libroadrunner-experimental 2.2.2

libRoadRunner: A simulation and analysis library for SBML

libRoadRunner

Summary

libroadrunner 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:

Installation

Python front end (stable):

pip install libroadrunner

Binaries:

Head over to the Releases page to download binaries.

Experimental front end:

pip install libroadrunner-experimental

Documentation

Python API Documentation

C API Documention

Copyright

Copyright 2013-2021

E. T. Somogyi ¹, J. K. Medley ³, M. T. Karlsson ², M. Swat ¹, M. Galdzicki ³, K. Choi ³, W. Copeland ³, L. Smith ³, C. Welsh ³ and H. M. Sauro ³

1. Biocomplexity Institute, Indiana University, Simon Hall MSB1, Bloomington, IN 47405
2. Dune Scientific, 10522 Lake City Way NE, #302 Seattle WA
3. Department of Bioengineering, University of Washington, Seattle, WA, 98195

The current (2021) developers are Lucian Smith and Ciaran Welsh.

Introduction

libRoadRunner is a high-performance and portable simulation engine for systems and synthetic biology.

Contributing

IMPORTANT! Contributors must follow the contribution 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 CVODE
• Supports SBML Level 2 to 3 but currently excludes algebraic rules and delay differential equations
• Uses latest libSBML distribution
• Defaults to LLVM code generation on the backend, resulting is very fast simulation times
• Optional generation of model C code and linking at run-time
• Add plugins, distribution comes with Levenberg-Marquardt optimizer plugin
• Compute steady state
• Metabolic Control Analysis
• Frequency Domain Analysis
• Access to:
  • Eigenvalues and Eigenvectors
  • Jacobian, full and reduced
  • Structural Matrices of the stoichiometry matrix

Availability

RoadRunner 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 http://sourceforge.net/projects/libroadrunner/files and can be installed ready for use.

Docker images

Currently we have a manylinux2014 build docker 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.x

and the build image:

docker pull ciaranwelsh/roadrunner-manylinux2014-build:llvm-13.x

Docker build scripts can be found under the docker directory from the roadrunner root directory.

We can also build roadrunner in alternative docker environments (ubuntu etc.) on request.

Acknowledgements

This work is funded by NIGMS grant: GM081070

Licence

Licensed 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 at

http://www.apache.org/licenses/LICENSE-2.0

Unless 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 logo

The libroadrunner logo is an adaptation of the image originally posted to Flickr by El Brujo+ at http://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.