Release of BioUML platform - 2019.4

[Ilya Kiselev]

New 2019.4 version was released and can be downloaded from new.bio-store.org.

New features and improvements:

• General:
  
  • Headless version of BioUML refined and improved. More information and example scripts can be found here.
    
  • All Curated Biomodels tested to be imported and simulated
    
  • Automatically select imported data element in repository tree
    
• Formats:
  
  • SBGN Process Description Level 1 version 2.0 supported: shapes of simple chemical and variable changed, equivalence operator implemented (not affecting simulation for now)
    
  • Better Reactome support (full support of new ID format, various fixes)
    
  • Option to use score satisfying UCSC сonventions during export in BED, GTF, GFF
    
• Tables:
  
  • Table importer: fixed quotes processing, better processing of incomplete lines (with empty trailing values)
    
  • Info about matching path is shown in the results of the table converting (with versions of used databases).
    
• Web version:
  
  • More precise edge selection in diagrams
    
  • Selected edges are highlighted with pink color
    
  • Move nodes on diagram using Ctrl+Arrow keys for 1px and Shift + Arrow keys for 5px shift
    
  • Copy and clone diagram element actions are separated
    
  • Initial integration with Jupyter
    
  • Track finder (user can set conditions and search for tracks in database (Ensembl, GTRD), the results can be added to the genome browser view from the tab)
    
• Bug fixing