Package: r2sbml 0.1.0

Satyaprakash Nayak

r2sbml: Read 'SBML' Models and Convert Them to Simulation Code

Reads models in the Systems Biology Markup Language ('SBML') (Hucka et al. (2003) <doi:10.1093/bioinformatics/btg015>) through the bundled 'libSBML' library (Bornstein et al. (2008) <doi:10.1093/bioinformatics/btn051>). Lists a model's species, parameters, compartments, reactions, rules, events and function definitions, and converts the model into ready-to-run simulation code for 'deSolve', 'mrgsolve', 'rxode2', 'MATLAB', 'Julia' or 'ubiquity'. Models are read, not modified.

Authors:Satyaprakash Nayak [aut, cre, cph], Sarah M. Keating [ctb], Frank T. Bergmann [ctb], Lucian P. Smith [ctb], Brett G. Olivier [ctb], Akiya Jouraku [ctb], Michael Hucka [ctb], Ben Bornstein [ctb], Jeroen Ooms [ctb], California Institute of Technology [cph], EMBL European Bioinformatics Institute [cph], University of Heidelberg [cph], University College London [cph], Japan Science and Technology Agency [cph], Gilles Vollant [cph], Mathias Svensson [cph], Even Rouault [cph], Nathan Moinvaziri [cph], Terry Thorsen [cph], Info-ZIP [cph], Ludwig Schwardt [cph], Kevin Ruland [cph], M. Petra Baranski [cph], Tim Gromeyer [cph]

r2sbml_0.1.0.tar.gz
r2sbml_0.1.0.zip(r-4.7-x86_64)r2sbml_0.1.0.zip(r-4.7-arm64)r2sbml_0.1.0.zip(r-4.6-x86_64)r2sbml_0.1.0.zip(r-4.6-arm64)
r2sbml_0.1.0.tar.gz(r-4.7-arm64)r2sbml_0.1.0.tar.gz(r-4.7-x86_64)r2sbml_0.1.0.tar.gz(r-4.6-arm64)r2sbml_0.1.0.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
r2sbml/json (API)

# Install 'r2sbml' in R:
install.packages('r2sbml', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/sn248/r2sbml/issues

Pkgdown/docs site:https://sn248.github.io

Uses libs:
  • libxml2– GNOME XML library
  • bzip2– High-quality block-sorting file compressor library
  • c++– GNU Standard C++ Library v3

On CRAN:

Conda:

libxml2bzip2cpp

3.00 score 5 scripts 16 exports 1 dependencies

Last updated from:5836b25357. Checks:9 OK, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK294
linux-devel-x86_64OK268
source / vignettesOK503
linux-release-arm64OK304
linux-release-x86_64OK300
windows-devel-arm64OK580
windows-devel-x86_64OK469
windows-release-arm64OK535
windows-release-x86_64OK408
wasm-releaseFAIL146

Exports:convertReactionsechoSBMLgetCmtNamesgetCmtSizesgetEventMathgetFunctionDefinitiongetModelgetNumSpeciesgetParameterTablegetReactionMathgetReactionTablegetRuleMathgetSpeciesICgetSpeciesNamesgetSpeciesTableprintSBML

Dependencies:Rcpp

Getting started with r2sbml
Reading a model | Functions that return data | Functions that print | Absent components are an error, not an empty result | Exporting mass balances | What happens before anything is written | The deSolve output | The other five targets | Model features that change the shape of the output | Assignment rules | Algebraic rules make the model a DAE | Changing compartment volumes | Practical notes | Where to go next
Rendered fromr2sbml.Rmdusingknitr::rmarkdown

Last update: 2026-11-03
Started: 2026-11-03

Limitations and unimplemented behaviour
The single most important table | How far the output has been checked | Scope: reading and exporting only | Per-target capability matrix | Algebraic rules | Rules linear in one unknown become assignments | Coupled or nonlinear rules become a DAE where the target can solve one | The DAE path has three further limits | Compartments whose volume changes | delay | Events | Mathematics | Values and names | Values the model leaves undefined | Ids the target reserves | No validation is performed | Quirks of the query functions | Initial values are reported as the file states them | Names fall back to the id | Absent components raise an error | Things that are correct but easy to misread | Generated code is a starting point | The SBML Test Suite cases that still fail | Where these are tracked
Rendered fromlimitations.Rmdusingknitr::rmarkdown

Last update: 2026-11-03
Started: 2026-11-03