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dweindl committed Nov 11, 2024
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Expand Up @@ -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
Expand All @@ -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
Expand Down Expand Up @@ -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
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