Package: libroadrunner
libRoadRunnerSummarylibRoadRunner is a C/C++ library that supports simulation of SBML based models. It uses LLVM) to generate extremely high performance code and is the fastest SBML-based simulator currently available (ref). Its main purpose is for use as a reusable library that can be hosted by other applications, particularly on large compute clusters for doing parameter optimization where performance is critical. It also has a set of python bindings that allow it to be easily used from python.We provide C/C++, Python and Julia bindings.DocumentationFull DocumentationLocal Documentation(May be used if above link is failing.)C API DocumentionInstallationBinariesfor Windows, MacOS (including universal binaries for the M1 processor), and LinuxPython wheels are available at the above binaries link, and can also be installed via pip:pip install libroadrunnerGoogle Colablibroadrunner can be used entirely in a browser usingGoogle Colab.  Ideally, it will work with the following steps (updated May 2023)run a cell with!apt-get install libncurses5run a cell with!pip install libroadrunner(Vert important) Restart the runtime (From the menu: 'Runtime / Restart runtime')Test by runningimport roadrunnerThe Python version behind Colab is reasonably stable but can change. This issue to changes in how colab handles packages. we try to keep abreast of changes at colab.Example Python usageOnce installed in Python (using pip or using the wheels directly), the following simple example script should demonstrate the basics of a roadrunner simulation:importroadrunnerrr=roadrunner.RoadRunner("https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000010.2?filename=BIOMD0000000010_url.xml")results=rr.simulate(0,2000,200)rr.plot()print(results)This simple script downloadsBioModels 10(the Kholodenko model of MAPK oscillation) and runs a simulation for 2000 seconds, storing the results inresults.  If your system is set up to display figures, it will display a plot of the simulation, then print the numerical values obtained.DependenciesAll libRoadRunner binaries are self-contained, and should include all libraries it depends on.  When building libRoadRunner from source, its dependencies may either be downloadeden massefrom thelibroadrunner-depsrepository, may be obtained directly from theirrespective sources, or the libraries may be installed directly on your operating system.  Compilation requires a C++17 compiler.The one exception to the above is that the libRoadRunner binaries depend on the 'ncurses' library on linux.CopyrightCopyright 2013-2022E. T. Somogyi1, J. K. Medley3, M. T. Karlsson2, M. Swat1, M. Galdzicki3, K. Choi3, W. Copeland3, L. Smith3, C. Welsh3and H. M. Sauro3Biocomplexity Institute, Indiana University, Simon Hall MSB1, Bloomington, IN 47405Dune Scientific, 10522 Lake City Way NE, #302 Seattle WADepartment of Bioengineering, University of Washington, Seattle, WA, 98195The current (2021-present) developer is Lucian Smith.ContributingContributors may submit pull requests at any time, and are asked to follow some generalcontribution guidelines.  Bug requests and feature suggestions are also welcomed on theissues page.libRoadRunner supports the following features:Time Dependent Simulation (with optional conservation law reduction) using CVODESupports SBML Level 2 to 3 but currently excludes algebraic rules and delay differential equationsUses latest libSBML distributionDefaults to LLVM code generation on the backend, resulting is very fast simulation timesOptional generation of model C code and linking at run-timeAdd plugins, distribution comes with Levenberg-Marquardt optimizer pluginCompute steady stateMetabolic Control AnalysisFrequency Domain AnalysisAccess to:Eigenvalues and EigenvectorsJacobian, full and reducedStructural Matrices of the stoichiometry matrixAvailabilityRoadRunner is licensed for free as an open source programmatic library for use in other
applications and as a standalone command line driven application. Its C++ API, C API, and
Python APIs have comprehensive documentation. On Windows, OS X, and Linux binary files can be
downloaded from theReleasespage, and the
Python bindings can additionally be downloaded via pip.Docker imagesCurrently we have a manylinux2014builddocker image. The
base provides the environment you need to be able to build roadrunner yourself on manylinux2014 (centos 8).To get the base image:docker pull sysbiouw/roadrunner-manylinux2014-base:llvm-13.xDocker build scripts can be found under thedockerdirectory from the roadrunner
root directory.We can also build roadrunner in alternative docker environments (ubuntu etc.) on request.CitingIf you use RoadRunner in your research, we would appreciate following citations in any works you publish:Ciaran Welsh, Jin Xu, Lucian Smith, Matthias König, Kiri Choi, Herbert M Sauro, libRoadRunner 2.0: a high performance SBML simulation and analysis library,Bioinformatics, Volume 39, Issue 1, January 2023, btac770,https://doi.org/10.1093/bioinformatics/btac770Endre T. Somogyi, Jean-Marie Bouteiller, James A. Glazier, Matthias König, J. Kyle Medley, Maciej H. Swat, Herbert M. Sauro, libRoadRunner: a high performance SBML simulation and analysis library,Bioinformatics, Volume 31, Issue 20, 15 October 2015, Pages 3315–3321,https://doi.org/10.1093/bioinformatics/btv363AcknowledgementsThis work is funded by NIGMS grant: GM081070LicenceLicensed under the Apache License, Version 2.0 (the License); you may not use this
file except in compliance with the License. You may obtain a copy of the License athttp://www.apache.org/licenses/LICENSE-2.0Unless required by applicable law or agreed to in writing, software distributed
under the License is distributed on an AS-IS BASIS, WITHOUT WARRANTIES OR CONDITIONS
OF ANY KIND, either express or implied. See the License for the specific language
governing permissions and limitations under the License.In plain english this means:You CAN freely download and use this software, in whole or in part, for personal,
company internal, or commercial purposes;You CAN use the software in packages or distributions that you create.You SHOULD include a copy of the license in any redistribution you may make;You are NOT required include the source of software, or of any modifications you may
have made to it, in any redistribution you may assemble that includes it.YOU CANNOT: redistribute any piece of this software without proper attribution;libRoadRunner logoThe libroadrunner logo is an adaptation of the image originally posted to Flickr by
El Brujo+ athttp://flickr.com/photos/11039104@N08/2954808342. It was reviewed on
9 August 2009 by the FlickreviewR robot and was confirmed to be licensed under the
terms of the cc-by-sa-2.0.