amici

High-performance sensitivity analysis for large ordinary differential equation models

Science Score: 77.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 5 DOI reference(s) in README
✓
Academic publication links
Links to: zenodo.org
✓
Committers with academic emails
8 of 30 committers (26.7%) from academic institutions
○
Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (16.4%) to scientific vocabulary

Keywords

adjoint-sensitivities cvode cvodes differentialequations forward-sensitivities hacktoberfest idas kinetic-modeling mechanistic-models modeling ode parameter-estimation petab pysb python sbml sensitivities sensitivity-analysis simulation systemsbiology

Last synced: 6 months ago · JSON representation ·

Repository

High-performance sensitivity analysis for large ordinary differential equation models

Basic Info

Host: GitHub
Owner: AMICI-dev
License: other
Language: C++
Default Branch: main
Homepage: https://amici.readthedocs.io/
Size: 211 MB

Statistics

Stars: 125
Watchers: 9
Forks: 31
Open Issues: 123
Releases: 124

Topics

Created over 10 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog Contributing License Code of conduct Citation Codeowners

README.md

Advanced Multilanguage Interface for CVODES and IDAS

About

AMICI provides a multi-language (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 or PySB and automatically compiles such models into Python modules, C++ libraries or Matlab .mex simulation files. The generated model expressions along with the corresponding sensitivity equations are transformed into native C++ code which allows for a significantly faster simulation.

NOTE: The MATLAB interface is no longer supported and will be removed soon.

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 it is also applicable to a wider range of differential equation constrained optimization problems.

Current build status

Features

SBML import
PySB import
Generation of C++ code for model simulation and sensitivity computation
Access to and high customizability of CVODES and IDAS solver
Python, C++, Matlab interface
Sensitivity analysis
- forward
- steady state
- adjoint
- first- and second-order
Pre-equilibration and pre-simulation conditions
Support for discrete events and logical operations

Interfaces & workflow

The AMICI workflow starts with importing a model from either SBML (Matlab, Python), PySB (Python), or a Matlab definition of the model (Matlab-only). From this input, all equations for model simulation are derived symbolically and C++ code is generated. This code is then compiled into a C++ library, a Python module, or a Matlab .mex file and is then used for model simulation.

AMICI workflow

Getting started

The AMICI source code is available at https://github.com/AMICI-dev/AMICI/. To install AMICI, first read the installation instructions for Python, C++ or Matlab. There are also instructions for using AMICI inside containers.

To get you started with Python-AMICI, the best way might be checking out this Jupyter notebook .

To get started with Matlab-AMICI, various examples are available in matlab/examples/.

Comprehensive documentation is available at https://amici.readthedocs.io/en/latest/.

Any contributions to AMICI are welcome (code, bug reports, suggestions for improvements, ...).

Getting help

In case of questions or problems with using AMICI, feel free to post an issue on GitHub. We are trying to get back to you quickly.

Projects using AMICI

There are several tools for parameter estimation offering good integration with AMICI:

pyPESTO: Python library for optimization, sampling and uncertainty analysis
pyABC: Python library for parallel and scalable ABC-SMC (Approximate Bayesian Computation - Sequential Monte Carlo)
parPE: C++ library for parameter estimation of ODE models offering distributed memory parallelism with focus on problems with many simulation conditions.

Publications

Citeable DOI for the latest AMICI release:

There is a list of publications using AMICI. If you used AMICI in your work, we are happy to include your project, please let us know via a GitHub issue.

When using AMICI in your project, please cite:

Fröhlich, F., Weindl, D., Schälte, Y., Pathirana, D., Paszkowski, Ł., Lines, G.T., Stapor, P. and Hasenauer, J., 2021. AMICI: High-Performance Sensitivity Analysis for Large Ordinary Differential Equation Models. Bioinformatics, btab227, DOI:10.1093/bioinformatics/btab227.

bibtex @article{frohlich2020amici, title={AMICI: High-Performance Sensitivity Analysis for Large Ordinary Differential Equation Models}, author={Fr{\"o}hlich, Fabian and Weindl, Daniel and Sch{\"a}lte, Yannik and Pathirana, Dilan and Paszkowski, {\L}ukasz and Lines, Glenn Terje and Stapor, Paul and Hasenauer, Jan}, journal = {Bioinformatics}, year = {2021}, month = {04}, issn = {1367-4803}, doi = {10.1093/bioinformatics/btab227}, note = {btab227}, eprint = {https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btab227/36866220/btab227.pdf}, }

When presenting work that employs AMICI, feel free to use one of the icons in doc/gfx/, which are available under a CC0 license:

AMICI Logo

Owner

Name: AMICI
Login: AMICI-dev
Kind: organization

Twitter: AMICI_toolbox
Repositories: 1
Profile: https://github.com/AMICI-dev

Advanced Multilanguage Interface to CVODES and IDAS

Citation (CITATION.cff)

authors:
   -
     family-names: "Fröhlich"
     given-names: "Fabian"
     orcid: "https://orcid.org/0000-0002-5360-4292"
   -
     family-names: "Weindl"
     given-names: "Daniel"
     orcid: "https://orcid.org/0000-0001-9963-6057"
   -
     family-names: "Schälte"
     given-names: "Yannik"
     orcid: "https://orcid.org/0000-0003-1293-820X"
   -
     family-names: "Pathirana"
     given-names: "Dilan"
     orcid: "https://orcid.org/0000-0001-7000-2659"
   -
     family-names: "Paszkowski"
     given-names: "Lukasz"
   -
     family-names: "Lines"
     given-names: "Glenn Terje"
     orcid: "https://orcid.org/0000-0002-6294-1805"
   -
     family-names: "Stapor"
     given-names: "Paul"
     orcid: "https://orcid.org/0000-0002-7567-3985"
   -
     family-names: "Hasenauer"
     given-names: "Jan"
     orcid: "https://orcid.org/0000-0002-4935-3312"
title: "AMICI: High-Performance Sensitivity Analysis for Large Ordinary Differential Equation Models"

preferred-citation:
   type: article
   title: "AMICI: High-Performance Sensitivity Analysis for Large Ordinary Differential Equation Models"
   doi: 10.1093/bioinformatics/btab227
   journal: "Bioinformatics"
   year: 2021
   month: 4
   start: 1
   end: 1
   authors:
      -
        family-names: "Fröhlich"
        given-names: "Fabian"
        orcid: "https://orcid.org/0000-0002-5360-4292"
      -
        family-names: "Weindl"
        given-names: "Daniel"
        orcid: "https://orcid.org/0000-0001-9963-6057"
      -
        family-names: "Schälte"
        given-names: "Yannik"
        orcid: "https://orcid.org/0000-0003-1293-820X"
      -
        family-names: "Pathirana"
        given-names: "Dilan"
        orcid: "https://orcid.org/0000-0001-7000-2659"
      -
        family-names: "Paszkowski"
        given-names: "Lukasz"
      -
        family-names: "Lines"
        given-names: "Glenn Terje"
        orcid: "https://orcid.org/0000-0002-6294-1805"
      -
        family-names: "Stapor"
        given-names: "Paul"
        orcid: "https://orcid.org/0000-0002-7567-3985"
      -
        family-names: "Hasenauer"
        given-names: "Jan"
        orcid: "https://orcid.org/0000-0002-4935-3312"
cff-version: 1.2.0
message: "If you use this software, please cite both the article from preferred-citation and the software itself."
url: "https://github.com/AMICI-dev/AMICI"
doi: 10.5281/zenodo.597928

GitHub Events

Total

Create event: 190
Release event: 11
Issues event: 143
Watch event: 13
Delete event: 170
Issue comment event: 870
Push event: 560
Pull request review comment event: 80
Pull request review event: 250
Pull request event: 424
Fork event: 1

Last Year

Create event: 190
Release event: 11
Issues event: 143
Watch event: 13
Delete event: 170
Issue comment event: 870
Push event: 560
Pull request review comment event: 80
Pull request review event: 250
Pull request event: 424
Fork event: 1

Committers

Last synced: almost 3 years ago

All Time

Total Commits: 3,005
Total Committers: 30
Avg Commits per committer: 100.167
Development Distribution Score (DDS): 0.619

Top Committers

Name	Email	Commits
fabian.froehlich	f**h@h**e	1,145
Daniel Weindl	d**l@h**e	804
Daniel Weindl	d**l@u**m	514
Fabian Fröhlich	f**n@s**m	221
Paul Stapor	p**r@h**e	149
Fabian Fröhlich	f**h@h**u	58
Yannik Schälte	3**e@u**m	32
Dilan Pathirana	5**h@u**m	21
lcontento	l**o@u**m	11
AMICI-developer	f**b@g**m	9
Polina Lakrisenko	p**o@g**m	7
Thomas S. Ligon	t**m@t**o	4
Leonard	l**r@h**e	4
dependabot[bot]	4**]@u**m	3
Jan Hasenauer	j**r@h**e	2
Łukasz Paszkowski	l**i@r**m	2
Łukasz Paszkowski	4**w@u**m	2
yannikschaelte	y**e@g**m	2
Paul Jonas Jost	7**t@u**m	2
Fabian Froehlich	F**h@m**e	2
MerktSimon	4**n@u**m	2
Kristian Meyer	km@m****m	1
Paul Lang	4**g@u**m	1
Stephan Grein	s**n@u**e	1
Stephan Grein	1**g@u**m	1
Doresic	8**c@u**m	1
Katrin Leinweber	9**r@u**m	1
LarsFroehling	6**g@u**m	1
Jakob Vanhoefer	3**r@u**m	1
willov	w**s@g**m	1

Committer Domains (Top 20 + Academic)

helmholtz-muenchen.de: 5 uni-bonn.de: 1 meyerct.com: 1 mytum.de: 1 radytek.com: 1 thomassligon.info: 1 hms.harvard.edu: 1 schaluck.com: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 270
Total pull requests: 742
Average time to close issues: 9 months
Average time to close pull requests: 12 days
Total issue authors: 28
Total pull request authors: 13
Average comments per issue: 1.69
Average comments per pull request: 1.32
Merged pull requests: 620
Bot issues: 0
Bot pull requests: 9

Past Year

Issues: 96
Pull requests: 495
Average time to close issues: about 1 month
Average time to close pull requests: 2 days
Issue authors: 7
Pull request authors: 4
Average comments per issue: 0.95
Average comments per pull request: 1.14
Merged pull requests: 394
Bot issues: 0
Bot pull requests: 3

View more stats

Top Authors

Issue Authors

dweindl (229)
FFroehlich (27)
paulstapor (6)
aidinbii (5)
yannikschaelte (4)
plakrisenko (3)
matthiaskoenig (3)
dilpath (2)
ahjanee (2)
m-philipps (2)
lcontento (2)
derleanfv (1)
winkmal (1)
lmriccardo (1)
PHvanLent (1)

Pull Request Authors

dweindl (833)
FFroehlich (101)
dependabot[bot] (16)
plakrisenko (5)
dilpath (4)
paulstapor (4)
BartoszBartmanski (2)
ChocolateCharlie (2)
willov (1)
Podde1 (1)
Doresic (1)
PaulJonasJost (1)
fbergmann (1)
stephanmg (1)

Top Labels

Issue Labels

enhancement (55) python (52) c++ (45) bug (42) SBML (26) ci (25) events (18) PEtab (17) documentation (15) cmake (13) new (11) refactoring (10) matlab (10) wontfix (8) good first issue (8) breaking change (7) question (7) steady state (6) windows (5) performance (5) swig (3) maintenance (2) DAE (1) 2nd order (1) HacktoberFest (1) PySB (1) help wanted (1) :mega: :mega: :mega: (1)

Pull Request Labels

codex (41) dependencies (16) github_actions (12) PEtab (2) performance (2) invalid (2) help wanted (1)

Packages

Total packages: 2
Total downloads:
- pypi 3,028 last-month
Total docker downloads: 2,876

Total dependent packages: 5
(may contain duplicates)
Total dependent repositories: 13
(may contain duplicates)
Total versions: 129
Total maintainers: 3

pypi.org: amici

Advanced multi-language Interface to CVODES and IDAS

Homepage: https://github.com/AMICI-dev/AMICI
Documentation: https://amici.readthedocs.io/en/latest/
License: other
Latest release: 0.34.1
published 6 months ago

Versions: 127
Dependent Packages: 5
Dependent Repositories: 13
Downloads: 3,028 Last month
Docker Downloads: 2,876

Rankings

Dependent packages count: 1.6%

Docker downloads count: 1.7%

Dependent repos count: 4.0%

Average: 4.4%

Downloads: 5.0%

Stargazers count: 6.9%

Forks count: 7.3%

Maintainers (2)

dweindl ffroehlich

Last synced: 6 months ago

spack.io: py-amici

Advanced Multilanguage Interface for CVODES and IDAS

Homepage: https://github.com/AMICI-dev/AMICI
License: []
Latest release: 0.16.0
published almost 3 years ago

Versions: 2
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent repos count: 0.0%

Stargazers count: 19.1%

Forks count: 19.2%

Average: 23.8%

Dependent packages count: 57.0%

Maintainers (1)

adamjstewart

Last synced: 6 months ago

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