Polina Lakrisenko

Start points from history

2

Add possibility to choose start points from a history file or a folder with history files. Would it be better to do it via setting `x_guesses` (#445 should be implemented)...

Allow setting different boundaries for starting points sampling

5

Currently `pypesto.problem.lb` and `pypesto.problem.ub` are used as boundaries for generating starting points. I would like to be able to set narrower boundaries than those for optimization. So, optimization would start...

Additional check for steady-state convergence

1

**Feature description** Currently WrmsNorm is used with the formula ^2)}), where  Maybe it would make sense to add possibility to check individual elements and not the sum: ![Figure](https://latex.codecogs.com/svg.image?\left|&space;\dot{x_i}&space;w_i&space;\right|

**Bug description** When running optimizations for a large-scale model (encountered with Fröhlich et al. 2018, 143 control conditions) with `MultiProcessEngine` if memory isn't sufficient some processes get killed without any...

State sensitivities computation at steady state

3

There are two approaches available in AMICI for state sensitivities computation at steady state: numerical integration and solving a linear system (`computeNewtonSensis`). There are now also three `SteadyStateSensitivityMode`s available: `newtonOnly`,...

The model of hepatocyte growth factor (HGF) signal transduction combined with global proteomics, captures HGF-induced signal transduction via the MAPK cascade, the PI3K pathway and mTOR signaling. https://doi.org/10.1038/s44320-023-00007-4 https://www.ebi.ac.uk/biomodels/MODEL2306280002 Available...

Add Mishra_MetabEng2023

1

A kinetic metabolic model of lipid metabolism in Saccharomyces cerevisiae that integrates fatty acid biosynthesis, glycerophospholipid metabolism, sphingolipid metabolism, storage lipids, lumped sterol synthesis, and the synthesis and transport of...