Difference between revisions of "BioUML wiki"

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__NOTOC__
 
__NOTOC__
Welcome to BioUML wiki!  
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Welcome to BioUML wiki! Now it is the main web site for BioUML platform.
  
BioUML is an open source integrated Java platform for building virtual cell and 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, JavaScript) and workflow support it provides powerful possibilities for analyses of high-throughput data. The plug-in based architecture (Eclipse run time from IBM is used) allows to add new functionality using plug-ins.
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BioUML - Biological Universal Modelling Language - is an integrated Java platform for biomedical research. 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, JavaScript) and workflow support it provides powerful possibilities for analyses of high-throughput data. The plug-in based architecture (OSGI) allows to add new functionality using plug-ins.
  
 
Currently we have '''[[:Special:Statistics|{{NUMBEROFARTICLES}} articles]]'''.
 
Currently we have '''[[:Special:Statistics|{{NUMBEROFARTICLES}} articles]]'''.
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* [[BioUML user interface]]
 
* [[BioUML user interface]]
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* [[Databases]]
  
 
* Modelling  
 
* Modelling  
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** [[Modular modeling]]
 
** [[Modular modeling]]
  
* Workflows & analyses
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* Analyses & workflows
** [[Projects]]
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** [[Project]]s
** [[Workflows]]
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** [[:Category:Analyses|Analyses]]
 
** [[:Category:Analyses|Analyses]]
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** [[Workflows]]
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** [[Using Galaxy in BioUML|Galaxy]]
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** [[Using R in BioUML|R]]
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** [[Using JavaScript in BioUML|JavaScript]]
 
** [[:Category:File formats|File formats]]
 
** [[:Category:File formats|File formats]]
  
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* [[BioUML installation]]
 
* [[BioUML installation]]
 
* [[BioUML Development Kit]]
 
* [[BioUML Development Kit]]
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* [[:Category:Plugins|Plugins]]
 
* [[:Category:Extension points|Extension points]]
 
* [[:Category:Extension points|Extension points]]
 
* [[Creating Galaxy tool]]
 
* [[Creating Galaxy tool]]
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=== Try BioUML web edition ===
 
=== Try BioUML web edition ===
* http://ie.biouml.org/bioumlweb (free)
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* Main web server (free)  http://ict.biouml.org
* http://platform.genexplain.com (trial, commercial)
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* Commercial server (free and licensed) http://platform.genexplain.com/bioumlweb/
 
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===Miscellaneous===
 
===Miscellaneous===
 
* [[Tests]]
 
* [[Tests]]
 
* [[Presentations]]
 
* [[Presentations]]
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* [http://www.biouml.org/vc/agenda.shtml Presentations] (video, slides)
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from workshop "From virtual cell to virtual human and virtual patient"
  
 
|valign="top" width="33%"|
 
|valign="top" width="33%"|
  
 
== Community ==
 
== Community ==
* [[News]]
 
 
* [http://forum.biouml.org/ Forum]
 
* [http://forum.biouml.org/ Forum]
 
* [[BioStore]]
 
* [[BioStore]]
 
* [[Contributors]]
 
* [[Contributors]]
** [[BioUML_team]]
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** [[BioUML team]]
 
** [[geneXplain]]
 
** [[geneXplain]]
  
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* [//www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
 
* [//www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
 
* [//www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
 
* [//www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]
 
 
* [https://toolserver.org/~diberri/cgi-bin/html2wiki/index.cgi HTML-to-wiki converter]
 
* [https://toolserver.org/~diberri/cgi-bin/html2wiki/index.cgi HTML-to-wiki converter]
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=== Examples ===
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* [[DAE Models examples]]
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* [[Optimization examples]]
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* [[Population models examples]]
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* [[SBGN examples]]
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* [[SedML examples]]
 
|}
 
|}
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<p align="center">[[Acknowledgements]]</p>
 
<p align="center">[[Acknowledgements]]</p>

Latest revision as of 17:25, 5 August 2020

Welcome to BioUML wiki! Now it is the main web site for BioUML platform.

BioUML - Biological Universal Modelling Language - is an integrated Java platform for biomedical research. 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, JavaScript) and workflow support it provides powerful possibilities for analyses of high-throughput data. The plug-in based architecture (OSGI) allows to add new functionality using plug-ins.

Currently we have 1,022 articles.

[edit] For BioUML users

[edit] For administrators/developers


[edit] Try BioUML web edition

[edit] Miscellaneous

from workshop "From virtual cell to virtual human and virtual patient"

[edit] Community


[edit] Editing this wiki

To edit this wiki you have to register in BioStore.

Consult the User's Guide for information on using the wiki software.

[edit] Examples


Acknowledgements

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