Difference between revisions of "BioUML development roadmap"

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(→‎Plans for 2016)
 
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This page describes the current plans for BioUML platform development in 2013 and includes a list of desired features that are not scheduled yet.
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This page describes the current plans for BioUML platform development in 2016 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.  
 
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 [http://forum.biouml.org/ BioUML forum].
 
For this purpose, please, use the [http://forum.biouml.org/ BioUML forum].
  
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===Plans for 2013===
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===Plans for 2016===
  
 
<center>
 
<center>
 
{| class="wikitable"
 
{| class="wikitable"
 
!Release!!Description!!Date
 
!Release!!Description!!Date
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|-
+
|- style="background-color: Lavender"
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|v. 0.9.6
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|v. 2016.4
 
|
 
|
−
*Modelling
+
 
−
**Rule based modelling (implementation of BioNetGen approach)
+
*Analysis
−
**Antimony support
+
**Parameters identifiability analysis (Raue et al., 2009)
−
**Synchronisation between textual and graphical model representation (BioNetGen, Antimony)
+
**Generating models population using Metropolis algorithm
−
*New methods for analysis transcription factor binding sites
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**Key node sensitivity analysis
−
|2013, August
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**New result types for Steady State: table, simulation result
 +
*Simulation
 +
**Automatic generation of kinetik laws from SBO
 +
**Option to set different output type for variables (quantity or concentration)
 +
**Options for algebraic solvers
 +
*SBML
 +
**Level 2 version 5 supported
 +
**All tests from SBML test suite v. 3.2.0 passed
 +
*BioUML IDE
 +
**NetBeans version updated to 8.2
 +
*Bug fixing
 +
|December
 +
2016
 
|-
 
|-
−
|v. 0.9.7
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|v. 2016.2
 
|
 
|
−
*Server installation
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*Modeling
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**repository - packages for Red Hat and Debian
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**Custom styles for diagram elements rendering for all types of models (see SBGN examples)
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**Puppet cookbooks for server updates
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**Automatic detection of model parameter types (Unused, ODE, Algebraic, Descrete, Parameter)
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*Server
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**Converter: SBML-SBGN diagram -> SBML-SBGN composite diagram
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**grid version - pilot task manager integration with SGE via DRMAA virtualisation       
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*Databases
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*Web interface
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**CHEBI support enhancement
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**mobile version (for web-browser)  
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*Analysis
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**web interface improvements diagrams - convenient for exchange and editing
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**Flux balance analysis enhancement
−
*NGS
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|July
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**ribo-seq
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2016
−
**miRNA
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−
**RNA-seq
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−
*Integration with GenABEL
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−
|2013, Q4
+
−
|-
+
−
|v. 0.9.8
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−
|
+
−
*Server
+
−
**grid version
+
−
*Further NGS analyses improvements
+
−
|2013, Q4
+
 
|}
 
|}
 
</center>
 
</center>
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|-
 
|-
 
|Core
 
|Core
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|*Major refactoring: complex, macromolecule state, reaction
+
|
 +
*Major refactoring: complex, macromolecule state, reaction
 
*Parameters fitting - optimization process as a workflow
 
*Parameters fitting - optimization process as a workflow
−
*SED-ML as workflow
 
 
*Save optimization results as the diagram state
 
*Save optimization results as the diagram state
−
*SBGN-XML support
 
 
*Implementation of OQL subset for access to databases via BioUML object model
 
*Implementation of OQL subset for access to databases via BioUML object model
 
|style="background-color:LightSalmon;"|moderate
 
|style="background-color:LightSalmon;"|moderate

Latest revision as of 14:56, 11 January 2017

This page describes the current plans for BioUML platform development in 2016 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.

[edit] Plans for 2016

Release Description Date
v. 2016.4
  • Analysis
    • Parameters identifiability analysis (Raue et al., 2009)
    • Generating models population using Metropolis algorithm
    • Key node sensitivity analysis
    • New result types for Steady State: table, simulation result
  • Simulation
    • Automatic generation of kinetik laws from SBO
    • Option to set different output type for variables (quantity or concentration)
    • Options for algebraic solvers
  • SBML
    • Level 2 version 5 supported
    • All tests from SBML test suite v. 3.2.0 passed
  • BioUML IDE
    • NetBeans version updated to 8.2
  • Bug fixing
December

2016

v. 2016.2
  • Modeling
    • Custom styles for diagram elements rendering for all types of models (see SBGN examples)
    • Automatic detection of model parameter types (Unused, ODE, Algebraic, Descrete, Parameter)
    • Converter: SBML-SBGN diagram -> SBML-SBGN composite diagram
  • Databases
    • CHEBI support enhancement
  • Analysis
    • Flux balance analysis enhancement
July

2016

[edit] Other desired features

Component Features Priority
Core
  • Major refactoring: complex, macromolecule state, reaction
  • Parameters fitting - optimization process as a workflow
  • Save optimization results as the diagram state
  • 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

[edit] See also

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