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AMICI biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container

Home Page: https://docs.biosimulators.org/Biosimulators_AMICI

License: MIT License

Dockerfile 3.42% Python 93.00% CSS 3.57%

sbml systems-biology computational-biology sed-ml combine omex mathematical-model simulation biosimulators

biosimulators_amici's Introduction

BioSimulators-AMICI

BioSimulators-compliant command-line interface to the AMICI simulation program.

This command-line interface and Docker image enable users to use AMICI to execute COMBINE/OMEX archives that describe one or more simulation experiments (in SED-ML format) of one or more models (in SBML format).

A list of the algorithms and algorithm parameters supported by AMICI is available at BioSimulators.

A simple web application and web service for using AMICI to execute COMBINE/OMEX archives is also available at runBioSimulations.

Installation

Dependencies

Python >= 3.7
pip
libatlas
g++
swig

Install Python package

pip install biosimulators-amici

Install Docker image

docker pull ghcr.io/biosimulators/amici

Usage

Local usage

usage: biosimulators-amici [-h] [-d] [-q] -i ARCHIVE [-o OUT_DIR] [-v]

BioSimulators-compliant command-line interface to the AMICI simulation program <https://github.com/AMICI-dev/AMICI>.

optional arguments:
  -h, --help            show this help message and exit
  -d, --debug           full application debug mode
  -q, --quiet           suppress all console output
  -i ARCHIVE, --archive ARCHIVE
                        Path to OMEX file which contains one or more SED-ML-
                        encoded simulation experiments
  -o OUT_DIR, --out-dir OUT_DIR
                        Directory to save outputs
  -v, --version         show program's version number and exit

Usage through Docker container

The entrypoint to the Docker image supports the same command-line interface described above.

For example, the following command could be used to use the Docker image to execute the COMBINE/OMEX archive ./modeling-study.omex and save its outputs to ./.

docker run \
  --tty \
  --rm \
  --mount type=bind,source="$(pwd)",target=/root/in,readonly \
  --mount type=bind,source="$(pwd)",target=/root/out \
  ghcr.io/biosimulators/amici:latest \
    -i /root/in/modeling-study.omex \
    -o /root/out

Documentation

Documentation is available at https://docs.biosimulators.org/Biosimulators_AMICI/.

License

This package is released under the MIT license.

Development team

This package was developed by the Center for Reproducible Biomedical Modeling and the Karr Lab at the Icahn School of Medicine at Mount Sinai in New York with assistance from the contributors listed here.

Questions and comments

Please contact the BioSimulators Team with any questions or comments.

biosimulators_amici's People

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biosimulators_amici's Issues

Annotate algorithm parameters with more specific KISAO terms

CVODES, IDAS
- KISAO_0000243: Flag to activate stability limit detection

Failed biomodels

Attached are a list of amici failures on the current suite of biomodels from https://github.com/sys-bio/temp-biomodels/tree/main/omex_files

Also included is the list of tellurium failures, because anything that fails on tellurium is probably also going to fail on amici, for the reasons listed.

tellurium_failures.xlsx
amici_failures.csv

Fix CI

The current CI for Amici fails in the 'build docker image' step with the following error:

      In file included from /tmp/pip-install-x9gsklsq/amici_0d1b10f132da4e86a60eafeef71a84e6/amici/src/solver_idas.cpp:4:
      /tmp/pip-install-x9gsklsq/amici_0d1b10f132da4e86a60eafeef71a84e6/amici/include/amici/model_dae.h: In constructor ‘amici::Model_DAE::Model_DAE(const amici::ModelDimensions&, amici::SimulationParameters, amici::SecondOrderMode, const std::vector<double>&, const std::vector<int>&, bool, int, int, int)’:
      /tmp/pip-install-x9gsklsq/amici_0d1b10f132da4e86a60eafeef71a84e6/amici/include/amici/model_dae.h:60:18: error: ‘reduce’ is not a member of ‘std’
                   std::reduce(idlist.begin(), idlist.end())
                        ^~~~~~
      /tmp/pip-install-x9gsklsq/amici_0d1b10f132da4e86a60eafeef71a84e6/amici/include/amici/model_dae.h:60:18: note: suggested alternative: ‘deque’
                   std::reduce(idlist.begin(), idlist.end())
                        ^~~~~~
                        deque
      ninja: build stopped: subcommand failed.

'reduce' is a feature of C++17, so the problem is probably that we need a newer C++ compiler on the Docker image. Though I don't know how it worked in the past with this problem? Maybe Amici's source itself was updated in the intervening year-ish since the last successful build.

Add support for BNGL

Can be handled by AMICI via PySB.

Add support for other parameters of CVODES

Create additional KiSAO terms
Map function arguments to new terms

Add support for IDAS

First, AMICI would need to provide IDAS support for SBML

macOS needs swig to install properly.

When calling pip install biosimulators-amici in my python3.10 conda environment, there was an error building the wheel due to the PEP517-style build. After using brew install swig and re-running my pypi download, it was successful. I am not sure if this is a Mac-specific issue.

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