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@ARTICLE{Dalman:811790,
      author       = {Dalman, Tolga and Wiechert, Wolfgang and Nöh, Katharina},
      title        = {{A} scientific workflow framework for 13{C} metabolic flux
                      analysis},
      journal      = {Journal of biotechnology},
      volume       = {232},
      issn         = {0168-1656},
      address      = {Amsterdam [u.a.]},
      publisher    = {Elsevier Science},
      reportid     = {FZJ-2016-04144},
      pages        = {12 - 24},
      year         = {2016},
      abstract     = {Metabolic flux analysis (MFA) with 13C labeling data is a
                      high-precision technique to quantify intracellular reaction
                      rates (fluxes). One of the major challenges of 13C MFA is
                      the interactivity of the computational workflow according to
                      which the fluxes are determined from the input data
                      (metabolic network model, labeling data, and physiological
                      rates). Here, the workflow assembly is inevitably determined
                      by the scientist who has to consider interacting biological,
                      experimental, and computational aspects. Decision-making is
                      context dependent and requires expertise, rendering an
                      automated evaluation process hardly possible.Here, we
                      present a scientific workflow framework (SWF) for creating,
                      executing, and controlling on demand 13C MFA workflows. 13C
                      MFA-specific tools and libraries, such as the
                      high-performance simulation toolbox 13CFLUX2, are wrapped as
                      web services and thereby integrated into a service-oriented
                      architecture. Besides workflow steering, the SWF features
                      transparent provenance collection and enables full
                      flexibility for ad hoc scripting solutions. To handle
                      compute-intensive tasks, cloud computing is supported. We
                      demonstrate how the challenges posed by 13C MFA workflows
                      can be solved with our approach on the basis of two
                      proof-of-concept use cases.},
      cin          = {IBG-1},
      ddc          = {540},
      cid          = {I:(DE-Juel1)IBG-1-20101118},
      pnm          = {583 - Innovative Synergisms (POF3-583)},
      pid          = {G:(DE-HGF)POF3-583},
      typ          = {PUB:(DE-HGF)16},
      UT           = {WOS:000380818700003},
      doi          = {10.1016/j.jbiotec.2015.12.032},
      url          = {https://juser.fz-juelich.de/record/811790},
}