Release of BioUML platform - 2023.3

[Ilya Kiselev]

New 2023.3 version was released and can be downloaded from https://bio-store.org.

• General
  
  • Export\import research project
  • Export\import optimization document to sbex format
  • Overall performance improved, bugs fixed
• Python library
  
  • bioumlsim library was created to facilitate using BioUML simulation capabilities via Python interface (http://wiki.biouml.org/index.php/Bioumlsim)
• Diagrams
  
  • Improved mathematical formulas representation in models description
  • Improved visual representation of variables including concentration\amount notation
  • Improved tabs for model elements editing
• Analysis
  
  • 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
  • Text highlight improved
  • Autoupdate mode
  • Keyword substanceOnly and initial quantity type (e.g. s1 = 5.0 / C)
  • Custom annotations added to antimony
    
    • SBGN annotation to specify:
      
      • Species type: macromolecule, simple chemical, etc.
      • Structure: complex elements, multiple modifications, units of information
      • Reaction type: process, inhibition etc.
      • Modifier type: catalysis, modulation etc.
      • Apecies clones.
      • Port titles
    • Glycan annotation to specify structure
    • Smiles annotation to specify structure
    • Multimers
• A bunch of published complex modular models has recently been constructed in BioUML:
  
  • Blood pressure regulation (https://doi.org/10.3389/fphys.2021.746300%20)
  • Antihypertensive therapy (https://doi.org/10.3389/fphys.2022.1070115)
  • Skeletal muscle metabolism (https://doi.org/10.3390/ijms221910353)
  • SARS-CoV-2 distribution in human organs (https://doi.org/10.3390/math10111925)
  • COVID-19 epidemiology (https://doi.org/10.1038/s41598-023-40008-9)
  • PBPK modeling of nanoparticles delivery to solid tumors in mice (https://doi.org/10.3390/math10071176)