Difference between revisions of "BioUML development roadmap"

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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 2015===
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===Plans for 2016===
  
 
<center>
 
<center>
 
{| class="wikitable"
 
{| class="wikitable"
 
!Release!!Description!!Date
 
!Release!!Description!!Date
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|-
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|- style="background-color: Lavender"
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|v. 0.9.9
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|v. 2016.4
 
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|
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*BioUML IDE<br>new branch of BioUML platform based on NetBeans IDE
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*General diagrams
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*Analysis
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**automatic redraw of diagram objects on mouse dragging
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**Parameters identifiability analysis (Raue et al., 2009)
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**context actions on right click: edit element, rotate
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**Generating models population using Metropolis algorithm
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*SBGN diagrams reworked and enhanced
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**Key node sensitivity analysis
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**special action for clone creation: user can choose for which reactions clone will be created.
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**New result types for Steady State: table, simulation result
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**"oriented" reactions with one input edge for products and one output edge for reactants. 
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*Simulation
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**Creation of phenotypes as processes with modifiers
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**Automatic generation of kinetik laws from SBO
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**entity pool node and process types can be selected from drop boxes rather then typed
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**Option to set different output type for variables (quantity or concentration)
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**complexes can be transformed to other EPNs and vice-versa
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**Options for algebraic solvers
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**separate fonts for node titles.
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*SBML
 
*SBML
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**species are saved with the same name as correspondent node on diagram without auomaic prepending of "compartmentName_".
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**Level 2 version 5 supported
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**Unit definitions can be created and changed via BioUML interface.
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**All tests from SBML test suite v. 3.2.0 passed
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**SBO terms can be set for reactions, equations, functions etc.
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*BioUML IDE
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**random variables with normal, unifrom and binomial distributions. Support of custom annotation (also supported by COPASI, Jarnac, Roadrunner).
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**NetBeans version updated to 8.2
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**"time", "avogadro" and "delay" csymbols.
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*Bug fixing
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*SedML l1v2 supported
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|December
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*Antimony 
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2016
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**added support for visual arrangment of species (complexes, state variables, different types of EPN)
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**fixed bug with disabling of "close document" action.
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*Agent-based modeling: introuced script-agents. Supported script languages: R, MATLAB, java-script.
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*Server
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*integration with DropBox, Google Drive, Microsoft One Drive
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|February
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2015
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|-
 
|-
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|v. 0.9.10
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|v. 2016.2
 
|
 
|
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*Server
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*Modeling
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**integration with Galaxy CloudMan
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**Custom styles for diagram elements rendering for all types of models (see SBGN examples)
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**cloud/grid version - further development and improvements
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**Automatic detection of model parameter types (Unused, ODE, Algebraic, Descrete, Parameter)
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**repository - packages for Debian and CentOS
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**Converter: SBML-SBGN diagram -> SBML-SBGN composite diagram
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*Web interface
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*Databases
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**mobile version (for web-browser)  
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**CHEBI support enhancement
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**web interface improvements diagrams
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*Analysis
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*SBGN-ML import and exported supported
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**Flux balance analysis enhancement
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*SBML
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|July
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** built-in constants pi and exponentiale
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2016
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** fbc 1.2 supported (except gene products). Now boundaries can be specified by parameters
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*Simulation
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** dynamic fbc implemented - flux balance analysis can be performed continuosly during ODE simulation. Special engine implemented.
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|2015
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|}
 
|}
 
</center>
 
</center>
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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
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*SED-ML as workflow
 
 
*Save optimization results as the diagram state
 
*Save optimization results as the diagram state
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*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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