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Update README
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dweindl committed Dec 11, 2023
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Expand Up @@ -48,7 +48,7 @@ described in [doc/petab_model_import.md](doc/petab_model_import.md).

For full functionality, parPE requires the following libraries:

* CMAKE (>=3.10)
* CMAKE (>=3.15)
* MPI ([OpenMPI](https://www.open-mpi.org/),
[MPICH](https://www.mpich.org/), ...)
* IPOPT (>= 1.2.7) (requires coinhsl)
Expand All @@ -60,7 +60,7 @@ For full functionality, parPE requires the following libraries:
* [AMICI](https://github.com/AMICI-dev/AMICI) (included in this repository)
(uses SuiteSparse, Sundials)
* C++17 compiler
* Python >= 3.7, including header files
* Python >= 3.9, including header files

On Debian-based systems, dependencies can be installed via:
```shell
Expand All @@ -72,6 +72,7 @@ sudo apt-get install \
curl \
gfortran \
libblas-dev \
libboost-chrono-dev \
libboost-serialization-dev \
libboost-thread-dev \
libceres-dev \
Expand Down Expand Up @@ -120,7 +121,7 @@ can be found on [dockerhub](https://hub.docker.com/r/dweindl/parpe/).

Some high-level documentation is available at
[https://parpe.readthedocs.io/en/latest/](https://parpe.readthedocs.io/en/latest/)
and among [Github issues](https://github.com/ICB-DCM/parPE/issues). No extensive
and among [GitHub issues](https://github.com/ICB-DCM/parPE/issues). No extensive
full-text documentation is available for the C++ interface yet. For usage of
the C++ interface see [`examples/`](examples/) and `*/tests`.

Expand All @@ -140,6 +141,11 @@ parPE is being used or has been used in the following projects:
(2022). [doi:10.1038/s41467-021-27374-6](https://doi.org/10.1038/s41467-021-27374-6)
(preprint: [doi:10.1101/859884](https://doi.org/10.1101/859884)).

- Paul F. Lang, David R. Penas, Julio R. Banga, Daniel Weindl, Bela Novak.
*Reusable rule-based cell cycle model explains compartment-resolved dynamics*
*of 16 observables in RPE-1 cells*. bioRxiv (2023).
[doi:10.1101/2023.05.04.539349](https://doi.org/10.1101/2023.05.04.539349)

- [CanPathPro](http://canpathpro.eu/)


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