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@INPROCEEDINGS{Yegenoglu:850028,
      author       = {Yegenoglu, Alper and Denker, Michael and Grün, Sonja},
      title        = {{C}ollaborative {HPC}-enabled workflows on the {HBP}
                      {C}ollaboratory using the {E}lephant framework},
      reportid     = {FZJ-2018-04114},
      year         = {2018},
      abstract     = {The degree of complexity in analyzing massively parallel,
                      heterogeneous data from electrophysiological experiments and
                      network simulations has reached levels where novel tools
                      forming workflows for managing data, metadata acquisition,
                      pre-processing, and analysis in a reproducible fashion are
                      in high demand. Moreover, this complexity calls for new
                      conceptual approaches in organizing scientific work. The
                      nature of these new, highly manifold projects requires work
                      to be performed in larger, multi-disciplinary
                      collaborations. The collaborators that need to interact
                      closely require the supported from powerful computing
                      resources, especially when dealing with large and diverse
                      data sets.The Human Brain Project (HBP,
                      http://humanbrainproject.eu/) aims at creating and operating
                      a scientific research infrastructure for the neurosciences
                      to address such needs for integrative software environments.
                      At its core, the HBP features the Collaboratory
                      (http://www.collab.humanbrainproject.eu), a web-based
                      platform to jointly implement research projects. It enables
                      the ability to create so-called “Collabs” that consist
                      of a joint workspace and associated apps (see also poster by
                      van Papen et al). An app provides the functionality to
                      launch Jupyter notebooks, which is in particular interesting
                      for interactive data analysis. Powerful as this approach
                      appears on paper, it is unclear how these developments
                      translate into implementing complete analysis workflows in a
                      real-world collaborative analysis scenario. Here, we show
                      how diverse tools, from software development, general
                      science and software specific for neuroscience can be
                      successfully combined in a to form a collaborative analysis
                      workflow hosted on the HBP Collaboratory. Three emerging
                      open-source software tools from neuroscience represent the
                      tool basis which builds the analysis pipeline: (i) data of
                      different origins are represented in a standard form using
                      the Neo framework, (ii) complex metadata accumulated in
                      relation to an electrophysiological experiment are managed
                      using the open metadata markup language (odML) and (iii)
                      analysis is performed utilizing the Electrophysiology
                      Analysis Toolkit (Elephant,
                      http://neuralensemble.org/elephant/). The Elephant tool is a
                      recent community-centered analysis framework for the
                      analysis of multi-scale high-dimensional activity data.
                      Elephant is a modular software component that provides
                      generic library functions to perform standard and advanced
                      analysis. All these domain-specific tools are augmented by
                      generic tools, such as version control systems or workflow
                      management solutions, to form a blueprint for performing
                      interdisciplinary, collaborative work including access to
                      high-performance computing facilities for advanced, but
                      computational demanding analyses.},
      month         = {Jul},
      date          = {2018-07-02},
      organization  = {INM-ICS Retreat 2018, Juelich
                       (Germany), 2 Jul 2018 - 3 Jul 2018},
      cin          = {INM-6 / IAS-6 / INM-10},
      cid          = {I:(DE-Juel1)INM-6-20090406 / I:(DE-Juel1)IAS-6-20130828 /
                      I:(DE-Juel1)INM-10-20170113},
      pnm          = {571 - Connectivity and Activity (POF3-571) / SMHB -
                      Supercomputing and Modelling for the Human Brain
                      (HGF-SMHB-2013-2017) / HBP SGA1 - Human Brain Project
                      Specific Grant Agreement 1 (720270) / HBP SGA2 - Human Brain
                      Project Specific Grant Agreement 2 (785907)},
      pid          = {G:(DE-HGF)POF3-571 / G:(DE-Juel1)HGF-SMHB-2013-2017 /
                      G:(EU-Grant)720270 / G:(EU-Grant)785907},
      typ          = {PUB:(DE-HGF)1},
      url          = {https://juser.fz-juelich.de/record/850028},
}