Biomodels - Revision history

Stan.lo@dote.ru at 08:14, 27 June 2013

2013-06-27T08:14:54Z

Stan.lo@dote.ru at 08:10, 27 June 2013

2013-06-27T08:10:32Z

Lan@dote.ru: +Category:Databases

2013-06-26T08:23:51Z

+Category:Databases

Lan@dote.ru: +picture

2013-06-26T08:21:22Z

+picture

Lan@dote.ru: Lucene search

2013-06-26T08:18:02Z

Lucene search

Stan.lo@dote.ru at 11:29, 25 June 2013

2013-06-25T11:29:48Z

Stan.lo@dote.ru: /* See also */

2013-06-25T10:44:46Z

‎See also

Stan.lo@dote.ru at 08:10, 25 June 2013

2013-06-25T08:10:55Z

Stan.lo@dote.ru: from GX manual

2013-06-25T08:10:13Z

from GX manual

New page

The BioModels database is a repository of peer-reviewed, published, computational models suitable for simulating biological processes.

These mathematical models are primarily from the field of systems biology, but more generally of biological interest. This resource allows biologists to store, search and retrieve published mathematical models. In addition, models in the database can be used to generate sub-models, can be simulated online, and can be converted between different representational formats. This resource also features programmatic access via Web Services.

The BioModels database is developed and maintained by the [http://www.biomodels.net/ BioModels.net] initiative.

[[BioUML]] provides possibility to visualize and browse the diagrams and models from the Biomodels database. The database (like any other) can be found in the [[repository pane]] with read access only. The '''Diagrams''' subdirectory currently contains 421 curated and 433 non-curated diagrams, of which only 50 items are shown at a time in the repository tree. To find a certain model you can either scroll down and subsequently expand the subdirectory by clicking on the '''Load next 50''' icon ([[File:Type-folder-icon.png]]) as necessary or just run a [[Search tools|text search]] through the database.

When a diagram is opened in the document pane, the '''Info''' tab in the [[information box]] shows some details about the model, including database links for the individual components. In the [[Viewparts|viewparts area]], under the tab '''My description''' a detailed description of the model is given; it shows the original reference, its abstract and the PubMed link; further information about how the model was constructed is added.

Under the '''Simulation''' tab you will find the default settings for the simulation, which can be changed before launching the simulation ([[File:Execute_icon.png]]). The simulation results will be graphically displayed in a new window, which can be saved as an image (in a number of formats) using the '''Export''' button ([[File:WebAction-toolbar-export-icon.png]]) in the [[general control panel]].

@@ Line 6: / Line 6: @@
 The BioModels database is developed and maintained by the [http://www.biomodels.net/ BioModels.net] initiative.
-[[BioUML]] provides possibility to visualize and browse the diagrams and models from the Biomodels database. The database can be found in the [[repository pane]] with read access only. The '''Diagrams''' subdirectory currently contains 421 curated and 433 non-curated diagrams. To find a certain model you can either scroll down and subsequently expand the subdirectory as necessary or just run a [[Lucene search|text search]] through the database.
+[[BioUML]] provides possibility to visualize and browse the diagrams and models from the Biomodels database. The database can be found in the [[repository pane]] with read access only. The '''Diagrams''' subdirectory currently contains 421 curated and 433 non-curated diagrams. To find a certain model you can either scroll down and (in the web edition) subsequently expand the subdirectory as necessary or just run a [[Lucene search|text search]] through the database.
 When a diagram is opened in the document pane, the '''Info''' tab in the [[information box]] shows some details about the model, including database links for the individual components. In the [[Viewparts|viewparts area]], under the tab '''My description''' a detailed description of the model is given; it shows the original reference, its abstract and the PubMed link; further information about how the model was constructed is added.

@@ Line 6: / Line 6: @@
 The BioModels database is developed and maintained by the [http://www.biomodels.net/ BioModels.net] initiative.
-[[BioUML]] provides possibility to visualize and browse the diagrams and models from the Biomodels database. The database can be found in the [[repository pane]] with read access only. The '''Diagrams''' subdirectory currently contains 421 curated and 433 non-curated diagrams, of which only 50 items are shown at a time in the repository tree. To find a certain model you can either scroll down and subsequently expand the subdirectory by clicking on the '''Load next 50''' icon ([[File:Type-folder-icon.png]]) as necessary or just run a [[Lucene search|text search]] through the database.
+[[BioUML]] provides possibility to visualize and browse the diagrams and models from the Biomodels database. The database can be found in the [[repository pane]] with read access only. The '''Diagrams''' subdirectory currently contains 421 curated and 433 non-curated diagrams. To find a certain model you can either scroll down and subsequently expand the subdirectory as necessary or just run a [[Lucene search|text search]] through the database.
 When a diagram is opened in the document pane, the '''Info''' tab in the [[information box]] shows some details about the model, including database links for the individual components. In the [[Viewparts|viewparts area]], under the tab '''My description''' a detailed description of the model is given; it shows the original reference, its abstract and the PubMed link; further information about how the model was constructed is added.

← Older revision		Revision as of 08:23, 26 June 2013
Line 16:		Line 16:
	* [[Lucene search]]		* [[Lucene search]]
	* [[Diagram document]]		* [[Diagram document]]
		+
		+	[[Category:Databases]]

← Older revision		Revision as of 08:21, 26 June 2013
Line 1:		Line 1:
		+	[[File:BioModels_Aguda_Cell_Cycle.png\|thumb\|BioModels diagram Aguda1999_CellCycle]]
	The BioModels database is a repository of peer-reviewed, published, computational models suitable for simulating biological processes.		The BioModels database is a repository of peer-reviewed, published, computational models suitable for simulating biological processes.

@@ Line 5: / Line 5: @@
 The BioModels database is developed and maintained by the [http://www.biomodels.net/ BioModels.net] initiative.
-[[BioUML]] provides possibility to visualize and browse the diagrams and models from the Biomodels database. The database can be found in the [[repository pane]] with read access only. The '''Diagrams''' subdirectory currently contains 421 curated and 433 non-curated diagrams, of which only 50 items are shown at a time in the repository tree. To find a certain model you can either scroll down and subsequently expand the subdirectory by clicking on the '''Load next 50''' icon ([[File:Type-folder-icon.png]]) as necessary or just run a [[Search tools|text search]] through the database.
+[[BioUML]] provides possibility to visualize and browse the diagrams and models from the Biomodels database. The database can be found in the [[repository pane]] with read access only. The '''Diagrams''' subdirectory currently contains 421 curated and 433 non-curated diagrams, of which only 50 items are shown at a time in the repository tree. To find a certain model you can either scroll down and subsequently expand the subdirectory by clicking on the '''Load next 50''' icon ([[File:Type-folder-icon.png]]) as necessary or just run a [[Lucene search|text search]] through the database.
 When a diagram is opened in the document pane, the '''Info''' tab in the [[information box]] shows some details about the model, including database links for the individual components. In the [[Viewparts|viewparts area]], under the tab '''My description''' a detailed description of the model is given; it shows the original reference, its abstract and the PubMed link; further information about how the model was constructed is added.
@@ Line 13: / Line 13: @@
 ==See also==
 * [[Databases]]
-* [[Search tools]]
+* [[Lucene search]]
 * [[Diagram document]]

← Older revision		Revision as of 10:44, 25 June 2013
Line 13:		Line 13:
	==See also==		==See also==
	* [[Databases]]		* [[Databases]]
		+	* [[Search tools]]
		+	* [[Diagram document]]

← Older revision		Revision as of 08:10, 25 June 2013
Line 10:		Line 10:

	Under the '''Simulation''' tab you will find the default settings for the simulation, which can be changed before launching the simulation ([[File:Execute_icon.png]]). The simulation results will be graphically displayed in a new window, which can be saved as an image (in a number of formats) using the '''Export''' button ([[File:WebAction-toolbar-export-icon.png]]) in the [[general control panel]].		Under the '''Simulation''' tab you will find the default settings for the simulation, which can be changed before launching the simulation ([[File:Execute_icon.png]]). The simulation results will be graphically displayed in a new window, which can be saved as an image (in a number of formats) using the '''Export''' button ([[File:WebAction-toolbar-export-icon.png]]) in the [[general control panel]].
		+
		+	==See also==
		+	* [[Databases]]