Package: libroadrunner-experimental
libRoadRunnerSummarylibroadrunner is a C/C++ library that supports simulation of SBML based models. It uses LLVM to generate extremely high performace code and is the fastest SBML based simulator currently avaialable. Its main purpose is for use as a resuable library that can be hosted by other applications, particularly on large compute clusters for doing parameter optimization where performance is critical.We provide C/C++, Python and Julia bindings.Sometimes the link to the C API docs goes bad in the readthedocs. If this happens, here is a permanent link that should remain whatever happens:InstallationPython front end (stable):pip install libroadrunnerBinaries:Head over to theReleasespage to download binaries.Experimental front end:pip install libroadrunner-experimentalDocumentationPython API DocumentationC API DocumentionCopyrightCopyright 2013-2021E. 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) developers are Lucian Smith and Ciaran Welsh.IntroductionlibRoadRunner is a high-performance and portable simulation engine for systems and synthetic biology.ContributingIMPORTANT!Contributorsmustfollow thecontribution guidelines. Contibuters are responsible for complying with the guidelines, including (but not limited to) making commits to the correct branch. Maintainers are not responsible for changes made to the wrong branch. Contributors take full responsibility for ensuring that their changes get merged into the develop branch.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 bedownloaded fromhttp://sourceforge.net/projects/libroadrunner/filesand can be installed
ready for use.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).There are two docker tags associated with roadrunner depending on which
version of llvm you want to build with. The options are llvm-13.x for newer
roadrunner versions (> v2.2.0) and llvm-6.x for older.To get the base image:docker pull ciaranwelsh/roadrunner-manylinux2014-base:llvm-13.xand the build image:docker pull ciaranwelsh/roadrunner-manylinux2014-build: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.AcknowledgementsThis 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 ÎAS 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.