Difference between revisions of "BioUML development roadmap"

• 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

2016

• 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

2016

• 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

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

• SBRML support
• Further integration with MATLAB