Metadata-Version: 2.1
Name: amici
Version: 0.10.5
Summary: Advanced multi-language Interface to CVODES and IDAS (%s)
Home-page: https://github.com/ICB-DCM/AMICI
Author: Fabian Froehlich, Jan Hasenauer, Daniel Weindl and Paul Stapor
Author-email: fabian_froehlich@hms.harvard.edu
License: BSD
Description: # About AMICI
        
        
        AMICI provides a multilanguage (Python, C++, Matlab) interface for the SUNDIALS solvers CVODES (for ordinary differential equations) and IDAS (for algebraic differential equations). AMICI allows the user to read differential equation models specified as SBML and automatically compiles such models as .mex simulation files, C++ executables or python modules. In contrast to the SUNDIALSTB interface, all necessary functions are transformed into native C++ code, which allows for a significantly faster simulation. Beyond forward integration, the compiled simulation file also allows for forward sensitivity analysis, steady state sensitivity analysis and adjoint sensitivity analysis for likelihood based output functions.
        
        The interface was designed to provide routines for efficient gradient computation in parameter estimation of biochemical reaction models but is also applicable to a wider range of differential equation constrained optimization problems.
        
        Online documentation is available as [github-pages](http://icb-dcm.github.io/AMICI/).
        
        ## Publications
        
        [![DOI](https://zenodo.org/badge/43677177.svg)](https://zenodo.org/badge/latestdoi/43677177)
        
        [Fröhlich, F., Kaltenbacher, B., Theis, F. J., & Hasenauer, J. (2017). Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks. Plos Computational Biology, 13(1), e1005331. doi: 10.1371/journal.pcbi.1005331](https://doi.org/10.1371/journal.pcbi.1005331)
        
        [Fröhlich, F., Theis, F. J., Rädler, J. O., & Hasenauer, J. (2017). Parameter estimation for dynamical systems with discrete events and logical operations. Bioinformatics, 33(7), 1049-1056. doi: 10.1093/bioinformatics/btw764](https://doi.org/10.1093/bioinformatics/btw764)
        
        [Full list](documentation/references.md)
        
        ## Current build status
        
        [![PyPI version](https://badge.fury.io/py/amici.svg)](https://badge.fury.io/py/amici)
        [![Build Status](https://travis-ci.com/ICB-DCM/AMICI.svg?branch=master)](https://travis-ci.com/ICB-DCM/AMICI)
        [![CodeCov](https://codecov.io/gh/ICB-DCM/AMICI/branch/master/graph/badge.svg)](https://codecov.io/gh/ICB-DCM/AMICI)
        [![Codacy](https://api.codacy.com/project/badge/Grade/945235766e344a7fa36278feab915ff6)](https://www.codacy.com/app/FFroehlich/AMICI?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=ICB-DCM/AMICI&amp;utm_campaign=Badge_Grade)
        
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: POSIX :: Linux
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Programming Language :: Python
Classifier: Programming Language :: C++
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.6
Description-Content-Type: text/markdown
Provides-Extra: wurlitzer
