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odeSD specifications

Information


Unique identifier OMICS_20238
Name odeSD
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, MATLAB
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 1.1
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Jorg Stelling <>

Publication for odeSD

odeSD citations

 (2)
library_books

Scalable Parameter Estimation for Genome Scale Biochemical Reaction Networks

2017
PMCID: 5256869
PMID: 28114351
DOI: 10.1371/journal.pcbi.1005331

[…] analysis, these matlab toolboxes could exploit forward sensitivity analysis available via amici, as amici yields computation times comparable to those of tailored numerical methods such as odesd [] ( section 5) or data2dynamics []. moreover amici comes with detailed documentation and is already now used by several research labs., our study of the model of erbb signaling suggests […]

library_books

Where next for the reproducibility agenda in computational biology?

2016
PMCID: 4946111
PMID: 27422148
DOI: 10.1186/s12918-016-0288-x

[…] ode solvers which can translate and solve models specified using a markup language, allowing modellers and readers to concentrate on the model rather than its implementation. for example, the odesd tool [] provides a model conversion framework for sbml models and integrators implemented in the matlab and c languages., like the bioinformatic analyses described above, simulations […]


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odeSD institution(s)
Supported by the EU FP6 project BaSysBio (LSHG-CT-2006-037469), the EU FP7 project UniCellSys (HEALTH-F4-2008-201142), the Swiss Initiative for Systems Biology SystemsX.ch (RTD project YeastX), by an ETH Excellence Scholarship and by Swiss National Science Foundation’s Individual Support Fellowships Nr. PBEZP2-127959 and Nr. PA00P2-134146.

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