Release of BioUML platform - 2019.1

[Ilya Kiselev]

We are pleased to announce new release of BioUML platform.
New 2019.1 version is now available at new.bio-store.org.

New features and improvements:

• General:
  
  • Installation process for linux systems improved
    
• Diagrams
  
  • “Fit to screen” option added in toolbar for diagrams
    
  • Create edges from reactions to newly added nodes on diagram, if edge information is present in reaction prototype
    
  • Copy&paste diagram nodes to specified location
    
  • Copy all elements of one diagram to another via drag-and-drop
    
  • Nodes shape size is now editable from info panel
    
  • User can remove parameters from Parameters view part
    
• Simulation
  
  • More convenient way to show on plot variables from modules several levels deep in the hierarchy
    
• Visualization
  
  • Nodes and compartments may be visualized using custom images uploaded by user, image width and length can be set in percents of original image
    
  • Reactome Image library supported
    
• Layout
  
  • Pin/unpin diagram elements via dropdown menu
    
  • Save and remember used automatic layouter for given diagram
    
  • Incremental layout of elements elements added from search
    
• Expression filters
  
  • All SBGN diagrams support filters (e.g. expression filter)
    
  • Display expression filter as gradient aura on diagrams
    
  • NaN values for expression filters supported
    
• Web version
  
  • Show multiple simulation plots in one window, stop simulation if plots are closed.
    
  • Collapsible array attributes in info block
    
  • Highlight inner nodes of complex in Keynodes visualization.
    
  • Selected info template is remembered for elements of the same type
    
  • Import improved
    
• Analysis
  
  • More user-friendly Identifiability analysis interface (absolute value of deviation instead of chi-square quantile, select parameters for analysis in optimization version)
    
• Formats
  
  • Partial support of VCF4.3 on import/export, FILTER property for .VCF track files supported
    
• External libraries
  
  • jfreechart update 1.0.18 -> 1.5.0;
    
  • jcommon updated 1.0.22 -> 1.0.24
    
  • underscore.js update 1.2.2 -> 1.9.1
    
• Many bugs were fixed