Difference between revisions of "BioUML development roadmap"

• 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

2015

• 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

• 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

• KEGG support improvements:
• Diagram export (KGML, BioPAX, SBML, +SVG, +PNG, +JPEG)
• Set up wizard

• SBRML support
• Further integration with MATLAB