BioUML - Revision history

Stan.lo@dote.ru: /* Collaborative research */

2013-10-09T09:43:57Z

‎Collaborative research

Stan.lo@dote.ru: /* Collaborative research */

2013-10-09T05:46:42Z

‎Collaborative research

Stan.lo@dote.ru: /* Collaborative research */

2013-10-09T05:46:06Z

‎Collaborative research

Alexander.kel@genexplain.com at 09:38, 9 September 2013

2013-09-09T09:38:19Z

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

2013-06-25T07:54:19Z

‎See also

Lan@dote.ru at 09:37, 17 June 2013

2013-06-17T09:37:03Z

Stan.lo@dote.ru: /* Visual modeling */

2013-06-07T09:16:55Z

‎Visual modeling

Stan.lo@dote.ru: /* Visual modeling */

2013-06-07T09:15:04Z

‎Visual modeling

Lan@dote.ru at 10:33, 17 May 2013

2013-05-17T10:33:01Z

Lan@dote.ru: -{{Stub}}

2013-05-13T09:43:39Z

-{{Stub}}

@@ Line 61: / Line 61: @@
 * [[collaborative diagram editing]],
 * access to [[diagram editing history]] (both session and version),
-* in-built [[User-to-user communication|group chat]].
+* in-built [[User to user communication|group chat]].
 ==Architecture overview==

@@ Line 59: / Line 59: @@
 * [[BioStore#InvitingOthers|sharing projects with other users]],
-* collaborative diagram editing,
+* [[collaborative diagram editing]],
 * access to [[diagram editing history]] (both session and version),
 * in-built [[User-to-user communication|group chat]].

@@ Line 61: / Line 61: @@
 * collaborative diagram editing,
 * access to [[diagram editing history]] (both session and version),
-* in-built [[group chat]].
+* in-built [[User-to-user communication|group chat]].
 ==Architecture overview==

← Older revision		Revision as of 09:38, 9 September 2013
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−	BioUML is an open source integrated Java platform for analysis of data ~~from~~ [[wikipedia:omics\|omics]] ~~sciences research and other~~ advanced [[wikipedia:computational biology\|computational biology]]~~, for building the~~ [[virtual cell]] and ~~the~~ [[wikipedia:Virtual Physiological Human\|virtual physiological human]]. It spans a comprehensive range of capabilities, including access to databases with experimental data, tools for formalized description of biological systems structure and functioning, as well as tools for their visualization, simulation, parameters fitting and analyses. Due to scripts ({{R}}, [[wikipedia:JavaScript\|JavaScript]]) and workflow support it provides powerful possibilities for analyses of high-throughput data. The [[#See also\|plug-in based architecture]] ([http://www.eclipse.org/ Eclipse] run time from IBM is used) allows to add new functionality using plug-ins.	+	BioUML is an open source integrated Java platform for analysis of data generated by [[wikipedia:omics\|omics]] technologies using advanced tools of [[wikipedia:computational biology\|computational biology]]. The BioUML vision is to provide a computational platform to build [[virtual cell]] and [[wikipedia:Virtual Physiological Human\|virtual physiological human]]. BioUML spans a comprehensive range of capabilities, including access to databases with experimental data, tools for formalized description of biological systems structure and functioning, as well as tools for their visualization, simulation, parameters fitting and analyses. Due to scripts ({{R}}, [[wikipedia:JavaScript\|JavaScript]]) and workflow support it provides powerful possibilities for analyses of high-throughput data. The [[#See also\|plug-in based architecture]] ([http://www.eclipse.org/ Eclipse] run time from IBM is used) allows to add new functionality using plug-ins.

	The whole system aims at covering, with time, all areas of computational applications in bioinformatics and systems biology. The architecture is open, so that users' own scripts can be easily loaded into the system, and new modules can be programmed and added by any skilled person.		The whole system aims at covering, with time, all areas of computational applications in bioinformatics and systems biology. The architecture is open, so that users' own scripts can be easily loaded into the system, and new modules can be programmed and added by any skilled person.

@@ Line 83: / Line 83: @@
 * [[Features]]
 * [[BioStore#InvitingOthers|Inviting other users to your project]]
 * [[BioUML development history]]
 * [[BioUML development roadmap]]

@@ Line 52: / Line 52: @@
 ===Reproducible research===
-Reproducible research is the common name for functionality for saving, representing and reproducing a set of data manipulation. BioUML provides special [[Projects]] collections, [[workflows]] and [[Workflows#research diagram|research diagram]]s for this purpose.
+Reproducible research is the common name for functionality for saving, representing and reproducing a set of data manipulation. BioUML provides special [[Project]] collections, [[workflows]] and [[Workflows#research diagram|research diagram]]s for this purpose.
 ===Collaborative research===

@@ Line 12: / Line 12: @@
 [[File:Data flow in BioUML.png|thumb|Visual modeling within the data workflow in BioUML]]
-Reconstruction of complex biological systems from a huge amount of experimental data requires a formal language that can be easily understood both by the human and the computer. It is known that graphic depiction of complex systems is the most suitable way of understanding their structure by humans. Graphic notation allows humans to completely and formally specify model so computer programs can analyze the model and simulate its behavior.
+Reconstruction of complex biological systems from a huge amount of experimental data requires a formal language that can be easily understood both by the human and the computer. It is known that graphic depiction of complex systems is the most suitable way of understanding their structure by humans. [[Graphic notation]] allows humans to completely and formally specify model so computer programs can analyze the model and simulate its behavior.
 This approach is widely used in engineering and computer science. Some examples are:

@@ Line 1: / Line 1: @@
-BioUML is an open source integrated Java platform for analysis of data from [http://en.wikipedia.org/wiki/Omics omics] sciences research and other advanced [http://en.wikipedia.org/wiki/Computational_biology computational biology], for building the [[virtual cell]] and the [http://en.wikipedia.org/wiki/Virtual_Physiological_Human virtual physiological human]. It spans a comprehensive range of capabilities, including access to databases with experimental data, tools for formalized description of biological systems structure and functioning, as well as tools for their visualization, simulation, parameters fitting and analyses. Due to scripts ([http://en.wikipedia.org/wiki/R_(programming_language) R], [http://en.wikipedia.org/wiki/JavaScript JavaScript]) and workflow support it provides powerful possibilities for analyses of high-throughput data. The [[#See also|plug-in based architecture]] ([http://www.eclipse.org/ Eclipse] run time from IBM is used) allows to add new functionality using plug-ins.
+BioUML is an open source integrated Java platform for analysis of data from [[wikipedia:omics|omics]] sciences research and other advanced [[wikipedia:computational biology|computational biology]], for building the [[virtual cell]] and the [[wikipedia:Virtual Physiological Human|virtual physiological human]]. It spans a comprehensive range of capabilities, including access to databases with experimental data, tools for formalized description of biological systems structure and functioning, as well as tools for their visualization, simulation, parameters fitting and analyses. Due to scripts ({{R}}, [[wikipedia:JavaScript|JavaScript]]) and workflow support it provides powerful possibilities for analyses of high-throughput data. The [[#See also|plug-in based architecture]] ([http://www.eclipse.org/ Eclipse] run time from IBM is used) allows to add new functionality using plug-ins.
 The whole system aims at covering, with time, all areas of computational applications in bioinformatics and systems biology. The architecture is open, so that users' own scripts can be easily loaded into the system, and new modules can be programmed and added by any skilled person.
 The community is invited to contribute to the development, either as public-domain or as a commercial part of the platform. [[BioUML team|The developers]] are confident that this way a most powerful and needed system of tools can grow.
-[[BioUML team|The team]] also hopes that BioUML will contribute to creation of virtual cell, virtual physiological human and [http://en.wikipedia.org/wiki/Virtual_patient virtual patient], which would be extremely useful in medicine as a means of computational identification of the most effective therapeutic interventions and for prediction of potential outcomes of intended treatments for a given patient.
+[[BioUML team|The team]] also hopes that BioUML will contribute to creation of virtual cell, virtual physiological human and [[wikipedia:virtual patient|virtual patient]], which would be extremely useful in medicine as a means of computational identification of the most effective therapeutic interventions and for prediction of potential outcomes of intended treatments for a given patient.
 ==Principles==
@@ Line 69: / Line 69: @@
 * [[BioUML server]] - provides access to data and analyses methods installed on the server side for BioUML clients (workbench and web edition) via the Internet.
 * [[BioUML workbench]] - Java application that can work standalone or as "thick" client for BioUML server.
-* [[BioUML web edition]] - "thin" client for BioUML server (you just need to start web browser) that provides most of functionality of BioUML workbench. It uses [http://en.wikipedia.org/wiki/Ajax_(programming) AJAX] and [http://en.wikipedia.org/wiki/Canvas_element HTML5 <canvas>] technology for visual modeling and interactive data editing.
+* [[BioUML web edition]] - "thin" client for BioUML server (you just need to start web browser) that provides most of functionality of BioUML workbench. It uses [[wikipedia:Ajax (programming)|AJAX]] and [[wikipedia:Canvas element|HTML5 <canvas>]] technology for visual modeling and interactive data editing.
 ===Plug-in based architecture===

← Older revision		Revision as of 09:43, 13 May 2013
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−	~~{{Stub}}~~
−
	BioUML is an open source integrated Java platform for analysis of data from [http://en.wikipedia.org/wiki/Omics omics] sciences research and other advanced [http://en.wikipedia.org/wiki/Computational_biology computational biology], for building the [[virtual cell]] and the [http://en.wikipedia.org/wiki/Virtual_Physiological_Human virtual physiological human]. It spans a comprehensive range of capabilities, including access to databases with experimental data, tools for formalized description of biological systems structure and functioning, as well as tools for their visualization, simulation, parameters fitting and analyses. Due to scripts ([http://en.wikipedia.org/wiki/R_(programming_language) R], [http://en.wikipedia.org/wiki/JavaScript JavaScript]) and workflow support it provides powerful possibilities for analyses of high-throughput data. The [[#See also\|plug-in based architecture]] ([http://www.eclipse.org/ Eclipse] run time from IBM is used) allows to add new functionality using plug-ins.		BioUML is an open source integrated Java platform for analysis of data from [http://en.wikipedia.org/wiki/Omics omics] sciences research and other advanced [http://en.wikipedia.org/wiki/Computational_biology computational biology], for building the [[virtual cell]] and the [http://en.wikipedia.org/wiki/Virtual_Physiological_Human virtual physiological human]. It spans a comprehensive range of capabilities, including access to databases with experimental data, tools for formalized description of biological systems structure and functioning, as well as tools for their visualization, simulation, parameters fitting and analyses. Due to scripts ([http://en.wikipedia.org/wiki/R_(programming_language) R], [http://en.wikipedia.org/wiki/JavaScript JavaScript]) and workflow support it provides powerful possibilities for analyses of high-throughput data. The [[#See also\|plug-in based architecture]] ([http://www.eclipse.org/ Eclipse] run time from IBM is used) allows to add new functionality using plug-ins.