biomass-dev/biomass
A Python Framework for Modeling and Analysis of Signaling Systems
PythonApache-2.0
Issues
- 1
Add JAK-STAT model to example models
#275 opened by himoto - 0
Support Python 3.12
#265 opened by himoto - 0
Sphinx version
#261 opened by himoto - 0
Sphinx v7 is incompatible due to usage of style key
#258 opened by himoto - 1
Read the Docs build failed
#254 opened by himoto - 1
Support for Python 3.11
#199 opened by himoto - 0
Use Sphinx 6 after `sphinx_rtd_theme` supports it
#250 opened by himoto - 0
Email address needs to be updated
#248 opened by himoto - 0
- 0
Move package setup to `pyproject.toml `
#242 opened by himoto - 0
Visualization of sensitivity analysis via heatmap
#239 opened by himoto - 0
- 0
Use `copy_to_current` function in example code
#233 opened by himoto - 0
Pre-commit error
#236 opened by himoto - 0
Raise `DetectionError` instead of creating wrong model
#231 opened by himoto - 4
Numerical structural identifiability analysis
#196 opened by formersbach - 0
Allowable type of method in `solve_ode`
#228 opened by himoto - 1
Example models
#226 opened by himoto - 2
Typo in state_transition rule
#220 opened by formersbach - 0
Supported `BioMASS.jl` version
#221 opened by himoto - 0
LGTM badge
#218 opened by himoto - 0
Error in example code for `Optimizer` class
#216 opened by himoto - 1
Add note for `run_analysis` function
#214 opened by himoto - 0
Fix code scanning alert - File is not always closed
#212 opened by himoto - 0
Fix code scanning alert - Explicit returns mixed with implicit (fall through) returns
#209 opened by himoto - 0
Template for BioMASS.jl
#203 opened by himoto - 0
Model template needs to be updated
#198 opened by himoto - 6
pytest on graphing fails with `pyvis==0.3`
#200 opened by himoto - 0
- 9
Unable to run provided models
#194 opened by lhdp0110 - 0
- 0
- 2
Unexpected behavior in reaction_rules
#187 opened by formersbach - 1
Phosphorylation generates duplicate ODE
#183 opened by formersbach - 0
Link to `graph visualization functions` is dead
#180 opened by himoto - 0
- 0
Kinetic Information to BioMass
#173 opened by formersbach - 0
`group` method in `reaction_network.py`
#160 opened by himoto - 0
- 0
Methods in `search_param.py`
#159 opened by himoto - 0
Generalization of Mass action kinetics
#171 opened by formersbach - 8
Unexpected behavior for reversible reaction
#166 opened by formersbach - 1
- 6
Using BioMASS without Graphviz
#161 opened by himoto - 0
Unused `exec` in name2idx/species.py
#155 opened by himoto - 0
- 2
Type of `show_controls` in the example code
#151 opened by himoto - 0
Docs for graph visualization
#145 opened by himoto - 1
- 0
Interactive graph
#143 opened by himoto