Difference between revisions of "BioUML development roadmap"

From BioUML platform
Jump to: navigation, search
(Plans for 2016)
 
(28 intermediate revisions by 5 users not shown)
Line 1: Line 1:
  
This page describes the current plans for BioUML platform development in 2013 and includes a list of desired features that are not scheduled yet.
+
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].
  
===Plans for 2013===
+
===Plans for 2016===
  
 
<center>
 
<center>
 
{| class="wikitable"
 
{| class="wikitable"
 
!Release!!Description!!Date
 
!Release!!Description!!Date
|-
+
|- style="background-color: Lavender"
|v. 0.9.5
+
|v. 2016.4
 
|
 
|
*SBML level 3 packages:
+
 
**hierarchic
+
*Analysis
**FBC test suite  
+
**Parameters identifiability analysis (Raue et al., 2009)
*Rule based modelling (implementation of BioNetGen approach)
+
**Generating models population using Metropolis algorithm
|2013, Q2
+
**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. 0.9.6
+
|v. 2016.2
 
|
 
|
*Server installation
+
*Modeling
**repository - packages for Red Hat and Debian
+
**Custom styles for diagram elements rendering for all types of models (see SBGN examples)
**Puppet cookbooks for server updates
+
**Automatic detection of model parameter types (Unused, ODE, Algebraic, Descrete, Parameter)
*Server
+
**Converter: SBML-SBGN diagram -> SBML-SBGN composite diagram
**grid version - pilot task manager integration with SGE via DRMAA virtualisation       
+
*Databases
*Web interface
+
**CHEBI support enhancement
**mobile version (for web-browser)  
+
*Analysis
**web interface improvements diagrams - convenient for exchange and editing
+
**Flux balance analysis enhancement
*NGS
+
|July
**ribo-seq
+
2016
**miRNA
+
**rna-seq
+
*Integration with genAbel - pilot
+
|2013, Q2/3
+
|-
+
|v. 0.9.7
+
|
+
*Server
+
**grid version (alpha)
+
*Further NGS analyses improvements
+
*Integration with genAbel (beta)
+
*SBGN-XML support
+
|2013, Q3
+
|-
+
|v. 0.9.8
+
|
+
*Server
+
**grid version (beta)
+
*Further NGS analyses improvements
+
|2013, Q4
+
 
|}
 
|}
 
</center>
 
</center>
 
  
 
===Other desired features===
 
===Other desired features===
Line 60: Line 52:
 
!Component!!Features!!Priority
 
!Component!!Features!!Priority
 
|-
 
|-
|rowspan="3"|Core
+
|Core
|Major refactoring: complex, macromolecule state, reaction
+
|
|style="background-color:LightSalmon;"|moderate
+
*Major refactoring: complex, macromolecule state, reaction
|-
+
*Parameters fitting - optimization process as a workflow
|Parameters fitting
+
*Save optimization results as the diagram state
 
+
*Implementation of OQL subset for access to databases via BioUML object model
- optimization process as a workflow
+
 
+
- SED-ML as workflow
+
 
+
- save optimization results as the diagram state
+
|style="background-color:LightSalmon;"|moderate
+
|-
+
|Implementation of OQL subset for access to databases via BioUML object model
+
 
|style="background-color:LightSalmon;"|moderate
 
|style="background-color:LightSalmon;"|moderate
 
|-
 
|-
 
|Databases
 
|Databases
|KEGG improvements:
+
|
 
+
*KEGG support improvements:
- omics data visualisation
+
*Diagram export (KGML, BioPAX, SBML, +SVG, +PNG, +JPEG)
 
+
*Set up wizard
- graph search engine improvements (not include small molecules, search for related maps)
+
 
+
- organism - filter and highlighter
+
 
+
- visualization of chemical structure for substances
+
 
+
- diagram editing
+
 
+
- diagram export (KGML, BioPAX, SBML, +SVG, +PNG, +JPEG)
+
 
+
- set up wizard
+
 
|style="background-color:CornflowerBlue;"|low
 
|style="background-color:CornflowerBlue;"|low
 
|-
 
|-
|rowspan="2"|Misc.
+
|Misc.
|SBRML support
+
|
|style="background-color:CornflowerBlue;"|low
+
*SBRML support
|-
+
*Further integration with MATLAB
|Further integration with Matlab
+
 
|style="background-color:CornflowerBlue;"|low
 
|style="background-color:CornflowerBlue;"|low
 
|}
 
|}
 
</center>
 
</center>
 
  
 
==See also==
 
==See also==

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

Personal tools
Namespaces

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