled by their names;
# The labelled oriented graph ''R'': vertices are ''G''<nowiki>'</nowiki>s elements, and arcs represent interactions between regulatory products, labelled with a sign when the interaction corresponds to an activation or an inhibition.
# The products levels: for each node, a specific variable represents the level of expression (or of activity) of the corresponding node. This level (me g) is related to the threshold above which an outgoing interaction becomes functional. It is represented by an integer in <nowiki>{</nowiki>0,...,max<nowiki>}</nowiki>, where max equals, at most, the number of outgoing interactions from this particular component. By default, two extreme values are considered, 0 (none outgoing interaction functional) and max=1 (all interactions functional). The user can then define additional values to represent functional intermediate levels for the activity of the corresponding node.
# The logical parameters: they allow the qualitative specification of the effects of combinations of interactions controlling a given element. A parameter is named by the set of incoming interactions which are functional. At present, a null value is assign to all parameters by default.

==== State transition graphs ====

Logical state transition graphs represent the dynamical behaviour of systems described by regulatory graphs, given a set of initial states. They are defined as follows,

# The graph defined by a set of nodes (vertices) and a set of arcs connecting pairs of nodes.
# The nodes represent states of the system, defined by a word resulting of ogique temporelle et model checking pour les rthe concatenation of the actual level of each regulatory product.
# The arcs represent spontaneous transitions between pairs of states.
In addition, we have to define an updating method to specify the temporal ordering of the transitions. Under the synchronous assumption, all orders of commutation are executed simultaneously at each time step. From a biological point of view, this assumption implies that all macromolecular processes are realised in identical amounts of time, which is clearly unrealistic and often at the origin of simulation artefacts. Under the asynchronous assumption, when multiple orders of commutations occur at a given state, additional information is needed to select specific transitions. As we have no such information, all possible transitions are considered.
==== References ====

# [http://gin.univ-mrs.fr/ http://gin.univ-mrs.fr/]

[[Category:File formats]]

@@ Line 2: / Line 2: @@
 :GinSim
 ;Element type
-:{{Type link|diagram}}
+:{{Type link|Diagram}}
 ;Plugin
 :[[Biouml.plugins.ginsim (plugin)|biouml.plugins.ginsim (Support for GinSim models)]]

@@ Line 2: / Line 2: @@
 :GinSim
 ;Element type
-:[[File:Type-diagram-icon.png]] [[Diagram (element type)|diagram]]
+:{{Type link|diagram}}
 ;Plugin
 :[[Biouml.plugins.ginsim (plugin)|biouml.plugins.ginsim (Support for GinSim models)]]

@@ Line 1: / Line 1: @@
 ;File format title
 :GinSim
 ;Plugin
 :[[Biouml.plugins.ginsim (plugin)|biouml.plugins.ginsim (Support for GinSim models)]]

← Older revision		Revision as of 07:13, 7 May 2013
Line 1:		Line 1:
		+	;File format title
		+	:GinSim
		+	;Plugin
		+	:[[Biouml.plugins.ginsim (plugin)\|biouml.plugins.ginsim (Support for GinSim models)]]
		+
	=== GINsim format ===		=== GINsim format ===

← Older revision		Revision as of 09:28, 4 April 2013
Line 39:		Line 39:

	[[Category:File formats]]		[[Category:File formats]]
		+	[[Category:Autogenerated pages]]

GinSim (file format) - Revision history

WikiBot: Automatic synchronization with BioUML

WikiBot: {{Type link}} used

WikiBot: Target element type added

WikiBot: Plugin link added

WikiBot: Protected "GinSim (file format)": Autogenerated page (‎[edit=sysop] (indefinite))

WikiBot: Added 'Autogenerated pages' category

WikiBot: Automatic synchronization with BioUML