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Pypet specifications


Unique identifier OMICS_29551
Name Pypet
Alternative name Python Parameter Explorations Toolkit
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Version 0.4.2
Stability Stable
tables, numpy, scipy, panda HTF5
Maintained Yes




No version available



  • person_outline Robert Meyer

Additional information

Publication for Python Parameter Explorations Toolkit

Pypet citations


Tlr1612 is the major repressor of cell aggregation in the light color dependent c di GMP signaling network of Thermosynechococcus vulcanus

Sci Rep
PMCID: 5871770
PMID: 29593349
DOI: 10.1038/s41598-018-23628-4

[…] Primers used are listed in Table . Plasmids were constructed using the In-Fusion System (TaKaRa). For constructing FRET biosensors, fluorescent proteins were cloned from pCyPet-His and pYPet-His (Addgene). We created monomerized variants of CyPet (mCyPet) and YPet (mYPet) by introducing A206K,. The DNA encoding the chimeric protein consisting of mCyPet, Tll0007-PilZ (or the full-len […]


Optogenetic protein clustering through fluorescent protein tagging and extension of CRY2

Nat Commun
PMCID: 5482817
PMID: 28646204
DOI: 10.1038/s41467-017-00060-2

[…] EYFP-C1, pmCitrine-C1, pDsRed-Express2-C1, and pmCherry-C1 were obtained from Clontech. Expression plasmids for pCypet-C1 (Addgene plasmid #54649, a gift from Patrick Daugherty and Michael Davidson), pYpet-C1 (Addgene plasmid #54648, a gift from Patrick Daugherty and Michael Davidson), FusionRed-C1 (Addgene plasmid #54777, a gift from Michael Davidson), mRFP-C1 (Addgene plasmid #54764, a gift from […]


A simple optogenetic MAPK inhibitor design reveals resonance between transcription regulating circuitry and temporally encoded inputs

Nat Commun
PMCID: 5437309
PMID: 28497795
DOI: 10.1038/ncomms15017

[…] repared by replacing enhanced green fluorescent protein (EGFP) in the corresponding vectors that we developed previously, with cds for monomeric-Cherry. The cds was also inserted in frame into vector pYpet-C1 we prepared by replacing mCherry in pmCherry-C1 with the Ypet cds obtained from plasmid JNKAR1EV (generous gift of Michiyuki Matsuda, Kyoto, Japan). We also transferred OptoJNKi.lsm, OptoJNKi […]


The Influence of Mexican Hat Recurrent Connectivity on Noise Correlations and Stimulus Encoding

Front Comput Neurosci
PMCID: 5423970
PMID: 28539881
DOI: 10.3389/fncom.2017.00034

[…] berg et al., ) using the BRIAN simulator package (Goodman and Brette, ) (data not shown, example run see Supplementary ). All data and parameter explorations were managed using the simulation toolkit pypet (Meyer et al., ). […]


Demonstration of protein fragment complementation assay using purified firefly luciferase fragments

BMC Biotechnol
PMCID: 3626928
PMID: 23536995
DOI: 10.1186/1472-6750-13-31

[…] The cDNAs for Ypet on pYpet-His (kindly provided by Dr. PS Daugherty) [] and Cerulean [] made from pEBFP-N1 plasmid (Clontech, Takara-Bio) were amplified using specific primers with 5′-terminal NotI and 3′-terminal XhoI si […]


Nonpolarized signaling reveals two distinct modes of 3D cell migration

PMCID: 3341168
PMID: 22547408
DOI: 10.1083/jcb.201201124

[…] The pECFP-Rac1 and -Cdc42 constructs () were generated by subcloning the full-length sequence into the EcoRI–BamH1 sites of pECFP-C1 (Takara Bio Inc.). pYPet–p21-binding domain (PBD) was generated by subcloning the sequence encoding amino acids 65–150 of human Pak1 into the EcoRI–BamH1 sites of pYPet-C1. pYPet-C1 was constructed by subcloning the seq […]


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Pypet institution(s)
Neuroinformatics Group, Department of Software Engineering and Theoretical Computer Science, Technical University, Berlin, Berlin, Germany; Bernstein Center for Computational Neuroscience, Berlin, Germany
Pypet funding source(s)
Supported by the Deutsche Forschungsgemeinschaft (GRK1589/1).

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