Release of BioUML 2023.3

[Ilya Kiselev]

Dear all!

We are glad to announce that new 2023.3 version of BioUML was released and can be downloaded from bio-store.org. Web version is available at https://ict.biouml.org/.

New features and improvements include

• General:
  
  • Export\import research project.
  • Export\import optimization (parameter fitting) document to sbex format.
  • Python library bioumlsim, providing python API for BioUML simulation tools.
  • Overall performance improved, bugs fixed.
• Diagrams:
  
  • Improved mathematical formulas representation in models description.
  • Improved visual representation of model variables including concentration\amount notation.
• Parameter Identifiability analysis improved to calculate confidence intervals more correctly
  
• Antimony support:
  
  • New elements: constraints, algebraic equations, subtypes, logical nodes, propagated ports, units (unit definitions, initializations with unit and keyword has), database references, phenotypes.
  • Keyword substanceOnly and initial quantity type (e.g. s1 = 5.0 / C).
  • Text highlight improved.
  • Diagram autoupdate on the base of text.
  • Custom annotation added to antimony.
    
    • SBGN annotation to specify:
      
      • entity type: macromolecule, simple chemical, etc.,
        
      • entity structure: complex elements, multiple modifications, units of information,
        
      • reaction type: process, inhibition etc.,
        
      • modifier type: catalysis, modulation etc.,
        
      • entity clones.
    •  Glycan annotation to specify structure.
    • Smiles annotation to specify structure.
• A bunch of complex modular models has recently been constructed in BioUML and published describing:
  • Blood pressure regulation.
  • Antihypertensive therapy.
  • Skeletal muscle metabolism.
  • SARS-CoV-2 distribution in human organs.
  • COVID-19 epidemiology.
  •  PBPK modeling of nanoparticles delivery to solid tumors in mice.

On the behalf of the BioUML team,

Ilya