Advanced Multilanguage Interface to CVODES and IDAS
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dweindl Merge pull request #501 from ICB-DCM/release_v0.8.2
Release v0.8.2

Features / improvements:
* Speedup symbolic processing for ODE generation in python

Bugfixes:
* Fix(python) Add missing deepcopy (introduced in 6847ba6)
* Fix(core) Prevent parameter scaling length mismatch (#488)
* Fix(python) Set distutils dependency to current version to fix </usr/lib/python3.6/distutils/dist.py:261: UserWarning: Unknown distribution option: 'long_description_content_type'>
* fix(python) add symlink to version.txt to be included in package

Backwards-compatibility:
* Replace 'newline' by literal to restore <R2016b compatibility (Fixes #493)

Maintenance:
* Remove obsolete swig library build via cmake and related file copying
* Provide issue template for bug reports
* Providing valid SBML document to import is not optional anymore
* Update documentation and tests
* Add python version check and raise required version to 3.6 to prevent cryptic error messages when encountering f-strings
Latest commit dce9bbc Jan 7, 2019
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.github/ISSUE_TEMPLATE Provide issue template for bug reports Dec 14, 2018
ThirdParty Feature swig interface (#279) May 22, 2018
cmake Feature swig interface (#279) May 22, 2018
documentation Document Amici/OpenMP usage with gcc/linux (Missed commits from PR #461 Nov 21, 2018
include/amici fix(steadystate) fix solver copying in createSteadyStateSimSolver (#482) Dec 4, 2018
matlab fix(matlab) Replace 'newline' by literal to restore <R2016b compatibi… Jan 7, 2019
models Pysb Import (#463) Nov 17, 2018
python Fix(python) Add missing deepcopy (introduced in 6847ba6) Dec 18, 2018
scripts Update scripts/run-doxygen.sh Jan 7, 2019
src fix(core) Check input dimensions in Model::setParameterScale (Fixes #488 Dec 12, 2018
swig refactor(build) Remove obsolete swig library build via cmake and rela… Dec 18, 2018
tests test(core) Add regression tests for parameter scaling length mismatch ( Dec 14, 2018
.clang-format Proposal for clang-format style file Aug 19, 2017
.gitignore Pysb Import (#463) Nov 17, 2018
.travis.yml setup develop branch with travis and version bump (#487) Dec 12, 2018
AMICI_guide.pdf Replace symengine by sympy (#467) Nov 19, 2018
CMakeLists.txt refactor(build) Remove obsolete swig library build via cmake and rela… Dec 18, 2018
CONTRIBUTING.md setup develop branch with travis and version bump (#487) Dec 12, 2018
INSTALL.md Maintenance fixes (#399) Aug 15, 2018
LICENSE.md Documentation update, fixes #233 (#317) May 30, 2018
README.md Update README.md (#484) Dec 11, 2018
bu_.appveyor.yml lets disable appveyor until somebody is brave enough to repair it May 12, 2017
codecov.yml Feature convenience wrappers, fixes #413 (#418) Sep 4, 2018
version.txt setup develop branch with travis and version bump (#487) Dec 12, 2018

README.md

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.

Publications

DOI

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

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

Current build status

PyPI version Build Status CodeCov Codacy