Data2Dynamics specifications

Information


Unique identifier OMICS_09501
Name Data2Dynamics
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages MATLAB
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Andreas Raue <>

Publications for Data2Dynamics

Data2Dynamics in publications

 (11)
PMCID: 5787704
PMID: 29371237
DOI: 10.15252/msb.20177733

[…] filter sets. automated segmentation was performed in matlab (mathworks) with algorithms from cellprofiler (carpenter et al, )., model simulations and fitting were performed using the matlab toolbox data2dynamics (raue et al, ). the implementation of the model and the computational methods are described in ., reporter cell lines are available upon request. the primary datasets and mathematical […]

PMCID: 5648249
PMID: 29049379
DOI: 10.1371/journal.pone.0186927

[…] receptor clustering for sfk-mediated dab1 trans-phosphorylation and does not require co-receptors to describe the measured data. the model is freely available within the open-source framework data2dynamics (www.data2dynamics.org). it can be used to generate predictions that can be validated experimentally, and provides a platform for model extensions both to downstream targets […]

PMCID: 5640784
PMID: 29062282
DOI: 10.3389/fphys.2017.00775

[…] multi-compartment model describing il-6 signaling in primary mouse hepatocytes was developed. the model is described by a set of coupled non-linear differential equations implemented using the data2dynamics software package (raue et al., ) in each simulated experiment, the model is equilibrated to steady state prior to treatment with inhibitors or stimulation. considering the size […]

PMCID: 5607260
PMID: 28944080
DOI: 10.1038/s41540-017-0030-3

[…] together with the rna sequencing data obtained from the ccle and the tcga research network (http://cancergenome.nih.gov/), respectively, have been deposited within freely available modeling toolbox data2dynamics (http://data2dynamics.org; repository folder examples/hass_npjsysbio2017). it includes matlab code and documented script files to readily perform all analysis steps outlined […]

PMCID: 5548920
PMID: 28804640
DOI: 10.1038/s41540-017-0023-2

[…] dns has the advantage, with respect to sf, of not introducing additional unknown parameters, dnss are rarely used. a reason can be that current parameter estimation software, such as copasi and data2dynamics, do not include dns support. a technical difficulty arises, because the normalisation has to be applied to each simulation run, after the run is completed. unlike the sfs, […]


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Data2Dynamics institution(s)
Institute of Physics, University of Freiburg, Freiburg im Breisgau, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg im Breisgau, Germany
Data2Dynamics funding source(s)
This work was supported by the German Ministry of Education and Research through the grants LungSys II (0316042A) and ReelinSys (0316174C). It was also supported by the Mechanism Based Integrated Systems for the Prediction of Drug Induced Liver Injury project, Innovative Medicines Initiative Joint Undertaking under Grant Agreement No. 115336.

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