The SBML ODE Solver Library: a native API for symbolic and fast numerical analysis of reaction networks
The SBML ODE Solver Library (SOSlib) is a programming library for symbolic and numerical analysis of chemical reaction network models encoded in the Systems Biology Markup Language (SBML). It is written in ISO C and distributed under the open source LGPL license. The package employs libSBML structur...
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| Veröffentlicht in: | Bioinformatics 2006-06, Vol.22 (11), p.1406-1407 |
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| creator | Machné, Rainer Finney, Andrew Müller, Stefan Lu, James Widder, Stefanie Flamm, Christoph |
| description | The SBML ODE Solver Library (SOSlib) is a programming library for symbolic and numerical analysis of chemical reaction network models encoded in the Systems Biology Markup Language (SBML). It is written in ISO C and distributed under the open source LGPL license. The package employs libSBML structures for formula representation and associated functions to construct a system of ordinary differential equations, their Jacobian matrix and other derivatives. SUNDIALS' CVODES is incorporated for numerical integration and sensitivity analysis. Preliminary benchmarking results give a rough overview on the behavior of different tools and are discussed in the Supplementary Material. The native application program interface provides fine-grained interfaces to all internal data structures, symbolic operations and numerical routines, enabling the construction of very efficient analytic applications and hybrid or multi-scale solvers with interfaces to SBML and non SBML data sources. Optional modules based on XMGrace and Graphviz allow quick inspection of structure and dynamics. Availability: Contact:xtof@tbi.univie.ac.at Supplementary information: Supplementary data are available at Bioinformatics online. |
| doi_str_mv | 10.1093/bioinformatics/btl086 |
| format | Article |
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| source | MEDLINE; Oxford Journals Open Access Collection; EZB-FREE-00999 freely available EZB journals; Alma/SFX Local Collection |
| subjects | Algorithms Biological and medical sciences Computational Biology - methods Computer Simulation Computers Fundamental and applied biological sciences. Psychology Gene Library General aspects Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) Models, Biological Models, Theoretical Programming Languages Software Design Systems Biology |
| title | The SBML ODE Solver Library: a native API for symbolic and fast numerical analysis of reaction networks |
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