Recent Releases of BioMASS
BioMASS - v0.8.2
What's Changed
- Move const in continuation.jl to
new_curve!args by @himoto in https://github.com/biomass-dev/BioMASS.jl/pull/63 - CompatHelper: bump compat for CSV to 0.10, (keep existing compat) by @github-actions in https://github.com/biomass-dev/BioMASS.jl/pull/64
Full Changelog: https://github.com/biomass-dev/BioMASS.jl/compare/v0.8.1...v0.8.2
- Julia
Published by himoto about 3 years ago
BioMASS - v0.8.1
What's Changed
- Remove unused package and .jl file by @himoto in https://github.com/biomass-dev/BioMASS.jl/pull/57
- Update docs and code for bifurcation analysis by @himoto in https://github.com/biomass-dev/BioMASS.jl/pull/59
- Fix appearacne by @himoto in https://github.com/biomass-dev/BioMASS.jl/pull/60
- Bump version to 0.8.1 by @himoto in https://github.com/biomass-dev/BioMASS.jl/pull/61
Full Changelog: https://github.com/biomass-dev/BioMASS.jl/compare/v0.8.0...v0.8.1
- Julia
Published by himoto about 3 years ago
BioMASS - v0.8.0 (November 2022)
What's Changed
- Drop support for GA by @himoto in https://github.com/biomass-dev/BioMASS.jl/pull/52
- Add citation info by @himoto in https://github.com/biomass-dev/BioMASS.jl/pull/50
- Release v0.8.0 by @himoto in https://github.com/biomass-dev/BioMASS.jl/pull/53
- Fix parameter_estimation in docs by @himoto in https://github.com/biomass-dev/BioMASS.jl/pull/54
- Don't use GC by @himoto in https://github.com/biomass-dev/BioMASS.jl/pull/55
- Remove unused package in example code by @himoto in https://github.com/biomass-dev/BioMASS.jl/pull/56
Full Changelog: https://github.com/biomass-dev/BioMASS.jl/compare/v0.7.2...v0.8.0
- Julia
Published by himoto over 3 years ago
BioMASS - v0.7.0 (June 2022)
What's Changed
- Release v 0.7.0 by @himoto in https://github.com/biomass-dev/BioMASS.jl/pull/47
| Old | New |
| --- | --- |
| set_model.jl | ode.jl|
| set_search_param.jl | search_param.jl |
| fitness.jl | problem.jl |
Full Changelog: https://github.com/biomass-dev/BioMASS.jl/compare/v0.6.0...v0.7.0
- Julia
Published by himoto over 3 years ago
BioMASS - v0.5.1
What's Changed
- CompatHelper: bump compat for Seaborn to 1, (keep existing compat) by @github-actions in https://github.com/biomass-dev/BioMASS.jl/pull/42
- CompatHelper: bump compat for CSV to 0.9, (keep existing compat) by @github-actions in https://github.com/biomass-dev/BioMASS.jl/pull/43
- Release v0.5.1 by @himoto in https://github.com/biomass-dev/BioMASS.jl/pull/44
Full Changelog: https://github.com/biomass-dev/BioMASS.jl/compare/v0.5.0...v0.5.1
- Julia
Published by himoto almost 4 years ago
BioMASS - v0.5.0 (July 2021)
- Move to biomass-dev
- Create
Modelstruct and function - Rename
run_simulationfunction
- Julia
Published by himoto over 4 years ago
BioMASS - v0.4.2
Updates
examples
- Renamed core functions
docs
- Fix example codes
Parameter estimation
- Add new local search method:
"CMAES" - The CMA Evolution Strategy is a stochastic method for derivative-free optimization of potentially non-linear, non-convex or noisy functions over continuous domains (Hansen 2016).
- Fix search bounds in SciPyOptimize
- Add new local search method:
- Julia
Published by himoto almost 5 years ago
BioMASS - v0.4.1
Update visualize
save_format::String (default: "pdf")- Either "png" or "pdf", indicating whether to save figures as png or pdf format.
Update optimize
initial_threshold::Float64 (default: 1e12)- Allowable error used to generate initial population. Default is 1e12 (numerically solvable).
- Julia
Published by himoto about 5 years ago
BioMASS - v0.4.0 (January 2021)
- Add a Delay differential Equation (DDE) model
```Julia using BioMASS
ddemodel = loadmodel("examples/nfkb_model");
visualize(ddemodel, viztype="original") ```
- Julia
Published by himoto about 5 years ago
BioMASS - v0.3.2
Updates:
Add new local search method: "DE"
- using differential evolution with 'best2bin' strategy in local search phase
Example usage
```julia using BioMASS
model = loadmodel("./examples/fosmodel")
optimize(model, 1, maxgeneration=1000, allowableerror=0.35, localsearchmethod="DE") ```
- Julia
Published by himoto about 5 years ago
BioMASS - v0.3.0 (December 2020)
Updates:
- Documentation
New Features:
- Bifurcation analysis
- Julia
Published by himoto about 5 years ago
BioMASS - v0.2.0 (November 2020)
Updates:
- Create visualize.jl
julia
visualize(model, viz_type="best", show_all=true)
- viztype : String
- "average":
The average of simulation results with parameter sets in "fitparam/".
- "best":
The best simulation result in "fitparam/".
- "original":
Simulation with the default parameters and initial values defined in ```setmodel.jl.
-"n(=1,2,...)"```:
Use the parameter set in "fitparam/n/".
- show_all : *Bool*
- Whether to show all simulation results.
- stdev : *Bool*
- If True, the standard deviation of simulated values will be shown (only available for "average" visualization type).
Change Sim.normalization type from Bool to Dict:
julia normalization = Dict{String, Dict{}}() for observable in observables normalization[observable] = Dict( "timepoint" => nothing, "condition" => [] ) end"timepoint": Union{Int, Nothing}- The time point at which simulated values are normalized. If nothing, the maximum value will be used for normalization.
"condition": Vector{Stirng}- The experimental conditions to use for normalization. If empty, all conditions defined int Sim.conditions will be used.
- Julia
Published by himoto over 5 years ago