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




No version available



  • 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

[…] vely 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.As […]


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

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

[…] agnitude. 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 Gauss-Ne […]

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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