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 2015
| Release |
Description |
Date
|
| v. 0.9.9
|
- BioUML IDE
new branch of BioUML platform based on NetBeans IDE
- General diagrams
- automatic redraw of diagram objects on mouse dragging
- context actions on right click: edit element, rotate
- SBGN diagrams reworked and enhanced
- special action for clone creation: user can choose for which reactions clone will be created.
- "oriented" reactions with one input edge for products and one output edge for reactants.
- Creation of phenotypes as processes with modifiers
- entity pool node and process types can be selected from drop boxes rather then typed
- 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
2015
|
| 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.
|
2015
|
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
