Release of BioUML platform - 2023.3
Posted: 15 Sep 2023, 15:43New 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
- SBGN annotation to specify:
- 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)