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BioPARKIN specifications


Unique identifier OMICS_20240
Alternative name PARKINcpp
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Input format SBML
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python, Shell (Bash)
License GNU Lesser General Public License version 3.0
Computer skills Medium
Version 1.2.23
Stability Stable
Maintained Yes




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  • person_outline Susanna Roblitz

Publications for BioPARKIN

BioPARKIN citations


Parameter Identification in a Tuberculosis Model for Cameroon

PLoS One
PMCID: 4395246
PMID: 25874885
DOI: 10.1371/journal.pone.0120607

[…] in each iteration by an adaptive trust-region method []. this method for solving a non-linear least squares problem is implemented in the software code nlscon [] and part of the software package bioparkin []. here, a matlab-based version of this software package, named poem 2.0, which is especially adapted to parameter identification in ordinary differential equation models, has been used., […]


Inferring Proteolytic Processes from Mass Spectrometry Time Series Data Using Degradation Graphs

PLoS One
PMCID: 3398944
PMID: 22815782
DOI: 10.1371/journal.pone.0040656

[…] this minimization problem can theoretically be solved by any available optimization technique. after testing different available techniques we decided to use poem, a matlab-based version of bioparkin , , to estimate the model parameters as well as the transformation parameters. we further use poem to estimate the initial concentration of the base peptide. poem is based on damped […]

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BioPARKIN institution(s)
Zuse Institute Berlin, Berlin-Dahlem, Germany; Heidelberg University Hospital, Radiology Clinic, Department for Nuclear Medicine, Heidelberg, Germany; Free University Berlin, Institute of Mathematics, Berlin-Dahlem, Germany

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