BioUML development roadmap - Revision history

Axec@dote.ru: /* Plans for 2016 */

2017-01-11T07:56:31Z

‎Plans for 2016

Axec@dote.ru: /* Plans for 2016 */

2017-01-11T07:47:09Z

‎Plans for 2016

Axec@dote.ru at 07:43, 11 January 2017

2017-01-11T07:43:53Z

Axec@dote.ru at 07:40, 11 January 2017

2017-01-11T07:40:13Z

Axec@dote.ru at 07:22, 11 January 2017

2017-01-11T07:22:14Z

Manikitos@yandex.ru: plans for 2016.4 added

2016-12-28T10:43:05Z

plans for 2016.4 added

Manikitos@yandex.ru: year updated

2016-09-29T08:44:42Z

year updated

Manikitos@yandex.ru: Date for 0.9.10 corrected

2016-03-11T11:05:53Z

Date for 0.9.10 corrected

Axec@dote.ru at 08:15, 12 January 2016

2016-01-12T08:15:24Z

Axec@dote.ru at 10:54, 9 December 2015

2015-12-09T10:54:42Z

@@ Line 17: / Line 17: @@
 **Generating models population using Metropolis algorithm
 **Key node sensitivity analysis
 *Simulation
 **Automatic generation of kinetik laws from SBO

@@ Line 20: / Line 20: @@
 **Automatic generation of kinetik laws from SBO
 **Option to set different output type for variables (quantity or concentration)
 *SBML
 **Level 2 version 5 supported

@@ Line 16: / Line 16: @@
 **Parameters identifiability analysis (Raue et al., 2009)
 **Generating models population using Metropolis algorithm
 *SBML
 **Level 2 version 5 supported

@@ Line 12: / Line 12: @@
 |v. 2016.4
+|
-*Bug fixing
 *Analysis
 **Parameters identifiability analysis (Raue et al., 2009)
@@ Line 21: / Line 21: @@
 *BioUML IDE
 **NetBeans version updated to 8.2
 |December

@@ Line 12: / Line 12: @@
 |v. 2016.4
+|
-'''BioUML core'''
+*Bug fixing
-*Fix bugs
 *Analysis
-**analysis to check parameters identifiability
+**Parameters identifiability analysis (Raue et al., 2009)
-'''BioUML IDE'''
+**Generating models population using Metropolis algorithm
-*update NetBeans version to 8.2
+*SBML
 |December

@@ Line 9: / Line 9: @@
 {| class="wikitable"
 !Release!!Description!!Date
 |-
 |v. 2016.2
@@ Line 17: / Line 28: @@
 **Converter: SBML-SBGN diagram -> SBML-SBGN composite diagram
 *Databases
-**CHEBI support enhanced
+**CHEBI support enhancement
 *Analysis
-**Flux balance analysis enhanced
+**Flux balance analysis enhancement
 |July

@@ 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.
 For this purpose, please, use the [http://forum.biouml.org/ BioUML forum].
-===Plans for 2015===
+===Plans for 2016===
 <center>
@@ Line 10: / Line 10: @@
 !Release!!Description!!Date
 |-
-|v. 0.9.9
+|v. 2016.2
+|
-*BioUML IDE<br>new branch of BioUML platform based on NetBeans IDE
+*Modeling
-*General diagrams
+**Custom styles for diagram elements rendering for all types of models (see SBGN examples)
-**automatic redraw of diagram objects on mouse dragging
+**Automatic detection of model parameter types (Unused, ODE, Algebraic, Descrete, Parameter)
-**context actions on right click: edit element, rotate
+**Converter: SBML-SBGN diagram -> SBML-SBGN composite diagram
-*SBGN diagrams reworked and enhanced
+*Databases
-**special action for clone creation: user can choose for which reactions clone will be created.
+**CHEBI support enhanced
-**"oriented" reactions with one input edge for products and one output edge for reactants.
+*Analysis
-**Creation of phenotypes as processes with modifiers
+**Flux balance analysis enhanced
-**entity pool node and process types can be selected from drop boxes rather then typed
+|July
-**complexes can be transformed to other EPNs and vice-versa
-**separate fonts for node titles.
-*SBML
-**species are saved with the same name as correspondent node on diagram without auomaic prepending of "compartmentName_".
-**Unit definitions can be created and changed via BioUML interface.
-**SBO terms can be set for reactions, equations, functions etc.
-**random variables with normal, unifrom and binomial distributions. Support of custom annotation (also supported by COPASI, Jarnac, Roadrunner).
-**"time", "avogadro" and "delay" csymbols.
-*SedML l1v2 supported
-*Antimony
-**added support for visual arrangment of species (complexes, state variables, different types of EPN)
-**fixed bug with disabling of "close document" action.
-*Agent-based modeling: introuced script-agents. Supported script languages: R, MATLAB, java-script.
-*Server
-*integration with DropBox, Google Drive, Microsoft One Drive
-−
-−
-|February
-−
-−
-|-
-|v. 0.9.10
-−
-*Server
-**integration with Galaxy CloudMan
-**cloud/grid version - further development and improvements
-**repository - packages for Debian and CentOS
-*Web interface
-**mobile version (for web-browser)
-**web interface improvements diagrams
-*SBGN-ML import and exported supported
-*SBML
-** built-in constants pi and exponentiale
-** fbc 1.2 supported (except gene products). Now boundaries can be specified by parameters
-*Simulation
-** dynamic fbc implemented - flux balance analysis can be performed continuosly during ODE simulation. Special engine implemented.
-|December
-−
 |}
 </center>

@@ Line 71: / Line 71: @@
 *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
 |style="background-color:LightSalmon;"|moderate