diff --git a/README.md b/README.md index b5a29b8f..e1ce8342 100644 --- a/README.md +++ b/README.md @@ -24,11 +24,15 @@ equation (ODE) models. parPE offers the following features: * MPI-based load-balancing of individual simulations + (if you don't need this, and don't require a C++ library, consider using + the [pypesto](https://pypesto.readthedocs.io/en/latest/) Python package + which is more mature and user-friendly) * improved load balancing by intermingling multiple optimization runs (multi-start local optimization) -* simple integration with [SBML](http://sbml.org/) models via +* integration with [SBML](http://sbml.org/) models via [AMICI](https://github.com/AMICI-dev/AMICI) and [PEtab](https://github.com/PEtab-dev/PEtab) + * hierarchical optimization (https://doi.org/10.1093/bioinformatics/btz581) * interfaces to [Ipopt](https://www.coin-or.org/Ipopt/), [Ceres](http://ceres-solver.org/), [FFSQP](https://www.isr.umd.edu/news/news_story.php?id=4088) and @@ -37,6 +41,12 @@ parPE offers the following features: * Good parallel scaling to up to several thousand cores (highly problem dependent) +**Note that this library has been developed for specific research questions +and certain assumptions may not always hold. Use with caution. +In particular, certain default settings may need adaptation (in particular, +parallelization settings and AMICI settings such as the sensitivity method). +PEtab support is patchy. Always verify your simulation results.** + ## Getting started Although various modules of parPE can be used independently, the most @@ -109,7 +119,7 @@ Other sample build scripts are provided as `/build*.sh`. ## Recently tested compilers -* GCC 13.2.0 +* GCC 14.2.0 * Clang 18.1.3 ## Containers