Difference between revisions of "BioUML development roadmap"

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(Plans for 2013)
(Plans for 2013)
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For this purpose, please, use the [http://forum.biouml.org/ BioUML forum].
 
For this purpose, please, use the [http://forum.biouml.org/ BioUML forum].
  
===Plans for 2013===
+
===Plans for 2013-2014===
  
 
<center>
 
<center>
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|v. 0.9.6
 
|v. 0.9.6
 
|
 
|
*Modelling
+
*BioUML workbench (desktop version)
**Rule based modelling (implementation of BioNetGen approach)
+
**integration of Galaxy
**Antimony support
+
**rule based modelling (implementation of BioNetGen approach, [[BioNetGen|details]])
 +
**Antimony support ([[Antimony|details]])
 
**Synchronisation between textual and graphical model representation (BioNetGen, Antimony)
 
**Synchronisation between textual and graphical model representation (BioNetGen, Antimony)
 +
 
*Interface improvements
 
*Interface improvements
 
**display name and actions for table cell values
 
**display name and actions for table cell values
 +
 +
*R integration
 +
**improved interface and bug fixes
 +
**possibility to call BioUML from R using rbiouml package (http://cran.r-project.org/web/packages/rbiouml)
 +
 +
*JavaScript support (web version)
 +
** new JavaScript editor, CodeMirror (http://codemirror.net/).
 +
 
*GTRD database
 
*GTRD database
 
**perspective
 
**perspective
 
**special start page
 
**special start page
 
**improved web interface
 
**improved web interface
 +
 
*New methods for analysis of transcription factor binding sites
 
*New methods for analysis of transcription factor binding sites
|2013, August
+
|2013, November
 
|-
 
|-
 
|v. 0.9.7
 
|v. 0.9.7
 
|
 
|
*BioUML workbench (desktop version)
 
**integration of Galaxy
 
 
*Server  
 
*Server  
 
**grid version - pilot task manager integration with SGE via DRMAA virtualisation         
 
**grid version - pilot task manager integration with SGE via DRMAA virtualisation         
 +
**repository - packages for Red Hat and Debian
 +
**Puppet cookbooks for server updates
 
*NGS
 
*NGS
 
**miRNA  
 
**miRNA  
 
**ribo-seq
 
**ribo-seq
*R - improved interface (similar with RStudio)
+
|2013, December
|2013, September
+
 
|-
 
|-
 
|v. 0.9.8
 
|v. 0.9.8
 
|
 
|
*Server installation
 
**repository - packages for Red Hat and Debian
 
**Puppet cookbooks for server updates
 
 
*Web interface
 
*Web interface
 
**mobile version (for web-browser)  
 
**mobile version (for web-browser)  
 
**web interface improvements diagrams - convenient for exchange and editing  
 
**web interface improvements diagrams - convenient for exchange and editing  
*NGS
+
|2014, Q1
**RNA-seq
+
*Integration with GenABEL
+
|2013, Q4
+
|-
+
|v. 0.9.9
+
|
+
*Server
+
**grid version
+
*Further NGS analyses improvements
+
|2013, Q4
+
 
|}
 
|}
 
</center>
 
</center>

Revision as of 01:39, 9 November 2013

This page describes the current plans for BioUML platform development in 2013 and includes a list of desired features that are not scheduled yet. Users, administrators and developers are welcome with their comments and suggestions about new features as well as feature implementation priorities. For this purpose, please, use the BioUML forum.

Plans for 2013-2014

Release Description Date
v. 0.9.6
  • BioUML workbench (desktop version)
    • integration of Galaxy
    • rule based modelling (implementation of BioNetGen approach, details)
    • Antimony support (details)
    • Synchronisation between textual and graphical model representation (BioNetGen, Antimony)
  • Interface improvements
    • display name and actions for table cell values
  • GTRD database
    • perspective
    • special start page
    • improved web interface
  • New methods for analysis of transcription factor binding sites
2013, November
v. 0.9.7
  • Server
    • grid version - pilot task manager integration with SGE via DRMAA virtualisation
    • repository - packages for Red Hat and Debian
    • Puppet cookbooks for server updates
  • NGS
    • miRNA
    • ribo-seq
2013, December
v. 0.9.8
  • Web interface
    • mobile version (for web-browser)
    • web interface improvements diagrams - convenient for exchange and editing
2014, Q1

Other desired features

Component Features Priority
Core *Major refactoring: complex, macromolecule state, reaction
  • Parameters fitting - optimization process as a workflow
  • SED-ML as workflow
  • Save optimization results as the diagram state
  • SBGN-XML support
  • Implementation of OQL subset for access to databases via BioUML object model
moderate
Databases
  • KEGG support improvements:
  • Diagram export (KGML, BioPAX, SBML, +SVG, +PNG, +JPEG)
  • Set up wizard
low
Misc.
  • SBRML support
  • Further integration with MATLAB
low

See also

Personal tools
Namespaces

Variants
Actions
BioUML platform
Community
Modelling
Analysis & Workflows
Collaborative research
Development
Virtual biology
Wiki
Toolbox