AMICI (@AMICI_toolbox) profile picture

AMICI

@AMICI_toolbox

AMICI is Python/C++/ Matlab interface for SUNDIALS solvers that enables scalable sensitivity analysis for ODE models. https://nitter.cf/t.co/nJmBo8f25b

github.com/AMICI-dev/AMICI
Joined February 2019
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  • Following2
  • Followers22
AMICI 0.23.0 is out with many bug fixes and QOL improvements: github.com/AMICI-dev/AMICI/r…. Thanks to @dweindl, @fabfrohlich, @PLakrisenko and Paul Jonas Jost for contributions!
Release AMICI v0.23.0 · AMICI-dev/AMICI

Release AMICI v0.23.0 · AMICI-dev/AMICI

Features SBML InitialAssignment are no longer absorbed into other model expressions, but are available as parameters or expressions (w) in the amici model by @dweindl in #2304, #2305, #2345, #235...

github.com
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AMICI 0.17.0 is out with SBML plugin and AlgebraicRule support and lots of other goodies: github.com/AMICI-dev/AMICI/r…. Thanks to @dweindl, @fabfrohlich, @dilan_pathirana, @PLakrisenko and Henrik Podéus for contributions!
Release AMICI v0.17.0 · AMICI-dev/AMICI

Release AMICI v0.17.0 · AMICI-dev/AMICI

AMICI v0.17.0 requires Python>=3.9 and a C++17 compatible compiler Features DAE support in SBML by @FFroehlich in #2017 SBML import: flatten SBML-comp models by @dweindl in #2063 Added sllh com...

github.com
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AMICI 0.16.1 is out bringing many smaller fixes, cosmetic improvements, and documentation updates: github.com/AMICI-dev/AMICI/r… Thanks to @dweindl, @fabfrohlich and @PLakrisenko for contributions!
Release AMICI v0.16.1 · AMICI-dev/AMICI

Release AMICI v0.16.1 · AMICI-dev/AMICI

Fixes: Additional package names for finding blas via pkg-config by @dweindl in #1959 Changed default interpolation type from hermite to polynomial by @dweindl in #1960 PySB import: Change default ...

github.com
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We are organising an AMICI workshop as satellite event to the Bonn Conference on Mathematical Life Sciences. This workshop will provide an in-depth overview of the toolbox and its various functions and features. We look forward to seeing you there! docs.google.com/document/d/1…
AMICI Workshop Agenda

AMICI Workshop Agenda

This is a satellite workshop of the Bonn Conference on Mathematical Life Sciences and will happen next door to the INCOME hackathon. Please register for the AMICI workshop using this link. The AMICI...

docs.google.com
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The workshop is co-organized by @fabfrohlich, @dweindl and @JanHasenauer. Whether you are new to AMICI or already have experience with it, you will gain valuable insights and hands-on experience that will help you get the most out of AMICI.
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Register and find out more about the main conference here: uni-bonn.de/en/research-and-…

Bonn Conference on Mathematical Life Sciences

Conference on Mathematical Life Sciences in Bonn, 17-20. April 2023, Topics include: Systems Biology, Integrative Pathway Modelling, Mathematical Image Analysis, Computational Immunology, Chemoinfo...

uni-bonn.de
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AMICI 0.16.0 is out with many improvements to documentation and QoL features github.com/AMICI-dev/AMICI/r… Thanks to @fabfrohlich and @dweindl for contributions!
Release AMICI v0.16.0 · AMICI-dev/AMICI

Release AMICI v0.16.0 · AMICI-dev/AMICI

Features Python 3.11 compatibility by @dweindl in #1876 AMICI now runs on binder (example) by @dweindl in #1935, #1937, #1939 More informative Solver.__repr__ and ExpData.__repr__ by @dweindl in #...

github.com
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AMICI 0.14.0 is out with several bug fixes and new convenience features github.com/AMICI-dev/AMICI/r…
Release AMICI v0.14.0 · AMICI-dev/AMICI

Release AMICI v0.14.0 · AMICI-dev/AMICI

Features: Added optional functionality to apply C99 math optimization to generated C++ code by @dweindl and @lcontento in #1377, #1878 Added option to treat fixed parameters as constants in PEt...

github.com
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The application note describing AMICI is now published in Oxford Bioinformatics: doi.org/10.1093/bioinformati… Thanks to @fabfrohlich @dweindl @yannik_schaelte @dilan_pathirana @StaporPaul and @JanHasenauer for contributions.
AMICI: high-performance sensitivity analysis for large ordinary differential equation models

AMICI: high-performance sensitivity analysis for large ordinary differential equation models

AbstractSummary. Ordinary differential equation models facilitate the understanding of cellular signal transduction and other biological processes. However

academic.oup.com
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AMICI 0.11.14 is out, adding support for events and various bugfixes: github.com/AMICI-dev/AMICI/r…… Thanks to @dweindl, @dilan_pathirana, @fabfrohlich, @yannik_schaelte and @StaporPaul for contributions

Release AMICI v0.11.14 · AMICI-dev/AMICI

New features: Python model import now supports SBML Events (#1443) Implement support for compilation without sensitivities (#1454) Fixes: Issue #1446: Check whether constant parameters are valid...

github.com
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AMICI 0.11.13 is out, bringing better handling of state reinitializations, improved documentation as well as several bugfixes: github.com/AMICI-dev/AMICI/r… Includes contributions by @dweindl, @fabfrohlich and Dilan Pathirana.
Release AMICI v0.11.13 · AMICI-dev/AMICI

Release AMICI v0.11.13 · AMICI-dev/AMICI

Breaking changes: AMICI requires Python>=3.7 Updated package installation (PEP517/518): Creating source distributions requires https://github.com/pypa/build (#1384) (but now handles all package...

github.com
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AMICI 0.11.11 is out, again with better SBML support and bugfixes. Notably we have significantly improved sensitivity computation for models containing Piecewise functions: github.com/AMICI-dev/AMICI/r… Includes contributions by @StaporPaul, @dweindl, @fabfrohlich and Dilan Pathirana.

Release AMICI v0.11.11 · AMICI-dev/AMICI

Python Restore support for species references (#1358) Add support for noise models in pysb (#1360) Proper handling of discontinuities in the ODE rhs (#1352) Fix directly calling AMICI from snakema...

github.com
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AMICI 0.11.9 is out, again with improvements to SBML supporta and small bugfixes: github.com/AMICI-dev/AMICI/r… Includes contributions by @StaporPaul, @dweindl, @fabfrohlich, Dilan Pathirana, Thomas Ligon and Lorenzo Contento.

Release AMICI v0.11.9 · AMICI-dev/AMICI

Python General improvements to SBML import (#1312, #1316, #1315, #1322 , #1324 #1333, #1329) Small bugfixes and improvements (#1321 ) Improve derivative computation for instances of power (#1320 )...

github.com
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AMICI 0.11.8 is out, including improved SBML support, better documentation and various bug fixes: github.com/AMICI-dev/AMICI/r… Contributions by @dweindl, Dilan Pathirana and @fabfrohlich

Release AMICI v0.11.8 · AMICI-dev/AMICI

Python Fix pysb-petab support (#1288) Fix ExpData constructor overloading (#1299) Fix support for positivity enforcement (#1306) Refactor SBML import, adds support for parameter rate rules and ini...

github.com
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Happy to present our computational toolbox @AMICI_toolbox for simulating ODE models today at 7:15 pm UTC in a lightning talk at COMBINE conference (combine2020.sched.com/event/…). Thanks to the organizers @combine_coord for the opportunity! #COMBINE2020
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Just release AMICI 0.11.7 which includes a big documentation overhaul and some efficiency improvements for interdependent expressions: github.com/AMICI-dev/AMICI/r…
Release AMICI v0.11.7 · AMICI-dev/AMICI

Release AMICI v0.11.7 · AMICI-dev/AMICI

Python Improve and extend available objective functions (#1235) Fix processing of compartment definitions (#1223) Fix replacement of reserved symbols (#1265) Use Hierarchical Derivatives for Expre...

github.com
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