pypet: A Python Toolkit for Data Management of Parameter Explorations

dc.contributor.authorMeyer, Robert
dc.contributor.authorObermayer, Klaus
dc.date.accessioned2019-11-06T10:00:50Z
dc.date.available2019-11-06T10:00:50Z
dc.date.issued2016-08-25
dc.date.updated2019-09-29T21:35:17Z
dc.description.abstractpypet (Python parameter exploration toolkit) is a new multi-platform Python toolkit for managing numerical simulations. Sampling the space of model parameters is a key aspect of simulations and numerical experiments. pypet is designed to allow easy and arbitrary sampling of trajectories through a parameter space beyond simple grid searches. pypet collects and stores both simulation parameters and results in a single HDF5 file. This collective storage allows fast and convenient loading of data for further analyses. pypet provides various additional features such as multiprocessing and parallelization of simulations, dynamic loading of data, integration of git version control, and supervision of experiments via the electronic lab notebook Sumatra. pypet supports a rich set of data formats, including native Python types, Numpy and Scipy data, Pandas DataFrames, and BRIAN(2) quantities. Besides these formats, users can easily extend the toolkit to allow customized data types. pypet is a flexible tool suited for both short Python scripts and large scale projects. pypet's various features, especially the tight link between parameters and results, promote reproducible research in computational neuroscience and simulation-based disciplines.en
dc.description.sponsorshipDFG, 103586207, GRK 1589: Verarbeitung sensorischer Informationen in neuronalen Systemenen
dc.identifier.eissn1662-5196
dc.identifier.urihttps://depositonce.tu-berlin.de/handle/11303/10248
dc.identifier.urihttp://dx.doi.org/10.14279/depositonce-9210
dc.language.isoenen
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/en
dc.subject.ddc610 Medizin und Gesundheitde
dc.subject.otherparameter explorationen
dc.subject.otherreproducibilityen
dc.subject.othersimulationen
dc.subject.otherpythonen
dc.subject.otherparallelizationen
dc.subject.othergrid computingen
dc.titlepypet: A Python Toolkit for Data Management of Parameter Explorationsen
dc.typeArticleen
dc.type.versionpublishedVersionen
dcterms.bibliographicCitation.articlenumber38en
dcterms.bibliographicCitation.doi10.3389/fninf.2016.00038en
dcterms.bibliographicCitation.journaltitleFrontiers in Neuroinformaticsen
dcterms.bibliographicCitation.originalpublishernameFrontiers Media S.A.en
dcterms.bibliographicCitation.originalpublisherplaceLausanneen
dcterms.bibliographicCitation.volume10en
tub.accessrights.dnbfreeen
tub.affiliationFak. 4 Elektrotechnik und Informatik>Inst. Softwaretechnik und Theoretische Informatik>FG Neuronale Informationsverarbeitungde
tub.affiliation.facultyFak. 4 Elektrotechnik und Informatikde
tub.affiliation.groupFG Neuronale Informationsverarbeitungde
tub.affiliation.instituteInst. Softwaretechnik und Theoretische Informatikde
tub.publisher.universityorinstitutionTechnische Universität Berlinen
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